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Functions return results\nas tidy tibbles and support optional filtering, sorting, and\nrow limits via the Socrata API. The package includes endpoints\nfor 311 service requests, DOB job applications, juvenile\njustice metrics, school safety, environmental data, event\npermitting, and additional citywide datasets.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "URL": "https://docs.ropensci.org/nycOpenData/,\nhttps://github.com/ropensci/nycOpenData", "BugReports": "https://github.com/ropensci/nycOpenData/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev libssl-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-11-02 17:01:56 UTC", "RemoteUrl": "https://github.com/ropensci/nycOpenData", "RemoteRef": "HEAD", "RemoteSha": "061e56554fd96fe400b745a0c58c43301f92ff40", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-02 18:39:00 UTC", "User": "root" }, "Author": "Christian Martinez [aut, cre] (GitHub: martinezc1, ORCID:\n),\nCrystal Adote [ctb] (GitHub: crystalna20),\nJonah Dratfield [ctb] 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Wraps 32 of the 37 'BrAPI'\nv2.1 entities across all four modules, Core, Germplasm,\nPhenotyping, and Genotyping, covering 49 of the specification's\n138 retrieval ('GET' and search) endpoints and returning tidy\ntibbles ready for analysis. Write and update endpoints are out\nof scope by design. Features include automatic pagination,\nasync search handling, response caching, parallel batch\nfetching, and convenience functions for genomic selection\nworkflows (e.g. dosage matrix extraction). 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definitions and short codes", "topics": [ "gbif_issues_lookup" ] }, { "page": "gbif_names", "title": "View highlighted terms in name results from GBIF.", "topics": [ "gbif_names" ] }, { "page": "gbif_oai", "title": "GBIF registry data via OAI-PMH", "topics": [ "gbif_oai", "gbif_oai_get_records", "gbif_oai_identify", "gbif_oai_list_identifiers", "gbif_oai_list_metadataformats", "gbif_oai_list_records", "gbif_oai_list_sets" ] }, { "page": "gbif_photos", "title": "View photos from GBIF.", "topics": [ "gbif_photos" ] }, { "page": "gbif_to_col", "title": "Convert GBIF Backbone taxon keys to COL Extended Release keys", "concept": [ "name" ], "topics": [ "gbif_to_col" ] }, { "page": "installation_search", "title": "Search for installations", "topics": [ "installation_search" ] }, { "page": "installation_uuid_funs", "title": "Get installation metadata using an installation key", "topics": [ "installation_comment", "installation_contact", "installation_dataset", "installation_endpoint", 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dimensions.", "topics": [ "occ_count_", "occ_count_basis_of_record", "occ_count_country", "occ_count_pub_country", "occ_count_year" ] }, { "page": "occ_data", "title": "Legacy alternative to occ_search", "topics": [ "occ_data" ] }, { "page": "occ_download", "title": "Spin up a download request for GBIF occurrence data.", "concept": [ "downloads" ], "topics": [ "occ_download", "occ_download_prep" ] }, { "page": "occ_download_cached", "title": "Check for downloads already in your GBIF account", "concept": [ "downloads" ], "topics": [ "occ_download_cached" ] }, { "page": "occ_download_cancel", "title": "Cancel a download creation process.", "concept": [ "downloads" ], "topics": [ "occ_download_cancel", "occ_download_cancel_staged" ] }, { "page": "occ_download_countries", "title": "List countries for a download", "topics": [ "occ_download_countries" ] }, { "page": "occ_download_dataset_activity", "title": "Lists the downloads activity of a dataset", "concept": [ "downloads" ], "topics": [ 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metadata by its unique key.", "concept": [ "downloads" ], "topics": [ "occ_download_meta" ] }, { "page": "occ_download_organizations", "title": "List organizations for a download", "topics": [ "occ_download_organizations" ] }, { "page": "occ_download_queue", "title": "Download requests in a queue", "concept": [ "downloads" ], "topics": [ "occ_download_queue" ] }, { "page": "occ_download_sql", "title": "Download occurrence data using a SQL query", "topics": [ "occ_download_sql", "occ_download_sql_prep", "occ_download_sql_validate" ] }, { "page": "occ_download_stats", "title": "Occurrence download statistics", "concept": [ "downloads" ], "topics": [ "occ_download_stats" ] }, { "page": "occ_download_stats_dataset", "title": "Downloads by dataset", "concept": [ "downloads" ], "topics": [ "occ_download_stats_dataset" ] }, { "page": "occ_download_stats_dataset_records", "title": "Downloaded records by dataset", "concept": [ "downloads" ], "topics": [ "occ_download_stats_dataset_records" ] }, { "page": "occ_download_stats_export", "title": "Export summary of occurrence downloads", "concept": [ "downloads" ], "topics": [ "occ_download_stats_export" ] }, { "page": "occ_download_stats_source", "title": "Downloads by source", "concept": [ "downloads" ], "topics": [ "occ_download_stats_source" ] }, { "page": "occ_download_stats_user_country", "title": "Downloads by user country", "concept": [ "downloads" ], "topics": [ "occ_download_stats_user_country" ] }, { "page": "occ_download_user_count", "title": "Count downloads for a user.", "topics": [ "occ_download_user_count" ] }, { "page": "occ_download_wait", "title": "Wait for an occurrence download to be done", "concept": [ "downloads" ], "topics": [ "occ_download_wait" ] }, { "page": "occ_facet", "title": "Facet GBIF occurrences", "topics": [ "occ_facet" ] }, { "page": "occ_get", "title": "Get data for GBIF occurrences by occurrence key", "topics": [ "occ_get", "occ_get_verbatim" ] }, { "page": "occ_issues", "title": "Parse and 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\"carolinapradier@gmail.com\", role = c(\"aut\"), comment = c(ORCID = \"0009-0007-5058-6352\")),\nperson(\"Diego\", \"Kozlowski\", email = \"diegokoz92@gmail.com\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-5396-3471\")),\nperson(\"Pablo\", \"Tiscornia\", email = \"pablotisco@gmail.com\", role = \"aut\"),\nperson(\"Guido\", \"Weksler\", email = \"guidowe45@gmail.com\", role = c(\"aut\")),\nperson(\"Natsumi\", \"Shokida\", email = \"natsumi.shokida@gmail.com\", role = \"aut\"),\nperson(\"German\", \"Rosati\", email = \"german.rosati@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-9775-0435\")),\nperson(\"Juan Gabriel\", \"Juara\", email = \"jg.juara@gmail.com\", role = \"ctb\"),\nperson(\"Juan Camilo\", \"Gutman Gomez\", email = \"gutmanjuancamilo@gmail.com\", role = c(\"aut\",\"cre\"), comment = c(ORCID = \"0009-0009-4870-5628\"))\n)", "Description": "Tools to download and manipulate the Permanent Household\nSurvey from Argentina (EPH is the Spanish acronym for Permanent\nHousehold Survey). e.g: get_microdata() for downloading the\ndatasets, get_poverty_lines() for downloading the official\npoverty baskets, calculate_poverty() for the calculation of\nstating if a household is in poverty or not, following the\nofficial methodology. organize_panels() is used to concatenate\nobservations from different periods, and organize_labels() adds\nthe official labels to the data. The implemented methods are\nbased on INDEC (2016)\n.\nAs this package works with the argentinian Permanent Household\nSurvey and its main audience is from this country, the\ndocumentation was written in Spanish.", "BugReports": "https://github.com/ropensci/eph/issues", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Language": "es", "URL": "https://github.com/ropensci/eph", "LazyData": "true", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libicu-dev libpng-dev libuv1-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-10-28 02:26:20 UTC", "RemoteUrl": "https://github.com/ropensci/eph", "RemoteRef": "HEAD", "RemoteSha": "8123dd844a45ce32c627594304bb422e82c00883", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-28 06:03:23 UTC", "User": "root" }, "Author": "Carolina Pradier [aut] (ORCID: ),\nDiego Kozlowski [aut] (ORCID: ),\nPablo Tiscornia [aut],\nGuido Weksler [aut],\nNatsumi Shokida [aut],\nGerman Rosati [aut] (ORCID: ),\nJuan Gabriel Juara [ctb],\nJuan Camilo Gutman Gomez [aut, cre] (ORCID:\n)", "Maintainer": "Juan Camilo Gutman Gomez ", "_user": "ropensci", "_type": "src", "_file": "eph_1.0.2.9000.tar.gz", "_fileid": "https://r2.ropensci.org/d5a46ed091ad1694556de779f01d7a61d7ffc344dba2314ecf1392954c146b13", "_filesize": 1524161, "_sha256": "d5a46ed091ad1694556de779f01d7a61d7ffc344dba2314ecf1392954c146b13", "_expires": "2027-02-05T06:06:56.000Z", "_created": "2026-10-28T06:03:23.000Z", "_published": "2026-10-28T06:06:58.445Z", "_upstream": "https://github.com/ropensci/eph", "_status": "success", "_maintainer": { "name": "Juan Camilo Gutman Gomez", "email": "gutmanjuancamilo@gmail.com", "login": "juancamilogutman", "orcid": "0009-0009-4870-5628", "description": "Economista argentino, investigador en formación en @ceped-fce-uba. 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"rows": 12, "table": true, "tojson": true }, { "name": "fs_v7_raw", "title": "The unparsed XML form_schema of a form from ODK Central v0.6 as nested list.", "object": "fs_v7_raw", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "geo_fs", "title": "The form_schema of a form containing geofields in GeoJSON.", "object": "geo_fs", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "path", "name", "type", "binary", "selectMultiple", "ruodk_name" ], "rows": 19, "table": true, "tojson": true }, { "name": "geo_gj", "title": "The parsed submissions of a form containing geofields in GeoJSON.", "object": "geo_gj", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "meta_instance_id", "device_id", "start_time", "username", "subscriber_id", "point_location_point_gps_longitude", "point_location_point_gps_latitude", "point_location_point_gps_altitude", "point_location_point_gps_accuracy", "point_location_point_gps", "point_location_point_map_longitude", "point_location_point_map_latitude", "point_location_point_map_altitude", "point_location_point_map_accuracy", "point_location_point_map", "point_location_point_manual_longitude", "point_location_point_manual_latitude", "point_location_point_manual_altitude", "point_location_point_manual_accuracy", "point_location_point_manual", "path_location_path_gps_longitude", "path_location_path_gps_latitude", "path_location_path_gps_altitude", "path_location_path_gps", "path_location_path_map_longitude", "path_location_path_map_latitude", "path_location_path_map_altitude", "path_location_path_map", "path_location_path_manual_longitude", "path_location_path_manual_latitude", "path_location_path_manual_altitude", "path_location_path_manual", "shape_location_shape_gps_longitude", "shape_location_shape_gps_latitude", "shape_location_shape_gps_altitude", "shape_location_shape_gps", "shape_location_shape_map_longitude", "shape_location_shape_map_latitude", "shape_location_shape_map_altitude", 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"path_location_path_manual_longitude", "path_location_path_manual_latitude", "path_location_path_manual_altitude", "path_location_path_manual", "shape_location_shape_gps_longitude", "shape_location_shape_gps_latitude", "shape_location_shape_gps_altitude", "shape_location_shape_gps", "shape_location_shape_map_longitude", "shape_location_shape_map_latitude", "shape_location_shape_map_altitude", "shape_location_shape_map", "shape_location_shape_manual_longitude", "shape_location_shape_manual_latitude", "shape_location_shape_manual_altitude", "shape_location_shape_manual", "odata_context" ], "rows": 1, "table": false, "tojson": true }, { "name": "geo_wkt", "title": "The parsed submissions of a form containing geofields in WKT.", "object": "geo_wkt", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "meta_instance_id", "device_id", "start_time", "username", "subscriber_id", "point_location_point_gps", "point_location_point_gps_longitude", "point_location_point_gps_latitude", "point_location_point_gps_altitude", "point_location_point_map", "point_location_point_map_longitude", "point_location_point_map_latitude", "point_location_point_map_altitude", "point_location_point_manual", "point_location_point_manual_longitude", "point_location_point_manual_latitude", "point_location_point_manual_altitude", "path_location_path_gps", "path_location_path_gps_longitude", "path_location_path_gps_latitude", "path_location_path_gps_altitude", "path_location_path_map", "path_location_path_map_longitude", "path_location_path_map_latitude", "path_location_path_map_altitude", "path_location_path_manual", "path_location_path_manual_longitude", "path_location_path_manual_latitude", "path_location_path_manual_altitude", "shape_location_shape_gps", "shape_location_shape_gps_longitude", "shape_location_shape_gps_latitude", "shape_location_shape_gps_altitude", "shape_location_shape_map", "shape_location_shape_map_longitude", "shape_location_shape_map_latitude", "shape_location_shape_map_altitude", "shape_location_shape_manual", "shape_location_shape_manual_longitude", "shape_location_shape_manual_latitude", "shape_location_shape_manual_altitude", "end_time", "id", "system_submission_date", "system_updated_at", "system_submitter_id", "system_submitter_name", "system_attachments_present", "system_attachments_expected", "system_status", "system_review_state", "system_device_id", "system_edits", "system_form_version", "system_deleted_at", "odata_context" ], "rows": 1, "table": true, "tojson": true }, { "name": "geo_wkt_raw", "title": "The unparsed submissions of a form containing geofields in WKT.", "object": "geo_wkt_raw", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "geo_wkt88", "title": "The parsed submissions of a form containing geofields in WKT with trailing empty coordinates present.", "object": "geo_wkt88", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "id", "device_id", "start_time", "subscriber_id", "end_time", "system_submission_date", "system_submitter_id", "system_submitter_name", "system_attachments_present", "system_attachments_expected", "meta_instance_id", "point_location_point_gps", "point_location_point_gps_longitude", "point_location_point_gps_latitude", "point_location_point_gps_altitude", "point_location_point_map", "point_location_point_map_longitude", "point_location_point_map_latitude", "point_location_point_map_altitude", "point_location_point_manual", "point_location_point_manual_longitude", "point_location_point_manual_latitude", "point_location_point_manual_altitude", "path_location_path_gps", "path_location_path_gps_longitude", "path_location_path_gps_latitude", "path_location_path_gps_altitude", "path_location_path_map", "path_location_path_map_longitude", "path_location_path_map_latitude", "path_location_path_map_altitude", "path_location_path_manual", "path_location_path_manual_longitude", "path_location_path_manual_latitude", "path_location_path_manual_altitude", "shape_location_shape_gps", "shape_location_shape_gps_longitude", "shape_location_shape_gps_latitude", "shape_location_shape_gps_altitude", "shape_location_shape_map", "shape_location_shape_map_longitude", "shape_location_shape_map_latitude", "shape_location_shape_map_altitude", "shape_location_shape_manual", "shape_location_shape_manual_longitude", "shape_location_shape_manual_latitude", "shape_location_shape_manual_altitude", "odata_context" ], "rows": 1, "table": true, "tojson": true } ], "_help": [ { "page": "app_user_create", "title": "Create a new App User.", "concept": [ "user-management" ], "topics": [ "app_user_create" ] }, { "page": "app_user_delete", "title": "Delete an App User.", "concept": [ "user-management" ], "topics": [ "app_user_delete" ] }, { "page": "app_user_list", "title": "List all App Users of a Project.", "concept": [ "user-management" ], "topics": [ "app_user_list" ] }, { "page": "assignment_actors", "title": "List all 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"entity_audits", "title": "Return server audit logs of one Entity.", "concept": [ "entity-management" ], "topics": [ "entity_audits" ] }, { "page": "entity_bulk_delete", "title": "Delete multiple Entities at once.", "concept": [ "entity-management" ], "topics": [ "entity_bulk_delete" ] }, { "page": "entity_bulk_restore", "title": "Restore multiple deleted Entities at once.", "concept": [ "entity-management" ], "topics": [ "entity_bulk_restore" ] }, { "page": "entity_changes", "title": "List changes to one Entity.", "concept": [ "entity-management" ], "topics": [ "entity_changes" ] }, { "page": "entity_create", "title": "Creates exactly one Entity in the Dataset.", "concept": [ "entity-management" ], "topics": [ "entity_create" ] }, { "page": "entity_creators", "title": "List all creators of Entities in one Entity List.", "concept": [ "entity-management" ], "topics": [ "entity_creators" ] }, { "page": "entity_delete", "title": "Delete one Entity.", "concept": [ "entity-management" ], "topics": [ "entity_delete" ] }, { "page": "entity_detail", "title": "Show metadata and current data of one Entity.", "concept": [ "entity-management" ], "topics": [ "entity_detail" ] }, { "page": "entity_geodata", "title": "Get Entity geodata as GeoJSON.", "concept": [ "entity-management" ], "topics": [ "entity_geodata" ] }, { "page": "entity_geojson", "title": "Get the GeoJSON of one Entity.", "concept": [ "entity-management" ], "topics": [ "entity_geojson" ] }, { "page": "entity_list", "title": "List all Entities of a kind.", "concept": [ "entity-management" ], "topics": [ "entity_list" ] }, { "page": "entity_restore", "title": "Restore a deleted Entity.", "concept": [ "entity-management" ], "topics": [ "entity_restore" ] }, { "page": "entity_update", "title": "Update one Entity.", "concept": [ "entity-management" ], "topics": [ "entity_update" ] }, { "page": "entity_versions", "title": "List versions of one Entity.", "concept": [ "entity-management" ], "topics": [ "entity_versions" ] }, { "page": "entitylist_create", "title": "Create an Entity List.", "concept": [ "entity-management" ], "topics": [ "entitylist_create" ] }, { "page": "entitylist_delete", "title": "Delete an Entity List.", "concept": [ "entity-management" ], "topics": [ "entitylist_delete" ] }, { "page": "entitylist_detail", "title": "Show Entity List details.", "concept": [ "entity-management" ], "topics": [ "entitylist_detail" ] }, { "page": "entitylist_download", "title": "Download an Entity List as CSV.", "concept": [ "entity-management" ], "topics": [ "entitylist_download" ] }, { "page": "entitylist_list", "title": "List all Entity Lists of one Project.", "concept": [ "entity-management" ], "topics": [ "entitylist_list" ] }, { "page": "entitylist_property_create", "title": "Add a property to an Entity List.", "concept": [ "entity-management" ], "topics": [ "entitylist_property_create" ] }, { "page": "entitylist_property_delete", "title": "Delete a property from an Entity List.", "concept": [ "entity-management" ], "topics": [ "entitylist_property_delete" ] }, { "page": "entitylist_trash_download", "title": "Download Entities of a deleted Entity List.", "concept": [ "entity-management" ], "topics": [ "entitylist_trash_download" ] }, { "page": "entitylist_update", "title": "Update Entity List details.", "concept": [ "entity-management" ], "topics": [ "entitylist_update" ] }, { "page": "form_assignment_actors", "title": "List all Actors assigned some Form Role.", "concept": [ "form-management" ], "topics": [ "form_assignment_actors" ] }, { "page": "form_assignment_grant", "title": "Assign an Actor to a Form Role.", "concept": [ "form-management" ], "topics": [ "form_assignment_grant" ] }, { "page": "form_assignment_list", "title": "Summarize all Form Assignments of one Project.", "concept": [ "user-management" ], "topics": [ "form_assignment_list" ] }, { "page": "form_assignment_revoke", "title": "Revoke a Form Role Assignment from an Actor.", "concept": [ "form-management" ], "topics": [ "form_assignment_revoke" ] }, { "page": "form_assignment_role_list", "title": "List Role-specific Form Assignments within a Project.", "concept": [ "project-management" ], "topics": [ "form_assignment_role_list" ] }, { "page": "form_attachment_download", "title": "Download one Form attachment.", "concept": [ "form-management" ], "topics": [ "form_attachment_download" ] }, { "page": "form_attachment_list", "title": "List all attachments of one Form.", "concept": [ "form-management" ], "topics": [ "form_attachment_list" ] }, { "page": "form_create", "title": "Create a new Form.", "concept": [ "form-management" ], "topics": [ "form_create" ] }, { "page": "form_dataset_diff", "title": "Show Datasets affected by one Form.", "concept": [ "form-management" ], "topics": [ "form_dataset_diff" ] }, { "page": "form_delete", "title": "Delete a Form.", "concept": [ "form-management" ], "topics": [ "form_delete" ] }, { "page": "form_detail", "title": "Show details for one form.", "concept": [ "form-management" ], "topics": [ "form_detail" ] }, { "page": "form_draft_attachment_delete", "title": "Clear a Draft Form attachment.", "concept": [ "form-management" ], "topics": [ "form_draft_attachment_delete" ] }, { "page": "form_draft_attachment_download", "title": "Download one Draft Form attachment.", "concept": [ "form-management" ], "topics": [ "form_draft_attachment_download" ] }, { "page": "form_draft_attachment_link", "title": "Link a Dataset to a Draft Form attachment.", "concept": [ "form-management" ], "topics": [ "form_draft_attachment_link" ] }, { "page": "form_draft_attachment_list", "title": "List all expected attachments of a Draft Form.", "concept": [ "form-management" ], "topics": [ "form_draft_attachment_list" ] }, { "page": "form_draft_attachment_upload", "title": "Upload a Draft Form attachment.", "concept": [ "form-management" ], "topics": [ "form_draft_attachment_upload" ] }, { "page": "form_draft_create", "title": "Create a Draft Form.", "concept": [ "form-management" ], "topics": [ "form_draft_create" ] }, { "page": "form_draft_dataset_diff", "title": "Show Dataset changes of a Draft Form.", "concept": [ "form-management" ], "topics": [ "form_draft_dataset_diff" ] }, { "page": "form_draft_delete", "title": "Delete a Draft Form.", "concept": [ "form-management" ], "topics": [ "form_draft_delete" ] }, { "page": "form_draft_detail", "title": "Show details of a Draft Form.", "concept": [ "form-management" ], "topics": [ "form_draft_detail" ] }, { "page": "form_draft_publish", "title": "Publish a Draft Form.", "concept": [ "form-management" ], "topics": [ "form_draft_publish" ] }, { "page": "form_draft_xlsx", "title": "Download the XLSForm of a Draft Form.", "concept": [ "form-management" ], "topics": [ "form_draft_xlsx" ] }, { "page": "form_draft_xml", "title": "Show the XML of a Draft Form.", "concept": [ "form-management" ], "topics": [ "form_draft_xml" ] }, { "page": "form_link", "title": "Show Form details by Form Link ID.", "concept": [ "form-management" ], "topics": [ "form_link" ] }, { "page": "form_list", "title": "List all forms.", "concept": [ "form-management" ], "topics": [ "form_list" ] }, { "page": "form_restore", "title": "Restore a deleted Form.", "concept": [ "form-management" ], "topics": [ "form_restore" ] }, { "page": "form_schema", "title": "Show the schema of one form.", "concept": [ "form-management" ], "topics": [ "form_schema" ] }, { "page": "form_schema_ext", "title": "Show the extended schema of one form.", "concept": [ "form-management" ], "topics": [ "form_schema_ext" ] }, { "page": "form_schema_parse", "title": "Parse a form_schema into a tibble of fields with name, type, and path.", "concept": [ "utilities" ], "topics": [ "form_schema_parse" ] }, { "page": "form_update", "title": "Modify a Form's state.", "concept": [ "form-management" ], "topics": [ "form_update" ] }, { "page": "form_version_attachment_download", "title": "Download one attachment of a published Form version.", "concept": [ "form-management" ], "topics": [ "form_version_attachment_download" ] }, { "page": "form_version_attachment_list", "title": "List expected attachments of one published Form version.", "concept": [ "form-management" ], "topics": [ "form_version_attachment_list" ] }, { "page": "form_version_detail", "title": "Show details of one published Form version.", "concept": [ "form-management" ], "topics": [ "form_version_detail" ] }, { "page": "form_version_list", "title": "List all published versions of one Form.", "concept": [ "form-management" ], "topics": [ "form_version_list" ] }, { "page": "form_version_xlsx", "title": "Download the XLSForm of one published Form version.", "concept": [ "form-management" ], "topics": [ "form_version_xlsx" ] }, { "page": "form_version_xml", "title": "Show the XML of one published Form version.", "concept": [ "form-management" ], "topics": [ "form_version_xml" ] }, { "page": "form_xlsx", "title": "Download the XLSForm of one Form.", "concept": [ "form-management" ], "topics": [ "form_xlsx" ] }, { "page": "form_xml", "title": "Show the XML representation of one form as list.", "concept": [ "form-management" ], "topics": [ "form_xml" ] }, { "page": "fq_attachments", "title": "A tibble of submission attachments.", "concept": [ "included" ], "topics": [ "fq_attachments" ] }, { "page": "fq_data", "title": "Parsed submission data for an ODK Central form.", "concept": [ "included" ], "topics": [ "fq_data" ] }, { "page": "fq_data_strata", "title": "Parsed submission data for a subgroup of an ODK Central form.", "concept": [ "included" ], "topics": [ "fq_data_strata" ] }, { "page": "fq_data_taxa", "title": "Parsed submission data for a subgroup of an ODK Central form.", "concept": [ "included" ], "topics": [ "fq_data_taxa" ] }, { "page": "fq_form_detail", "title": "A tibble of form metadata.", "concept": [ "included" ], "topics": [ "fq_form_detail" ] }, { "page": "fq_form_list", "title": "A tibble of forms.", "concept": [ "included" ], "topics": [ "fq_form_list" ] }, { "page": "fq_form_schema", "title": "JSON form schema for an ODK Central form.", "concept": [ "included" ], "topics": [ "fq_form_schema" ] }, { "page": "fq_form_xml", "title": "A nested list of a form definition.", "concept": [ "included" ], "topics": [ "fq_form_xml" ] }, { "page": "fq_meta", "title": "OData metadata document for an ODK Central form.", "concept": [ "included" ], "topics": [ "fq_meta" ] }, { "page": "fq_project_detail", "title": "A tibble of project metadata.", "concept": [ "included" ], "topics": [ "fq_project_detail" ] }, { "page": "fq_project_list", "title": "A tibble of project metadata.", "concept": [ "included" ], "topics": [ "fq_project_list" ] }, { "page": "fq_raw", "title": "OData submission data for an ODK Central form.", "concept": [ "included" ], "topics": [ "fq_raw" ] }, { "page": "fq_raw_strata", "title": "OData submission data for a subgroup of an ODK Central form.", "concept": [ "included" ], "topics": [ "fq_raw_strata" ] }, { "page": "fq_raw_taxa", "title": "OData submission data for a subgroup of an ODK Central form.", "concept": [ "included" ], "topics": [ "fq_raw_taxa" ] }, { "page": "fq_submission_list", "title": "A tibble of submission metadata.", "concept": [ "included" ], "topics": [ "fq_submission_list" ] }, { "page": "fq_submissions", "title": "A nested list of submission data.", "concept": [ "included" ], "topics": [ "fq_submissions" ] }, { "page": "fq_svc", "title": "OData service document for an ODK Central form.", "concept": [ "included" ], "topics": [ "fq_svc" ] }, { "page": "fq_zip_data", "title": "A tibble of the main data table of records from a test form.", "concept": [ "included" ], "topics": [ "fq_zip_data" ] }, { "page": "fq_zip_strata", "title": "A tibble of a repeated sub-group of records from a test form.", "concept": [ "included" ], "topics": [ "fq_zip_strata" ] }, { "page": "fq_zip_taxa", "title": "A tibble of a repeated sub-group of records from a test form.", "concept": [ "included" ], "topics": [ "fq_zip_taxa" ] }, { "page": "fs_v7", "title": "The parsed XML form_schema of a form from ODK Central v0.6.", "concept": [ "included" ], "topics": [ "fs_v7" ] }, { "page": "fs_v7_raw", "title": "The unparsed XML form_schema of a form from ODK Central v0.6 as nested list.", "concept": [ "included" ], "topics": [ "fs_v7_raw" ] }, { "page": "geo_fs", "title": "The form_schema of a form containing geofields in GeoJSON.", "concept": [ "included" ], "topics": [ "geo_fs" ] }, { "page": "geo_gj", "title": "The parsed submissions of a form containing geofields in GeoJSON.", "concept": [ "included" ], "topics": [ "geo_gj" ] }, { "page": "geo_gj_raw", "title": "The unparsed submissions of a form containing geofields in GeoJSON.", "concept": [ "included" ], "topics": [ "geo_gj_raw" ] }, { "page": "geo_gj88", "title": "The parsed submissions of a form containing geofields in GeoJSON with trailing empty coordinates present.", "concept": [ "included" ], "topics": [ "geo_gj88" ] }, { "page": "geo_wkt", "title": "The parsed submissions of a form containing geofields in WKT.", "concept": [ "included" ], "topics": [ "geo_wkt" ] }, { "page": "geo_wkt_raw", "title": "The unparsed submissions of a form containing geofields in WKT.", "concept": [ "included" ], "topics": [ "geo_wkt_raw" ] }, { "page": "geo_wkt88", "title": "The parsed submissions of a form containing geofields in WKT with trailing empty coordinates present.", "concept": [ "included" ], "topics": [ "geo_wkt88" ] }, { "page": "get_one_attachment", "title": "Download one media attachment.", "concept": [ "utilities" ], "topics": [ "get_one_attachment" ] }, { "page": "get_one_submission", "title": "Download one submission.", "concept": [ "utilities" ], "topics": [ "get_one_submission" ] }, { "page": "get_one_submission_att_list", "title": "List all attachments of one submission.", "concept": [ "utilities" ], "topics": [ "get_one_submission_att_list" ] }, { "page": "get_one_submission_audit", "title": "Download server audit logs for one submission.", "concept": [ "utilities" ], "topics": [ "get_one_submission_audit" ] }, { "page": "handle_ru_attachments", "title": "Download and link submission attachments according to a form schema.", "concept": [ "utilities" ], "topics": [ "handle_ru_attachments" ] }, { "page": "handle_ru_datetimes", "title": "Parse datetimes of submission data according to a form schema.", "concept": [ "utilities" ], "topics": [ "handle_ru_datetimes" ] }, { "page": "handle_ru_geopoints", "title": "Split all geopoints of a submission tibble into their components.", "concept": [ "utilities" ], "topics": [ "handle_ru_geopoints" ] }, { "page": "handle_ru_geoshapes", "title": "Split all geoshapes of a submission tibble into their components.", "concept": [ "utilities" ], "topics": [ "handle_ru_geoshapes" ] }, { "page": "handle_ru_geotraces", "title": "Split all geotraces of a submission tibble into their components.", "concept": [ "utilities" ], "topics": [ "handle_ru_geotraces" ] }, { "page": "odata_entitylist_data_get", "title": "Get the Data Document from the OData Dataset Service.", "concept": [ "entity-management" ], "topics": [ "odata_entitylist_data_get" ] }, { "page": "odata_entitylist_metadata_get", "title": "Get the Metadata Document from the OData Dataset Service.", "concept": [ "entity-management" ], "topics": [ "odata_entitylist_metadata_get" ] }, { "page": "odata_entitylist_service_get", "title": "Get the Service Document from the OData Dataset Service.", "concept": [ "entity-management" ], "topics": [ "odata_entitylist_service_get" ] }, { "page": "odata_metadata_get", "title": "Retrieve metadata from an OData URL ending in .svc as list of lists.", "concept": [ "odata-api" ], "topics": [ "odata_metadata_get" ] }, { "page": "odata_service_get", "title": "Retrieve service metadata from an OData URL ending in .svc as tibble.", "concept": [ "odata-api" ], "topics": [ "odata_service_get" ] }, { "page": "odata_submission_get", "title": "Retrieve and rectangle form submissions, parse dates, geopoints, download and link attachments.", "concept": [ "odata-api" ], "topics": [ "odata_submission_get" ] }, { "page": "odata_submission_rectangle", "title": "Rectangle the output of 'odata_submission_get(parse=FALSE)' into a tidy tibble and unnest all levels.", "concept": [ "utilities" ], "topics": [ "odata_submission_rectangle" ] }, { "page": "odata_svc_parse", "title": "Retrieve URL, project ID, and form ID from an ODK Central OData service URL.", "concept": [ "ru_settings" ], "topics": [ "odata_svc_parse" ] }, { "page": "parse_odkc_version", "title": "Parse a given ODK Central version string or number into a 'semver'.", "concept": [ "ru_settings" ], "topics": [ "parse_odkc_version" ] }, { "page": "print.odata_entitylist_data_get", "title": "Print an OData EntityList data object.", "concept": [ "entity-management" ], "topics": [ "print.odata_entitylist_data_get" ] }, { "page": "print.odata_entitylist_metadata_get", "title": "Print an OData EntityList metadata object.", "concept": [ "entity-management" ], "topics": [ "print.odata_entitylist_metadata_get" ] }, { "page": "print.odata_entitylist_service_get", "title": "Print an OData EntityList service object.", "concept": [ "entity-management" ], "topics": [ "print.odata_entitylist_service_get" ] }, { "page": "print.ru_settings", "title": "Print ruODK settings.", "concept": [ "ru_settings" ], "topics": [ "print.ru_settings" ] }, { "page": "project_assignment_actors", "title": "List all Actors assigned some Project Role.", "concept": [ "project-management" ], "topics": [ "project_assignment_actors" ] }, { "page": "project_assignment_grant", "title": "Assign an Actor to a Project Role.", "concept": [ "project-management" ], "topics": [ "project_assignment_grant" ] }, { "page": "project_assignment_list", "title": "List all Assignments of one Project.", "concept": [ "user-management" ], "topics": [ "project_assignment_list" ] }, { "page": "project_assignment_revoke", "title": "Revoke a Project Role Assignment from an Actor.", "concept": [ "project-management" ], "topics": [ "project_assignment_revoke" ] }, { "page": "project_create", "title": "Create a new project.", "concept": [ "project-management" ], "topics": [ "project_create" ] }, { "page": "project_delete", "title": "Delete a Project.", "concept": [ "project-management" ], "topics": [ "project_delete" ] }, { "page": "project_detail", "title": "List all details of one project.", "concept": [ "project-management" ], "topics": [ "project_detail" ] }, { "page": "project_enable_encryption", "title": "Enable Project Managed Encryption.", "concept": [ "project-management" ], "topics": [ "project_enable_encryption" ] }, { "page": "project_list", "title": "List all projects.", "concept": [ "project-management" ], "topics": [ "project_list" ] }, { "page": "project_replace", "title": "Replace a Project.", "concept": [ "project-management" ], "topics": [ "project_replace" ] }, { "page": "project_update", "title": "Modify a Project.", "concept": [ "project-management" ], "topics": [ "project_update" ] }, { "page": "public_link_create", "title": "Create a Public Access Link for one Form.", "concept": [ "form-management" ], "topics": [ "public_link_create" ] }, { "page": "public_link_delete", "title": "Delete a Public Access Link.", "concept": [ "form-management" ], "topics": [ "public_link_delete" ] }, { "page": "public_link_detail", "title": "Show details of one Public Access Link.", "concept": [ "form-management" ], "topics": [ "public_link_detail" ] }, { "page": "public_link_list", "title": "List all Public Access Links of one Form.", "concept": [ "form-management" ], "topics": [ "public_link_list" ] }, { "page": "public_link_update", "title": "Set Actor Property values on a Public Access Link.", "concept": [ "form-management" ], "topics": [ "public_link_update" ] }, { "page": "role_detail", "title": "Show details of one Role.", "concept": [ "user-management" ], "topics": [ "role_detail" ] }, { "page": "role_list", "title": "List all Roles.", "concept": [ "user-management" ], "topics": [ "role_list" ] }, { "page": "ru_msg_abort", "title": "Abort with an error message.", "concept": [ "messaging" ], "topics": [ "ru_msg_abort" ] }, { "page": "ru_msg_info", "title": "Print an info message.", "concept": [ "messaging" ], "topics": [ "ru_msg_info" ] }, { "page": "ru_msg_noop", "title": "Print a noop message.", "concept": [ "messaging" ], "topics": [ "ru_msg_noop" ] }, { "page": "ru_msg_success", "title": "Print a success message.", "concept": [ "messaging" ], "topics": [ "ru_msg_success" ] }, { "page": "ru_msg_warn", "title": "Signal a warning message.", "concept": [ "messaging" ], "topics": [ "ru_msg_warn" ] }, { "page": "ru_settings", "title": "Get or set 'ruODK' settings.", "concept": [ "ru_settings" ], "topics": [ "get_default_fid", "get_default_odkc_version", "get_default_orders", "get_default_pid", "get_default_pp", "get_default_pw", "get_default_tz", "get_default_un", "get_default_url", "get_retries", "get_ru_verbose", "get_test_fid", "get_test_fid_att", "get_test_fid_gap", "get_test_fid_wkt", "get_test_fid_zip", "get_test_odkc_version", "get_test_pid", "get_test_pp", "get_test_pw", "get_test_un", "get_test_url", "ru_settings" ] }, { "page": "ru_setup", "title": "Configure default 'ruODK' settings.", "concept": [ "ru_settings" ], "topics": [ "ru_setup" ] }, { "page": "semver_gt", "title": "Show whether a given semver is greater than a baseline version.", "concept": [ "ru_settings" ], "topics": [ "semver_gt" ] }, { "page": "semver_lt", "title": "Show whether a given semver is lesser than a baseline version.", "concept": [ "ru_settings" ], "topics": [ "semver_lt" ] }, { "page": "split_geopoint", "title": "Annotate a dataframe containing a geopoint column with lon, lat, alt.", "concept": [ "utilities" ], "topics": [ "split_geopoint" ] }, { "page": "split_geoshape", "title": "Annotate a dataframe containing a geoshape column with lon, lat, alt of the geotrace's first point.", "concept": [ "utilities" ], "topics": [ "split_geoshape" ] }, { "page": "split_geotrace", "title": "Annotate a dataframe containing a geotrace column with lon, lat, alt of the geotrace's first point.", "concept": [ "utilities" ], "topics": [ "split_geotrace" ] }, { "page": "submission_audit_get", "title": "Get submission audits for a list of submission instance IDs.", "concept": [ "submission-management" ], "topics": [ "submission_audit_get" ] }, { "page": "submission_changes", "title": "Show changes between versions of one Submission.", "concept": [ "submission-management" ], "topics": [ "submission_changes" ] }, { "page": "submission_comment_create", "title": "Post a comment to one Submission.", "concept": [ "submission-management" ], "topics": [ "submission_comment_create" ] }, { "page": "submission_comment_list", "title": "List all comments of one Submission.", "concept": [ "submission-management" ], "topics": [ "submission_comment_list" ] }, { "page": "submission_create", "title": "Create a Submission.", "concept": [ "submission-management" ], "topics": [ "submission_create" ] }, { "page": "submission_csv", "title": "Export the root Submission table to CSV.", "concept": [ "submission-management" ], "topics": [ "submission_csv" ] }, { "page": "submission_delete", "title": "Delete a Submission.", "concept": [ "submission-management" ], "topics": [ "submission_delete" ] }, { "page": "submission_detail", "title": "Show metadata for one submission.", "concept": [ "submission-management" ], "topics": [ "submission_detail" ] }, { "page": "submission_draft_attachment_delete", "title": "Clear an attachment of a Draft Submission.", "concept": [ "submission-management" ], "topics": [ "submission_draft_attachment_delete" ] }, { "page": "submission_draft_attachment_download", "title": "Download one attachment of a Draft Submission.", "concept": [ "submission-management" ], "topics": [ "submission_draft_attachment_download" ] }, { "page": "submission_draft_attachment_list", "title": "List expected attachments of one Draft Submission.", "concept": [ "submission-management" ], "topics": [ "submission_draft_attachment_list" ] }, { "page": "submission_draft_attachment_upload", "title": "Upload an attachment of a Draft Submission.", "concept": [ "submission-management" ], "topics": [ "submission_draft_attachment_upload" ] }, { "page": "submission_draft_create", "title": "Create a Submission on a Draft Form.", "concept": [ "submission-management" ], "topics": [ "submission_draft_create" ] }, { "page": "submission_draft_export", "title": "Export Draft Submissions to CSV.", "concept": [ "submission-management" ], "topics": [ "submission_draft_export" ] }, { "page": "submission_draft_get", "title": "Download one Draft Submission.", "concept": [ "submission-management" ], "topics": [ "submission_draft_get" ] }, { "page": "submission_draft_keys", "title": "List encryption keys of Draft Submissions.", "concept": [ "submission-management" ], "topics": [ "submission_draft_keys" ] }, { "page": "submission_draft_list", "title": "List all Submissions of a Draft Form.", "concept": [ "submission-management" ], "topics": [ "submission_draft_list" ] }, { "page": "submission_edit", "title": "Edit one Submission field and leave a comment.", "concept": [ "submission-management" ], "topics": [ "submission_edit" ] }, { "page": "submission_export", "title": "Export all form submissions including repeats and attachments to CSV.", "concept": [ "submission-management" ], "topics": [ "submission_export" ] }, { "page": "submission_geodata", "title": "Get Submissions geodata as GeoJSON.", "concept": [ "submission-management" ], "topics": [ "submission_geodata" ] }, { "page": "submission_geojson", "title": "Get the GeoJSON of one Submission.", "concept": [ "submission-management" ], "topics": [ "submission_geojson" ] }, { "page": "submission_get", "title": "Get submissions for a list of submission instance IDs.", "concept": [ "submission-management" ], "topics": [ "submission_get" ] }, { "page": "submission_list", "title": "List all submissions of one form.", "concept": [ "submission-management" ], "topics": [ "submission_list" ] }, { "page": "submission_restore", "title": "Restore a deleted Submission.", "concept": [ "submission-management" ], "topics": [ "submission_restore" ] }, { "page": "submission_review", "title": "Review a Submission.", "concept": [ "submission-management" ], "topics": [ "submission_review" ] }, { "page": "submission_submitters", "title": "List all submitting Actors of one Form.", "concept": [ "submission-management" ], "topics": [ "submission_submitters" ] }, { "page": "submission_update", "title": "Update Submission data.", "concept": [ "submission-management" ], "topics": [ "submission_update" ] }, { "page": "submission_version_attachment_delete", "title": "Clear one attachment of a Submission version.", "concept": [ "submission-management" ], "topics": [ "submission_version_attachment_delete" ] }, { "page": "submission_version_attachment_download", "title": "Download one attachment of a Submission version.", "concept": [ "submission-management" ], "topics": [ "submission_version_attachment_download" ] }, { "page": "submission_version_attachment_list", "title": "List expected attachments of one Submission version.", "concept": [ "submission-management" ], "topics": [ "submission_version_attachment_list" ] }, { "page": "submission_version_detail", "title": "Show details of one Submission version.", "concept": [ "submission-management" ], "topics": [ "submission_version_detail" ] }, { "page": "submission_version_geojson", "title": "Get the GeoJSON of one Submission version.", "concept": [ "submission-management" ], "topics": [ "submission_version_geojson" ] }, { "page": "submission_version_xml", "title": "Show the XML of one Submission version.", 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Delineation entails\nthe identification of corridor boundaries, segmentation of the\ncorridor, and delineation of the river space using\ntwo-dimensional spatial information from street network data\nand digital elevation data in a projected CRS. The resulting\ndelineation can be used to characterise spatial phenomena that\ncan be related to the river as a central element.", "License": "Apache License (>= 2)", "URL": "https://cityriverspaces.github.io/rcrisp/,\nhttps://github.com/CityRiverSpaces/rcrisp,\nhttps://doi.org/10.5281/zenodo.15793526", "BugReports": "https://github.com/CityRiverSpaces/rcrisp/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE, roclets = c(\"namespace\", \"rd\",\n\"srr::srr_stats_roclet\"))", "Config/roxygen2/version": "8.1.1", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibglpk-dev libicu-dev libjpeg-dev libpng-dev libxml2-dev\nlibssl-dev libproj-dev libsqlite3-dev libudunits2-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-10-20 18:48:41 UTC", "RemoteUrl": "https://github.com/CityRiverSpaces/rcrisp", "RemoteRef": "main", "RemoteSha": 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"ElementProvider", "ElementProvider_en_US", "ElementProvider_nl_NL", "FileProvider", "FileProvider_en_US", "fraudster", "FraudsterClient", "InternetProvider", "InternetProvider_bg_BG", "InternetProvider_cs_CZ", "InternetProvider_de_DE", "InternetProvider_en_AU", "InternetProvider_en_NZ", "InternetProvider_en_US", "InternetProvider_fa_IR", "InternetProvider_fr_FR", "InternetProvider_hr_HR", "ISBNProvider", "JobProvider", "JobProvider_da_DK", "JobProvider_en_US", "JobProvider_fa_IR", "JobProvider_fi_FI", "JobProvider_fr_CH", "JobProvider_fr_FR", "JobProvider_hr_HR", "JobProvider_nl_NL", "JobProvider_pl_PL", "JobProvider_ru_RU", "JobProvider_uk_UA", "JobProvider_zh_TW", "LoremProvider", "LoremProvider_ar_AA", "LoremProvider_el_GR", "LoremProvider_en_US", "LoremProvider_he_IL", "LoremProvider_ja_JP", "LoremProvider_la", "LoremProvider_ru_RU", "LoremProvider_zh_CN", "LoremProvider_zh_TW", "MiscProvider", "MissingDataProvider", "NumericsProvider", "PersonProvider", "PersonProvider_bg_BG", "PersonProvider_cs_CZ", "PersonProvider_da_DK", "PersonProvider_de_AT", "PersonProvider_de_DE", "PersonProvider_en_GB", "PersonProvider_en_NZ", "PersonProvider_en_US", "PersonProvider_es_ES", "PersonProvider_es_MX", "PersonProvider_fa_IR", "PersonProvider_fi_FI", "PersonProvider_fr_CH", "PersonProvider_fr_FR", "PersonProvider_hr_HR", "PersonProvider_it_IT", "PersonProvider_ja_JP", "PersonProvider_ko_KR", "PersonProvider_lt_LT", "PersonProvider_lv_LV", "PersonProvider_ne_NP", "PersonProvider_nl_NL", "PersonProvider_no_NO", "PersonProvider_pl_PL", "PhoneNumberProvider", "PhoneNumberProvider_bg_BG", "PhoneNumberProvider_bs_BA", "PhoneNumberProvider_cs_CZ", "PhoneNumberProvider_da_DK", "PhoneNumberProvider_de_DE", "PhoneNumberProvider_dk_DK", "PhoneNumberProvider_el_GR", "PhoneNumberProvider_en_AU", "PhoneNumberProvider_en_CA", "PhoneNumberProvider_en_GB", "PhoneNumberProvider_en_NZ", "PhoneNumberProvider_en_US", "PhoneNumberProvider_es_ES", "PhoneNumberProvider_es_MX", "PhoneNumberProvider_es_PE", "PhoneNumberProvider_fa_IR", "PhoneNumberProvider_fi_FI", "PhoneNumberProvider_fr_CH", "PhoneNumberProvider_fr_FR", "PhoneNumberProvider_he_IL", "PhoneNumberProvider_hi_IN", "PhoneNumberProvider_hr_HR", "PhoneNumberProvider_hu_HU", "PhoneNumberProvider_id_ID", "PhoneNumberProvider_it_IT", "PhoneNumberProvider_ja_JP", "PhoneNumberProvider_ko_KR", "PhoneNumberProvider_lt_LT", "PhoneNumberProvider_lv_LV", "PhoneNumberProvider_ne_NP", "PhoneNumberProvider_nl_BE", "PhoneNumberProvider_nl_NL", "PhoneNumberProvider_nn_NO", "PhoneNumberProvider_no_NO", "PhoneNumberProvider_pl_PL", "PhoneNumberProvider_pt_BR", "PhoneNumberProvider_pt_PT", "PhoneNumberProvider_ru_RU", "PhoneNumberProvider_sk_SK", "PhoneNumberProvider_sv_SE", "PhoneNumberProvider_th_TH", "PhoneNumberProvider_tr_TR", "PhoneNumberProvider_uk_UA", "PhoneNumberProvider_zh_TW", "SequenceProvider", "SSNProvider", "SSNProvider_en_US", "SSNProvider_nl_NL", "subclass", "TaxonomyProvider", "TaxonomyProvider_en_US", "UserAgentProvider", "UserAgentProvider_en_US" ], "_datasets": [ { "name": "available_locales_df", "title": "Available locales", "object": "available_locales_df", "class": [ "data.frame" ], "fields": [ "Language", "Country", "Variant", "Name" ], "rows": 52, "table": true, "tojson": true }, { "name": "available_providers", "title": "Available Providers", "object": "available_providers", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "charlatan-package", "title": "charlatan", "topics": [ "charlatan-package", "charlatan" ] }, { "page": "AddressProvider", "title": "AddressProvider", "concept": [ "ParentProviders" ], "topics": [ "AddressProvider" ] }, { "page": "AddressProvider_en_GB", "title": "AddressProvider for English, Great Britain", "concept": [ "GB", "en" ], "topics": [ "AddressProvider_en_GB" ] }, { "page": "AddressProvider_en_NZ", "title": "AddressProvider for New-Zealand", "concept": [ "NZ", "en" ], "topics": [ "AddressProvider_en_NZ" ] }, { "page": "AddressProvider_en_US", "title": "AddressProvider for United States of America", "concept": [ "US", "en" ], "topics": [ "AddressProvider_en_US" ] }, { "page": "AddressProvider_nl_NL", "title": "AddressProvider for The Netherlands", "concept": [ "NL", "nl" ], "topics": [ "AddressProvider_nl_NL" ] }, { "page": "arabic-language", "title": "Arabic Language", "concept": [ "ar", "languages" ], "topics": [ "arabic-language" ] }, { "page": "available_locales_df", "title": "Available locales", "topics": [ "available_locales_df" ] }, { "page": "available_providers", "title": "Available Providers", "topics": [ "available_providers" ] }, { "page": "BareProvider", "title": "A NonLocalized Provider that contains all the selection and creation elements, but not the locales. That way we can still inherit an do useful stuff for providers that have no locale.", "topics": [ "BareProvider" ] }, { "page": "BaseProvider", "title": "BaseProvider", "topics": [ "BaseProvider" ] }, { "page": "bosnian-language", "title": "Bosnian Language", "concept": [ "bs", "languages" ], "topics": [ "bosnian-language" ] }, { "page": "bulgarian-language", "title": "Bulgarian Language", "concept": [ "bg", "languages" ], "topics": [ "bulgarian-language" ] }, { "page": "ch_color", "title": "Create fake colors", "topics": [ "ch_color", "ch_color_name", "ch_hex_color", "ch_rgb_color", "ch_rgb_css_color", "ch_safe_color_name", "ch_safe_hex_color" ] }, { "page": "ch_company", "title": "Create fake company names and other company bits", "topics": [ "ch_company" ] }, { "page": "ch_credit", "title": "Create fake credit card data", "topics": [ "ch_credit", "ch_credit_card_number", "ch_credit_card_provider", "ch_credit_card_security_code" ] }, { "page": "ch_currency", "title": "Create fake currencies", "topics": [ "ch_currency" ] }, { "page": "ch_doi", "title": "Create fake DOIs (Digital Object Identifiers)", "topics": [ "ch_doi" ] }, { "page": "ch_gene_sequence", "title": "Create fake gene sequences", "topics": [ "ch_gene_sequence" ] }, { "page": "ch_generate", "title": "Generate a fake dataset", "topics": [ "ch_generate" ] }, { "page": "ch_job", "title": "Create fake jobs", "topics": [ "ch_job" ] }, { "page": "ch_missing", "title": "Create missing data", "topics": [ "ch_missing" ] }, { "page": "ch_name", "title": "Create fake person names", "topics": [ "ch_name" ] }, { "page": "ch_phone_number", "title": "Create fake phone numbers", "topics": [ "ch_phone_number" ] }, { "page": "ch_ssn", "title": "Create fake Social Security Numbers", "topics": [ "ch_ssn" ] }, { "page": "charlatan_locales", "title": "Available locales", "topics": [ "charlatan_locales" ] }, { "page": "charlatan_settings", "title": "charlatan settings", "topics": [ "charlatan_settings" ] }, { "page": "chinese-language", "title": "Chinese Language", "concept": [ "languages", "zh" ], "topics": [ "chinese-language" ] }, { "page": "ColorProvider", "title": "ColorProvider", "concept": [ "ParentProviders" ], "topics": [ "ColorProvider" ] }, { "page": "ColorProvider_en_US", "title": "ColorProvider", "concept": [ "US", "en" ], "topics": [ "ColorProvider_en_US" ] }, { "page": "ColorProvider_uk_UA", "title": "ColorProvider Ukrainian (Ukraine)", "concept": [ "UA", "uk" ], "topics": [ "ColorProvider_uk_UA" ] }, { "page": "CompanyProvider", "title": "CompanyProvider", "concept": [ "ParentProviders" ], "topics": [ "CompanyProvider" ] }, { "page": "CompanyProvider_bg_BG", "title": "CompanyProvider for Bulgarian (Bulgaria)", "concept": [ "BG", "bg" ], "topics": [ "CompanyProvider_bg_BG" ] }, { "page": "CompanyProvider_cs_CZ", "title": "CompanyProvider for Czech", "concept": [ "CZ", "cs" ], "topics": [ "CompanyProvider_cs_CZ" ] }, { "page": "CompanyProvider_de_DE", "title": "CompanyProvider for German (Germany)", "concept": [ "DE", "de" ], "topics": [ "CompanyProvider_de_DE" ] }, { "page": "CompanyProvider_en_US", "title": "CompanyProvider for English (United States)", "concept": [ "US", "en" ], "topics": [ "CompanyProvider_en_US" ] }, { "page": "CompanyProvider_es_MX", "title": "CompanyProvider Spanish (Mexico)", "concept": [ "MX", "es" ], "topics": [ "CompanyProvider_es_MX" ] }, { "page": "CompanyProvider_fa_IR", "title": "CompanyProvider Persian (Iran)", "concept": [ "IR", "fa" ], "topics": [ "CompanyProvider_fa_IR" ] }, { "page": "CompanyProvider_fr_FR", "title": "CompanyProvider for France (French)", "concept": [ "FR", "fr" ], "topics": [ "CompanyProvider_fr_FR" ] }, { "page": "CompanyProvider_hr_HR", "title": "CompanyProvider Croatian (Croatia)", "concept": [ "HR", "hr" ], "topics": [ "CompanyProvider_hr_HR" ] }, { "page": "CompanyProvider_it_IT", "title": "CompanyProvider Italian (Italy)", "concept": [ "IT", "it" ], "topics": [ "CompanyProvider_it_IT" ] }, { "page": "coordinates", "title": "Create fake coordinates", "topics": [ "ch_lat", "ch_lon", "ch_position", "coordinates" ] }, { "page": "croatian-language", "title": "Croatian Language", "concept": [ "hr", "languages" ], "topics": [ "croatian-language" ] }, { "page": "czech-language", "title": "Czech Language", "concept": [ "cs", "languages" ], "topics": [ "czech-language" ] }, { "page": "danish-language", "title": "Danish Language", "concept": [ "da", "languages" ], "topics": [ "danish-language" ] }, { "page": "date_time", "title": "Create dates and times", "topics": [ "ch_date_time", "ch_timezone", "ch_unix_time", "date_time" ] }, { "page": "DateTimeProvider", "title": "DateTimeProvider", "topics": [ "DateTimeProvider" ] }, { "page": "dutch-language", "title": "Dutch Language", "concept": [ "languages", "nl" ], "topics": [ "dutch-language" ] }, { "page": "ElementProvider_en_US", "title": "ElementProvider for USA", "concept": [ "US", "en" ], "topics": [ "ElementProvider_en_US" ] }, { "page": "ElementProvider_nl_NL", "title": "ElementProvider for the Netherlands", "concept": [ "NL", "nl" ], "topics": [ "ElementProvider_nl_NL" ] }, { "page": "elements", "title": "Get elements", "topics": [ "ch_element_element", "ch_element_symbol", "elements" ] }, { "page": "english-language", "title": "English Language", "concept": [ "en", "languages" ], "topics": [ "english-language" ] }, { "page": "farsi-language", "title": "Farsi Language", "concept": [ "fa", "languages" ], "topics": [ "farsi-language" ] }, { "page": "FileProvider_en_US", "title": "File Provider for United States English", "concept": [ "US", "en" ], "topics": [ "FileProvider_en_US" ] }, { "page": "finnish-language", "title": "Finnish Language", "concept": [ "fl", "languages" ], "topics": [ "finnish-language" ] }, { "page": "fraudster", "title": "Fraudster - catch all client to make all types of fake data", "topics": [ "fraudster" ] }, { "page": "french-language", "title": "French Language", "concept": [ "fr", "languages" ], "topics": [ "french-language" ] }, { "page": "german-language", "title": "German Language", "concept": [ "de", "languages" ], "topics": [ "german-language" ] }, { "page": "greek-language", "title": "Greek Language", "concept": [ "el", "languages" ], "topics": [ "greek-language" ] }, { "page": "hebrew-language", "title": "Hebrew Language", "concept": [ "he", "languages" ], "topics": [ "hebrew-language" ] }, { "page": "hindi-language", "title": "Hindi Language", "concept": [ "hi", "languages" ], "topics": [ "hindi-language" ] }, { "page": "hungarian-language", "title": "Hungarian Language", "concept": [ "hu", "languages" ], "topics": [ "hungarian-language" ] }, { "page": "indonesian-language", "title": "Indonesian Language", "concept": [ "id", "languages" ], "topics": [ "indonesian-language" ] }, { "page": "InternetProvider", "title": "InternetProvider", "concept": [ "ParentProviders" ], "topics": [ "InternetProvider" ] }, { "page": "InternetProvider_bg_BG", "title": "Internet provider for Bulgarian (Bulgaria)", "concept": [ "BG", "bg" ], "topics": [ "InternetProvider_bg_BG" ] }, { "page": "InternetProvider_cs_CZ", "title": "Internet provider Czech", "concept": [ "CZ", "cs" ], "topics": [ "InternetProvider_cs_CZ" ] }, { "page": "InternetProvider_de_DE", "title": "Internet provider German (Germany)", "concept": [ "DE", "de" ], "topics": [ "InternetProvider_de_DE" ] }, { "page": "InternetProvider_en_AU", "title": "Internet provider English (Australia)", "concept": [ "AU", "en" ], "topics": [ "InternetProvider_en_AU" ] }, { "page": "InternetProvider_en_NZ", "title": "Internet provider for New-Zealand", "concept": [ "BG", "bg" ], "topics": [ "InternetProvider_en_NZ" ] }, { "page": "InternetProvider_en_US", "title": "Internet provider for United States", "concept": [ "US", "en" ], "topics": [ "InternetProvider_en_US" ] }, { "page": "InternetProvider_fa_IR", "title": "Internet provider for Iran", "concept": [ "IR", "fa" ], "topics": [ "InternetProvider_fa_IR" ] }, { "page": "InternetProvider_fr_FR", "title": "Internet provider for France", "concept": [ "FR", "fr" ], "topics": [ "InternetProvider_fr_FR" ] }, { "page": "InternetProvider_hr_HR", "title": "Internet provider for Croatian (Croatia)", "concept": [ "HR", "hr" ], "topics": [ "InternetProvider_hr_HR" ] }, { "page": "ISBNProvider", "title": "ISBNProvider", "topics": [ "ISBNProvider" ] }, { "page": "italian-language", "title": "Italian Language", "concept": [ "it", "languages" ], "topics": [ "italian-language" ] }, { "page": "japanese-language", "title": "Japanese Language", "concept": [ "ja", "languages" ], "topics": [ "japanese-language" ] }, { "page": "JobProvider", "title": "JobProvider", "concept": [ "ParentProviders" ], "topics": [ "JobProvider" ] }, { "page": "JobProvider_da_DK", "title": "Job provider for Danish", "concept": [ "DK", "da" ], "topics": [ "JobProvider_da_DK" ] }, { "page": "JobProvider_en_US", "title": "Job provider for United States", "concept": [ "US", "en" ], "topics": [ "JobProvider_en_US" ] }, { "page": "JobProvider_fa_IR", "title": "Job provider for Iran (Persian)", "concept": [ "IR", "fa" ], "topics": [ "JobProvider_fa_IR" ] }, { "page": "JobProvider_fi_FI", "title": "Job provider for Finnish", "concept": [ "FI", "fi" ], "topics": [ "JobProvider_fi_FI" ] }, { "page": "JobProvider_fr_CH", "title": "Job provider for Zwitserland", "concept": [ "CH", "fr" ], "topics": [ "JobProvider_fr_CH" ] }, { "page": "JobProvider_fr_FR", "title": "Job provider for France", "concept": [ "FR", "fr" ], "topics": [ "JobProvider_fr_FR" ] }, { "page": "JobProvider_hr_HR", "title": "Job provider for Croatia", "concept": [ "HR", "hr" ], "topics": [ "JobProvider_hr_HR" ] }, { "page": "JobProvider_nl_NL", "title": "Job provider for Netherlands", "concept": [ "NL", "nl" ], "topics": [ "JobProvider_nl_NL" ] }, { "page": "JobProvider_pl_PL", "title": "Job provider for Poland", "concept": [ "PL", "pl" ], "topics": [ "JobProvider_pl_PL" ] }, { "page": "JobProvider_ru_RU", "title": "Job provider for Russia", "concept": [ "RU", "ru" ], "topics": [ "JobProvider_ru_RU" ] }, { "page": "JobProvider_uk_UA", "title": "Job provider for Ukraine", "concept": [ "UA", "uk" ], "topics": [ "JobProvider_uk_UA" ] }, { "page": "JobProvider_zh_TW", "title": "Job provider for Taiwan", "concept": [ "TW", "zh" ], "topics": [ "JobProvider_zh_TW" ] }, { "page": "korean-language", "title": "Korean Language", "concept": [ "ko", "languages" ], "topics": [ "korean-language" ] }, { "page": "latin-language", "title": "Latin Language", "concept": [ "la", "languages" ], "topics": [ "latin-language" ] }, { "page": "latvian-language", "title": "Latvian Language", "concept": [ "languages", "lv" ], "topics": [ "latvian-language" ] }, { "page": "lithuanian-language", "title": "Lithuanian Language", "concept": [ "languages", "lt" ], "topics": [ "lithuanian-language" ] }, { "page": "LoremProvider", "title": "LoremProvider", "concept": [ "ParentProviders" ], "topics": [ "LoremProvider" ] }, { "page": "LoremProvider_ar_AA", "title": "Lorem provider Arabic", "concept": [ "AA", "ar" ], "topics": [ "LoremProvider_ar_AA" ] }, { "page": "LoremProvider_el_GR", "title": "Lorem provider Greek (Greece)", "concept": [ "GR", "el" ], "topics": [ "LoremProvider_el_GR" ] }, { "page": "LoremProvider_en_US", "title": "Lorem provider English (USA)", "concept": [ "US", "en" ], "topics": [ "LoremProvider_en_US" ] }, { "page": "LoremProvider_he_IL", "title": "Lorem provider Hebrew", "concept": [ "IL", "he" ], "topics": [ "LoremProvider_he_IL" ] }, { "page": "LoremProvider_ja_JP", "title": "Lorem provider Japanese", "concept": [ "JP", "ja" ], "topics": [ "LoremProvider_ja_JP" ] }, { "page": "LoremProvider_la", "title": "Lorem provider Latin", "concept": [ "la" ], "topics": [ "LoremProvider_la" ] }, { "page": "LoremProvider_ru_RU", "title": "Lorem provider Russian (Russia)", "concept": [ "RU", "ru" ], "topics": [ "LoremProvider_ru_RU" ] }, { "page": "LoremProvider_zh_CN", "title": "Lorem provider Chinese (China)", "concept": [ "CN", "zh" ], "topics": [ "LoremProvider_zh_CN" ] }, { "page": "LoremProvider_zh_TW", "title": "Lorem provider Chinese (Taiwan)", "concept": [ "TW", "zh" ], "topics": [ "LoremProvider_zh_TW" ] }, { "page": "norwegian-language", "title": "Norwegian Language", "concept": [ "languages", "no" ], "topics": [ "norwegian-language" ] }, { "page": "numerics", "title": "Create numbers", "topics": [ "ch_beta", "ch_double", "ch_integer", "ch_lnorm", "ch_norm", "ch_unif", "numerics" ] }, { "page": "PersonProvider", "title": "PersonProvider", "concept": [ "ParentProviders" ], "topics": [ "PersonProvider" ] }, { "page": "PersonProvider_bg_BG", "title": "Person Provider for Bulgarian (Bulgaria)", "concept": [ "BG", "bg" ], "topics": [ "PersonProvider_bg_BG" ] }, { "page": "PersonProvider_cs_CZ", "title": "Person Provider for Czech (Czech Republic)", "concept": [ "CZ", "cs" ], "topics": [ "PersonProvider_cs_CZ" ] }, { "page": "PersonProvider_da_DK", "title": "Person Provider for Danish (Denmark)", "concept": [ "DK", "da" ], "topics": [ "PersonProvider_da_DK" ] }, { "page": "PersonProvider_de_AT", "title": "Person Provider for Austrian German", "concept": [ "AT", "de" ], "topics": [ "PersonProvider_de_AT" ] }, { "page": "PersonProvider_de_DE", "title": "Person Provider for German (Germany)", "concept": [ "DE", "de" ], "topics": [ "PersonProvider_de_DE" ] }, { "page": "PersonProvider_en_GB", "title": "Person Provider for English (Great Brittain)", "concept": [ "GB", "en" ], "topics": [ "PersonProvider_en_GB" ] }, { "page": "PersonProvider_en_NZ", "title": "Person Provider for English (New Zealand)", "concept": [ "NZ", "en" ], "topics": [ "PersonProvider_en_NZ" ] }, { "page": "PersonProvider_en_US", "title": "Person Provider for English (United States)", "concept": [ "US", "en" ], "topics": [ "PersonProvider_en_US" ] }, { "page": "PersonProvider_es_ES", "title": "Person Provider for Spanish (Spain)", "concept": [ "ES", "es" ], "topics": [ "PersonProvider_es_ES" ] }, { "page": "PersonProvider_es_MX", "title": "Person Provider for Spanish (Mexico)", "concept": [ "MX", "es" ], "topics": [ "PersonProvider_es_MX" ] }, { "page": "PersonProvider_fa_IR", "title": "Person Provider for Farsi (Iran)", "concept": [ "IR", "fa" ], "topics": [ "PersonProvider_fa_IR" ] }, { "page": "PersonProvider_fi_FI", "title": "Person Provider for Finnish (Finland)", "concept": [ "FI", "fi" ], "topics": [ "PersonProvider_fi_FI" ] }, { "page": "PersonProvider_fr_CH", "title": "Person Provider for French (Switzerland)", "concept": [ "CH", "fr" ], "topics": [ "PersonProvider_fr_CH" ] }, { "page": "PersonProvider_fr_FR", "title": "Person Provider for French (France)", "concept": [ "FR", "fr" ], "topics": [ "PersonProvider_fr_FR" ] }, { "page": "PersonProvider_hr_HR", "title": "Person Provider for Croatian (Croatia)", "concept": [ "HR", "hr" ], "topics": [ "PersonProvider_hr_HR" ] }, { "page": "PersonProvider_it_IT", "title": "Person Provider for Italian (Italy)", "concept": [ "IT", "it" ], "topics": [ "PersonProvider_it_IT" ] }, { "page": "PersonProvider_ja_JP", "title": "Person Provider for Japanese (Japan)", "concept": [ "JP", "ja" ], "topics": [ "PersonProvider_ja_JP" ] }, { "page": "PersonProvider_ko_KR", "title": "Person Provider for Korean (Republic of Korea)", "concept": [ "KR", "ko" ], "topics": [ "PersonProvider_ko_KR" ] }, { "page": "PersonProvider_lt_LT", "title": "Person Provider for Lithuanian (Lithuania)", "concept": [ "LT", "lt" ], "topics": [ "PersonProvider_lt_LT" ] }, { "page": "PersonProvider_lv_LV", "title": "Person Provider for Latvian (Latvia)", "concept": [ "LV", "lv" ], "topics": [ "PersonProvider_lv_LV" ] }, { "page": "PersonProvider_ne_NP", "title": "Person Provider for Nepali (Nepal)", "concept": [ "NP", "ne" ], "topics": [ "PersonProvider_ne_NP" ] }, { "page": "PersonProvider_nl_NL", "title": "Person Provider for Dutch (Netherlands)", "concept": [ "NL", "nl" ], "topics": [ "PersonProvider_nl_NL" ] }, { "page": "PersonProvider_no_NO", "title": "Person Provider for Norwegian (Norway)", "concept": [ "NO", "no" ], "topics": [ "PersonProvider_no_NO" ] }, { "page": "PersonProvider_pl_PL", "title": "Person Provider for Polish (Poland)", "concept": [ "PL", "pl" ], "topics": [ "PersonProvider_pl_PL" ] }, { "page": "PhoneNumberProvider", "title": "PhoneNumberProvider", "concept": [ "ParentProviders" ], "topics": [ "PhoneNumberProvider" ] }, { "page": "PhoneNumberProvider_bg_BG", "title": "PhoneNumberProvider for Bulgaria", "concept": [ "BG", "bg" ], "topics": [ "PhoneNumberProvider_bg_BG" ] }, { "page": "PhoneNumberProvider_bs_BA", "title": "PhoneNumberProvider for Bosnia and Herzegovina", "concept": [ "BA", "bs" ], "topics": [ "PhoneNumberProvider_bs_BA" ] }, { "page": "PhoneNumberProvider_cs_CZ", "title": "PhoneNumberProvider for Chechia", "concept": [ "CZ", "cs" ], "topics": [ "PhoneNumberProvider_cs_CZ" ] }, { "page": "PhoneNumberProvider_da_DK", "title": "PhoneNumberProvider for Denmark", "concept": [ "DK", "da" ], "topics": [ "PhoneNumberProvider_da_DK" ] }, { "page": "PhoneNumberProvider_de_DE", "title": "PhoneNumberProvider for Germany", "concept": [ "DE", "de" ], "topics": [ "PhoneNumberProvider_de_DE" ] }, { "page": "PhoneNumberProvider_dk_DK", "title": "PhoneNumberProvider for Denmark", "concept": [ "DK", "dk" ], "topics": [ "PhoneNumberProvider_dk_DK" ] }, { "page": "PhoneNumberProvider_el_GR", "title": "PhoneNumberProvider for Greece", "concept": [ "GR", "el" ], "topics": [ "PhoneNumberProvider_el_GR" ] }, { "page": "PhoneNumberProvider_en_AU", "title": "PhoneNumberProvider for Australia", "concept": [ "AU", "en" ], "topics": [ "PhoneNumberProvider_en_AU" ] }, { "page": "PhoneNumberProvider_en_CA", "title": "PhoneNumberProvider for Canada", "concept": [ "CA", "en" ], "topics": [ "PhoneNumberProvider_en_CA" ] }, { "page": "PhoneNumberProvider_en_GB", "title": "PhoneNumberProvider for Great Britain", "concept": [ "GB", "en" ], "topics": [ "PhoneNumberProvider_en_GB" ] }, { "page": "PhoneNumberProvider_en_NZ", "title": "PhoneNumberProvider for New Zealand", "concept": [ "NZ", "en" ], "topics": [ "PhoneNumberProvider_en_NZ" ] }, { "page": "PhoneNumberProvider_en_US", "title": "PhoneNumberProvider for United States of America", "concept": [ "US", "en" ], "topics": [ "PhoneNumberProvider_en_US" ] }, { "page": "PhoneNumberProvider_es_ES", "title": "PhoneNumberProvider for Spain", "concept": [ "ES", "es" ], "topics": [ "PhoneNumberProvider_es_ES" ] }, { "page": "PhoneNumberProvider_es_MX", "title": "PhoneNumberProvider for Mexico", "concept": [ "MX", "en" ], "topics": [ "PhoneNumberProvider_es_MX" ] }, { "page": "PhoneNumberProvider_es_PE", "title": "PhoneNumberProvider for Peru", "concept": [ "PE", "es" ], "topics": [ "PhoneNumberProvider_es_PE" ] }, { "page": "PhoneNumberProvider_fa_IR", "title": "PhoneNumberProvider for Iran", "concept": [ "IR", "fa" ], "topics": [ 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It performs\nseveral typical preprocessing steps such as download,\nmosaicking, reprojecting and resizing data acquired on a\nspecified time period. All processing parameters can be set\nusing a user-friendly GUI. Users can select which layers of the\noriginal MODIS HDF files they want to process, which additional\nquality indicators should be extracted from aggregated MODIS\nquality assurance layers and, in the case of surface\nreflectance products, which spectral indexes should be computed\nfrom the original reflectance bands. For each output layer,\noutputs are saved as single-band raster files corresponding to\neach available acquisition date. Virtual files allowing access\nto the entire time series as a single file are also created.\nCommand-line execution exploiting a previously saved processing\noptions file is also possible, allowing users to automatically\nupdate time series related to a MODIS product whenever a new\nimage is available. For additional documentation refer to the\nfollowing article: Busetto and Ranghetti (2016)\n.", "License": "GPL-3", "Config/Needs/website": "tidyr, tibbletime", "SystemRequirements": "GDAL (>= 2.1.2) with support for HDF4 format, PROJ\n(>= 4.9.1).", "URL": "https://github.com/ropensci/MODIStsp/,\nhttps://docs.ropensci.org/MODIStsp/", "BugReports": "https://github.com/ropensci/MODIStsp/issues", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Roxygen": "list(markdown = TRUE)", "Encoding": "UTF-8", "Language": "en-US", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibicu-dev libjq-dev libprotobuf-dev libxml2-dev libssl-dev\nlibproj-dev protobuf-compiler libprotoc-dev libsqlite3-dev\nlibudunits2-dev libnode-dev libx11-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-10-06 10:52:05 UTC", "RemoteUrl": "https://github.com/ropensci/MODIStsp", "RemoteRef": "HEAD", "RemoteSha": "dbf9d14feae97239f12474f167884bd7db6df6fb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-06 09:07:18 UTC", "User": "root" }, "Author": "Lorenzo Busetto [aut] (ORCID: ),\nLuigi Ranghetti [aut, cre] (ORCID:\n),\nLeah Wasser [rev] (Leah Wasser reviewed the package for rOpenSci, see\nhttps://github.com/ropensci/software-review/issues/184),\nJeff Hanson [rev] (Jeff Hanson reviewed the package for rOpenSci, see\nhttps://github.com/ropensci/software-review/issues/184),\nBabak Naimi [ctb] (Babak Naimi wrote the function ModisDownload(), on\nwhich some MODIStsp internal functions are based)", "Maintainer": "Luigi Ranghetti ", "_user": "ropensci", "_type": "src", "_file": "MODIStsp_2.1.0.9001.tar.gz", "_fileid": "https://r2.ropensci.org/fd4c69465711d23865684c9f6b12e77e375c2dd3834fcffae6e3953145538831", "_filesize": 3496236, "_sha256": "fd4c69465711d23865684c9f6b12e77e375c2dd3834fcffae6e3953145538831", "_expires": "2027-02-14T09:55:15.000Z", "_created": "2026-11-06T09:07:18.000Z", "_published": "2026-11-06T09:55:17.509Z", 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"topics": [ "MODIStsp-package" ] }, { "page": "bbox_from_file", "title": "Retrieve bbox from a spatial file", "topics": [ "bbox_from_file" ] }, { "page": "check_files_existence", "title": "Check if all files required for a given date already exist", "topics": [ "check_files_existence" ] }, { "page": "check_projection", "title": "Check the validity of the input projection", "topics": [ "check_projection", "check_projection.character", "check_projection.crs", "check_projection.default", "check_projection.numeric" ] }, { "page": "get_mod_dates", "title": "Find MODIS dates included in selected processing period", "topics": [ "get_mod_dates" ] }, { "page": "get_mod_dirs", "title": "Get list of MODIS acquisition dates from NASA CMR", "topics": [ "get_mod_dirs" ] }, { "page": "get_mod_filenames", "title": "Find the names of MODIS images corresponding to the selected dates", "topics": [ "get_mod_filenames" ] }, { "page": "get_reqbands", "title": "Identify the MODIS original bands needed for a 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Suggested the use of local_timzeone().\")),\nperson(\"Max\", \"Moldovan\", email = \"max.moldovan@adelaide.edu.au\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-9680-8474\", \"Contributed valuable feedback on package usage leading to improvements in the package structure and functionality.\")),\nperson(\"Stephen\", \"Bradshaw\", email = \"stephen.bradshaw@dpird.wa.gov.au\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-3096-8787\", \"Identified data structure issues and provided insights that improved package data quality and usability.\")),\nperson(\"Jimmy\", \"Ng\", email = \"jimmy.ng@dpird.wa.gov.au\", role = \"ctb\"),\nperson(\"Steve\", \"Collins\", email = \"steve.collins@dpird.wa.gov.au\", role = \"ctb\",\ncomment = \"Designed the hex logo for 'weatherOz' hex logo.\"),\nperson(\"Adam H.\", \"Sparks\", email = \"adamhsparks@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-0061-8359\")),\nperson(\"Laurens\", \"Geffert\", email = \"laurensgeffert@gmail.com\", role = \"rev\"),\nperson(\"Sam\", \"Rogers\", email = \"sam.rogers@adelaide.edu.au\", role = \"rev\"),\nperson(\"Western Australia Agriculture Authority (WAAA)\", role = \"cph\"),\nperson(\"Curtin University\", role = \"cph\")\n)", "Description": "Provides automated downloading, parsing and formatting of\nweather data for Australia through API endpoints provided by\nthe Department of Primary Industries and Regional Development\n(DPIRD) of Western Australia and by the Science and Technology\nDivision of the Queensland Government's Department of\nEnvironment and Science (DES). As well as the Bureau of\nMeteorology (BOM) of the Australian government precis and\ncoastal forecasts, and downloading and importing radar and\nsatellite imagery files. DPIRD weather data are accessed\nthrough public APIs provided by DPIRD,\n, providing\naccess to weather station data from the DPIRD weather station\nnetwork. Australia-wide weather data are based on data from\nthe Australian Bureau of Meteorology (BOM) data and accessed\nthrough SILO (Scientific Information for Land Owners) Jeffrey\net al. (2001) . DPIRD data\nare made available under a Creative Commons Attribution 3.0\nLicence (CC BY 3.0 AU) license\n. SILO\ndata are released under a Creative Commons Attribution 4.0\nInternational licence (CC BY 4.0)\n. 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Suggested the use of\nlocal_timzeone().),\nMax Moldovan [ctb] (ORCID: ,\nContributed valuable feedback on package usage leading to\nimprovements in the package structure and functionality.),\nStephen Bradshaw [ctb] (ORCID: ,\nIdentified data structure issues and provided insights that\nimproved package data quality and usability.),\nJimmy Ng [ctb],\nSteve Collins [ctb] (Designed the hex logo for 'weatherOz' hex logo.),\nAdam H. 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The\npackage converts between wide revision triangles and tidy long\nvintages, extracts selected releases, computes revision series,\nvisualizes vintage paths, and summarizes revision properties\nsuch as bias, dispersion, autocorrelation, and news-noise\ndiagnostics. It also identifies efficient releases and\nestimates state-space models for revision nowcasting. Methods\nare based on Howrey (1978) , Jacobs and\nVan Norden (2011) , and\nKishor and Koenig (2012) .", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "Roxygen": "list (markdown = TRUE, roclets = c (\"namespace\", \"rd\",\n\"srr::srr_stats_roclet\"))", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "URL": "https://docs.ropensci.org/reviser/,\nhttps://github.com/ropensci/reviser", "BugReports": "https://github.com/ropensci/reviser/issues", "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-09-14 09:52:25 UTC", "RemoteUrl": "https://github.com/ropensci/reviser", "RemoteRef": "main", "RemoteSha": "2a96be4be728c7b8c4210456379e1e3779818db1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-22 11:58:07 UTC", "User": "root" }, "Author": "Marc Burri [aut, cre, cph] (ORCID:\n),\nPhilipp Wegmueller [aut, cph] (ORCID:\n)", "Maintainer": "Marc Burri ", 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"title": "trans_id", "topics": [ "transID", "trans_id" ] }, { "page": "update_door_database", "title": "update response matrix", "topics": [ "update_door_database" ] }, { "page": "update_door_odorinfo", "title": "update_door_odorinfo", "topics": [ "updateOdorInfo", "update_door_odorinfo" ] } ], "_readme": "https://github.com/ropensci/DoOR.functions/raw/master/README.md", "_rundeps": [ "DoOR.data" ], "_vignettes": [ { "source": "DoOR_tools.Rmd", "filename": "DoOR_tools.html", "title": "DoOR analysis tools", "author": "Daniel Münch", "engine": "knitr::rmarkdown", "headings": [ "Content", "Loading data", "Identifying the sensillum we are recording from with identify_sensillum()", "using correlations", "using Euclidean distances", "returning data instead of plots", "Finding neuron-specific odorants with private_odorant()", "Mapping response data from an unknown source with map_receptor()", "Changing the response unit (spikes, deltaF/F, ...) with back_project()", "Quantifying tuning curves with sparse()" ], "created": "2015-07-23 15:47:32", "modified": "2022-02-14 14:02:12", "commits": 19 }, { "source": "DoOR.functions_main.Rmd", "filename": "DoOR.functions_main.html", "title": "The Database of Odor Responses - DoOR functions package", "author": "Daniel Münch", "engine": "knitr::rmarkdown", "headings": [ "", "Content", "Loading DoOR", "Modifying, building and updating DoOR", "Importing new data with import_new_data()", "Looking up InChIKeys If you do not know the InChIKeys of the odorants in", "Building the complete data base with", "Updating parts of the data base with", "Using the heuristic approach This is the faster way to perform a merge of", "Trying all permutations The more exhaustive way to update the data base is", "model_response() and model_response_seq()", "Merging using the heuristic with model_response() model_response()", "Merging in a specific sequence with model_response_seq()", "Removing a study with remove_study(){#remove_study} remove_study() will", 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response profiles dplot_response_profile()", "Comparing response profiles dplot_compare_profiles()", "Comparing original data sets", "Comparing DoOR response profiles", "Visualizing responses across responding units with dplot_across_ru()", "Visualizing odorant responses across OSNs with dplot_across_osns()" ], "created": "2015-07-21 15:33:19", "modified": "2022-02-14 14:02:12", "commits": 22 } ], "_score": 6.227783900853718, "_indexed": true, "_nocasepkg": "door.functions", "_universes": [ "ropensci", "dahaniel" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.0.3.9000", "date": "2026-10-17T08:19:07.000Z", "distro": "resolute", "commit": "15e415e4d84dfbbba6febefdfd0f2c1ddcf31cd6", "fileid": "https://r2.ropensci.org/2dc6932a826cd68629e0c8dc3e549f95c1e6056c4455b91af8114844d3d0fc11", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/39016576999" }, { "r": "4.6.1", "os": "linux", "version": "2.0.3.9000", "date": 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Currently available\ndatabases: 14cpalaeolithic, 14sea, adrac, agrichange, aida,\naustarch, bda, calpal, caribbean, eubar, euroevol, irdd, jomon,\nkatsianis, kiteeastafrica, medafricarbon, mesorad, neonet,\nneonetatl, nerd, p3k14c, pacea, palmisano, rado.nb, rxpand,\nsard, tegiszhol, xronos.", "Version": "5.3.0", "Authors@R": "c(person(given = \"Clemens\",\nfamily = \"Schmid\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"clemens@nevrome.de\",\ncomment = c(ORCID = \"0000-0003-3448-5715\")),\nperson(given = \"Dirk\",\nfamily = \"Seidensticker\",\nrole = \"aut\",\nemail = \"dirk.seidensticker@gmail.com\",\ncomment = c(ORCID = \"0000-0002-8155-7702\")),\nperson(given = \"Daniel\",\nfamily = \"Knitter\",\nrole = \"aut\",\nemail = \"knitter@geographie.uni-kiel.de\",\ncomment = c(ORCID = \"0000-0003-3014-4497\")),\nperson(given = \"Martin\",\nfamily = \"Hinz\",\nrole = \"aut\",\nemail = \"martin.hinz@iaw.unibe.ch\",\ncomment = c(ORCID = \"0000-0002-9904-6548\")),\nperson(given = \"David\",\nfamily = \"Matzig\",\nrole = \"aut\",\nemail = \"matzigdavid@gmail.com\",\ncomment = c(ORCID = \"0000-0001-7349-5401\")),\nperson(given = \"Wolfgang\",\nfamily = \"Hamer\",\nrole = \"aut\",\nemail = \"hamer@geographie.uni-kiel.de\",\ncomment = c(ORCID = \"0000-0002-5943-5020\")),\nperson(given = \"Kay\",\nfamily = \"Schmuetz\",\nrole = \"aut\",\nemail = \"kschmuetz@ufg.uni-kiel.de\"),\nperson(given = \"Thomas\",\nfamily = \"Huet\",\nrole = \"ctb\",\nemail = \"thomashuet7@gmail.com\",\ncomment = c(ORCID = \"0000-0002-1112-6122\")),\nperson(given = \"Nils\",\nfamily = \"Mueller-Scheessel\",\nrole = \"ctb\",\nemail = \"nils.mueller-scheessel@ufg.uni-kiel.de\",\ncomment = c(ORCID = \"0000-0001-7992-8722\")),\nperson(given = \"Joe\",\nfamily = \"Roe\",\nemail = \"joe@joeroe.io\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-1011-1244\")),\nperson(given = \"Ben\",\nfamily = \"Marwick\",\nrole = \"rev\",\ncomment = c(ORCID = \"0000-0001-7879-4531\")),\nperson(given = \"Enrico R.\",\nfamily = \"Crema\",\nrole = \"rev\",\ncomment = c(ORCID = \"0000-0001-6727-5138\")))", "URL": "https://docs.ropensci.org/c14bazAAR,\nhttps://github.com/ropensci/c14bazAAR", "BugReports": "https://github.com/ropensci/c14bazAAR/issues", "Language": "en", "License": "GPL-2 | file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "libssl-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-08-10 18:52:59 UTC", "RemoteUrl": "https://github.com/ropensci/c14bazAAR", "RemoteRef": "master", "RemoteSha": "8e06055a8e4c915de476b789e068462c64e73763", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-09 10:22:57 UTC", "User": "root" }, "Author": "Clemens Schmid [aut, cre, cph] (ORCID:\n),\nDirk Seidensticker [aut] (ORCID:\n),\nDaniel Knitter [aut] (ORCID: ),\nMartin Hinz [aut] (ORCID: ),\nDavid Matzig [aut] (ORCID: ),\nWolfgang Hamer [aut] (ORCID: ),\nKay Schmuetz [aut],\nThomas Huet [ctb] (ORCID: ),\nNils Mueller-Scheessel [ctb] (ORCID:\n),\nJoe Roe [ctb] (ORCID: ),\nBen Marwick [rev] (ORCID: ),\nEnrico R. 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"https://cranlogs.r-pkg.org/downloads/total/last-month/c14bazAAR" }, "_devurl": "https://github.com/ropensci/c14bazaar", "_pkgdown": "https://docs.ropensci.org/c14bazAAR", "_searchresults": 56, "_metadata": { "review": { "id": 333, "status": "reviewed", "version": "1.0.3.9000", "organization": "rOpenSci Software Review", "url": "https://github.com/ropensci/software-review/issues/333" }, "ropensci_category": "data-access" }, "_rbuild": "4.6.1", "_assets": [ "extra/c14bazAAR.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_realowner": "ropensci", "_cranurl": false, "_releases": [ { "version": "1.0.2", "date": "2018-10-28" }, { "version": "1.0.3", "date": "2019-08-02" }, { "version": "1.2.0", "date": "2020-01-12" } ], "_exports": [ "as.c14_date_list", "as.sf", "calibrate", "classify_material", "coordinate_precision", "determine_country_by_coordinate", "enforce_types", "finalize_country_name", "fix_database_country_name", "fuse", "get_14cpalaeolithic", "get_14sea", "get_adrac", "get_agrichange", "get_aida", "get_all_dates", "get_austarch", "get_bda", "get_c14data", "get_calpal", "get_caribbean", "get_context", "get_db_url", "get_db_version", "get_db_version_number", "get_emedyd", "get_eubar", "get_euroevol", "get_irdd", "get_jomon", "get_katsianis", "get_kiteeastafrica", "get_medafricarbon", "get_mesorad", "get_neonet", "get_neonetatl", "get_nerd", "get_p3k14c", "get_pacea", "get_palmisano", "get_rado.nb", "get_radon", "get_radonb", "get_rxpand", "get_sard", "get_tegiszhol", "get_xronos", "is.c14_date_list", "mark_duplicates", "order_variables", "remove_duplicates", "standardize_country_name", "write_c14" ], "_datasets": [ { "name": "db_info_table", "title": "Database lookup table", "object": "db_info_table", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "db", "version", "version_number", "url_num", "url" ], "rows": 31, "table": true, "tojson": true }, { "name": "example_c14_date_list", "title": "Example c14_date_list", "object": "example_c14_date_list", "class": [ "c14_date_list", "tbl_df", "tbl", "data.frame" ], "fields": [ "sourcedb", "method", "labnr", "c14age", "c14std", "c13val", "site", "sitetype", "feature", "period", "culture", "material", "species", "region", "country", "lat", "lon", "shortref", "comment" ], "rows": 9, "table": true, "tojson": true } ], "_help": [ { "page": "as.sf", "title": "Convert a *c14_date_list* to a sf object", "topics": [ "as.sf", "as.sf.c14_date_list", "as.sf.default" ] }, { "page": "c14_date_list", "title": "*c14_date_list*", "topics": [ "as.c14_date_list", "c14_date_list", "format.c14_date_list", "is.c14_date_list", "plot.c14_date_list", "print.c14_date_list" ] }, { "page": "calibrate", "title": "Calibrate all valid dates in a *c14_date_list*", "topics": [ "calibrate", "calibrate.c14_date_list", "calibrate.default" ] }, { "page": "country_attribution", "title": "Determine the country of all dates in a *c14_date_list* from their coordinates", "topics": [ "country_attribution", "determine_country_by_coordinate", "determine_country_by_coordinate.c14_date_list", "determine_country_by_coordinate.default" ] }, { "page": "db_info_table", "title": "Database lookup table", "concept": [ "lookup_tables" ], "topics": [ "db_info_table" ] }, { "page": "deprecated_functions", "title": "Deprecated functions", "topics": [ "classify_material", "coordinate_precision", "deprecated_functions", "finalize_country_name", "fix_database_country_name", "get_context", "get_emedyd", "get_radon", "get_radonb", "mark_duplicates", "standardize_country_name" ] }, { "page": "duplicates", "title": "Remove duplicates in a *c14_date_list*", "topics": [ "duplicates", "remove_duplicates", "remove_duplicates.c14_date_list", "remove_duplicates.default" ] }, { "page": "enforce_types", "title": "Enforce variable types in a *c14_date_list*", "topics": [ "enforce_types", "enforce_types.c14_date_list", "enforce_types.default" ] }, { "page": "example_c14_date_list", "title": "Example c14_date_list", "concept": [ "c14_date_lists" ], "topics": [ "example_c14_date_list" ] }, { "page": "fuse", "title": "Fuse multiple *c14_date_list*s", "topics": [ "fuse", "fuse.c14_date_list", "fuse.default" ] }, { "page": "db_getter_backend", "title": "Backend functions for data download", "topics": [ "get_14cpalaeolithic", "get_14sea", "get_adrac", "get_agrichange", "get_aida", "get_all_dates", "get_austarch", "get_bda", "get_calpal", "get_caribbean", "get_eubar", "get_euroevol", "get_irdd", "get_jomon", "get_katsianis", "get_kiteeastafrica", "get_medafricarbon", "get_mesorad", "get_neonet", "get_neonetatl", "get_nerd", "get_p3k14c", "get_pacea", "get_palmisano", "get_rado.nb", "get_rxpand", "get_sard", "get_tegiszhol", "get_xronos" ] }, { "page": "db_getter", "title": "Download radiocarbon source databases and convert 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"filename": "simple_plotting.html", "title": "Simple plotting options for radiocarbon dates in c14_date_lists", "author": "Clemens Schmid", "engine": "knitr::rmarkdown", "headings": [ "Temporal plotting of radiocarbon ages", "Ridgeplots of density distributions", "Calcurve plot", "Spatial mapping of radiocarbon dates", "Interactive map view", "Static map plot" ], "created": "2019-08-01 11:01:46", "modified": "2025-02-08 12:19:02", "commits": 7 } ], "_score": 6.111800006898345, "_indexed": true, "_nocasepkg": "c14bazaar", "_universes": [ "ropensci", "nevrome" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "5.3.0", "date": "2026-10-09T10:25:30.000Z", "distro": "resolute", "commit": "8e06055a8e4c915de476b789e068462c64e73763", "fileid": "https://r2.ropensci.org/41da2dbf79913914a1b2eeedd1d297b7767a6c222d5a38c8a3793f527aed9cc4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/37916821919" }, { "r": "4.6.1", "os": "linux", 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for rOpenSci, see\\n .\")),\nperson(\"Hazel\", \"Kavili\", role = \"rev\",\ncomment = \"Hazel Kavili reviewed nasapower for rOpenSci, see\\n .\"),\nperson(\"Alison\", \"Boyer\", role = \"rev\",\ncomment = \"Alison Boyer reviewed nasapower for rOpenSci, see\\n .\"),\nperson(\"Fernando\", \"Miguez\", , \"femiguez@iastate.edu\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4627-8329\", \"Fernando Miguez provided assistance in identifying\\n improper missing value handling in the POWER data, see \\n .\")),\nperson(\"Maëlle\", \"Salmon\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-2815-0399\", \"Maëlle Salmon contributed a patch to fix issues with using the R\\n package, 'vcr', for testing the API queries, see\\n .\")),\nperson(\"Phillip D.\", \"Alderman\", , \"phillip.alderman@okstate.edu\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-1467-2337\", \"Phillip Alderman contributed a patch to fix an issue with, 'The\\n `file` argument of `vroom()` must use `I()` for literal data as\\n of vroom 1.5.0.', see\\n .\")),\nperson(\"Aleksandar\", \"Blagotić\", , \"alex@rapporter.net\", role = c(\"ctb\", \"cph\"),\ncomment = \"Author of the CRAN package 'rapportools', from which\\n the '.is_boolean()' was derived.\"),\nperson(\"Gergely\", \"Daróczi\", , \"daroczig@rapporter.net\", role = c(\"ctb\", \"cph\"),\ncomment = \"Author of the CRAN package 'rapportools', from which\\n the '.is_boolean()' was derived.\"),\nperson(\"Curtin University\", role = \"cph\",\ncomment = c(\"http://www.curtin.edu.au/\", ROR = \"02n415q13\"))\n)", "Description": "An API client for NASA POWER global meteorology, surface\nsolar energy and climatology data API. POWER (Prediction Of\nWorldwide Energy Resources) data are freely available for\ndownload with varying spatial resolutions dependent on the\noriginal data and with several temporal resolutions depending\non the POWER parameter and community. This work is funded\nthrough the NASA Earth Science Directorate Applied Science\nProgram. For more on the data themselves, the methodologies\nused in creating, a web-based data viewer and web access,\nplease see .", "License": "MIT + file LICENSE", "URL": "https://codeberg.org/ropensci/nasapower,\nhttps://docs.ropensci.org/nasapower/", "BugReports": "https://codeberg.org/ropensci/nasapower/issues", "VignetteBuilder": "knitr", "Config/Needs/build": "moodymudskipper/devtag", "Config/Needs/documentation": "roxylint", "Config/roxygen2/version": "8.1.0", "Config/roxylint": "list(linters = roxylint::tidy)", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "Encoding": "UTF-8", "Language": "en-US", "NeedsCompilation": "no", "Roxygen": "list(markdown = TRUE, roclets = c(\"collate\", \"namespace\",\n\"rd\", \"roxylint::roxylint\", \"devtag::dev_roclet\"))", "Config/pak/sysreqs": "libssl-dev libx11-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-08-09 23:35:04 UTC", "RemoteUrl": "https://github.com/ropensci/nasapower", "RemoteRef": "main", "RemoteSha": "6b9f6892f3c94068597e36efb3b9af03fac26e9a", "Packaged": { "Date": "2026-10-09 07:52:31 UTC", "User": "root" }, "Author": "Adam H. Sparks [aut, cre] (ORCID:\n),\nScott Chamberlain [rev] (ORCID:\n, Scott Chamberlain reviewed\nnasapower for rOpenSci, see\n.),\nHazel Kavili [rev] (Hazel Kavili reviewed nasapower for rOpenSci, see\n.),\nAlison Boyer [rev] (Alison Boyer reviewed nasapower for rOpenSci, see\n.),\nFernando Miguez [ctb] (ORCID: ,\nFernando Miguez provided assistance in identifying improper missing\nvalue handling in the POWER data, see\n.),\nMaëlle Salmon [ctb] (ORCID: ,\nMaëlle Salmon contributed a patch to fix issues with using the R\npackage, 'vcr', for testing the API queries, see\n.),\nPhillip D. Alderman [ctb] (ORCID:\n, Phillip Alderman\ncontributed a patch to fix an issue with, 'The `file` argument of\n`vroom()` must use `I()` for literal data as of vroom 1.5.0.', see\n.),\nAleksandar Blagotić [ctb, cph] (Author of the CRAN package\n'rapportools', from which the '.is_boolean()' was derived.),\nGergely Daróczi [ctb, cph] (Author of the CRAN package 'rapportools',\nfrom which the '.is_boolean()' was derived.),\nCurtin University [cph] (http://www.curtin.edu.au/, ROR:\n)", "Maintainer": "Adam H. 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Based on 'future' (Bengtsson, 2024\n) and 'mirai' (Gao et al.,\n2025 ) parallel back-ends,\n'terra' (Hijmans et al., 2025\n) and 'sf' (Pebesma et al.,\n2024 ) functions as well as\nconvenience functions in the package can be distributed over\nmultiple threads. The simplest way of parallelizing generic\ngeospatial computation is to start from par_pad_*() functions\nto par_grid(), par_hierarchy(), or par_multirasters()\nfunctions. Virtually any functions accepting classes in 'terra'\nor 'sf' packages can be used in the three parallelization\nfunctions. A common raster-vector overlay operation is provided\nas a function extract_at(), which uses 'exactextractr' (Baston,\n2023 ), with options\nfor kernel weights for summarizing raster values at vector\ngeometries. Other convenience functions for vector-vector\noperations including simple areal interpolation\n(summarize_aw()) and summation of exponentially decaying\nweights (summarize_sedc()) are also provided.", "License": "MIT + file LICENSE", "URL": "https://docs.ropensci.org/chopin/,\nhttps://github.com/ropensci/chopin", "BugReports": "https://github.com/ropensci/chopin/issues", "SystemRequirements": "netcdf", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "xz", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibglpk-dev libxml2-dev libnetcdf-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-08-09 15:33:42 UTC", "RemoteUrl": "https://github.com/ropensci/chopin", "RemoteRef": "main", "RemoteSha": "fd8a4a9b9a68d53f52eb981a9df9e5949dbae9bb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-16 10:56:11 UTC", "User": "root" }, "Author": "Insang Song [aut, cre] (ORCID: ),\nKyle Messier [aut, ctb] (ORCID:\n),\nAlec L. Robitaille [rev] (Alec reviewed the package version 0.6.3 for\nrOpenSci, see\n),\nEric R. Scott [rev] (Eric reviewed the package version 0.6.3 for\nrOpenSci, see\n)", "Maintainer": "Insang Song ", "_user": "ropensci", "_type": "src", "_file": "chopin_0.9.9-6.tar.gz", "_fileid": "https://r2.ropensci.org/385e7becdc97f3e7fd9580b9cf5929aaf404e223c3317252b2812be90b075e88", "_filesize": 5082076, "_sha256": "385e7becdc97f3e7fd9580b9cf5929aaf404e223c3317252b2812be90b075e88", "_expires": "2027-01-24T11:03:02.000Z", "_created": "2026-10-16T10:56:11.000Z", "_published": "2026-10-16T11:03:04.972Z", "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/38889840003", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116938992442, "time": 290, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12042241486" }, { "job": 116938992444, "time": 248, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12041817030" }, { "job": 116938992488, "time": 202, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", 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The Glottolog database contains the\ncatalogue of languages of the world. This package helps\nresearchers to make a linguistic maps, using philosophy of the\nCross-Linguistic Linked Data project , which\nallows for while at the same time facilitating uniform access\nto the data across publications. A tutorial for this package is\navailable on GitHub pages\n and package vignette.\nMaps created by this package can be used both for the\ninvestigation and linguistic teaching. In addition, package\nprovides an ability to download data from typological databases\nsuch as WALS, AUTOTYP and some others and to create your own\ndatabase website.", "License": "GPL (>= 2)", "URL": "https://CRAN.R-project.org/package=lingtypology,\nhttps://github.com/ropensci/lingtypology/,\nhttps://ropensci.github.io/lingtypology/", "BugReports": "https://github.com/ropensci/lingtypology/issues", "LazyData": "TRUE", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libpng-dev libuv1-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-07-26 08:23:57 UTC", "RemoteUrl": "https://github.com/ropensci/lingtypology", "RemoteRef": "master", "RemoteSha": "24d5c48d4c35b95454f8eb4de331e5abd50b7baa", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-15 08:56:35 UTC", "User": "root" }, "Author": "George Moroz [aut, cre] (ORCID:\n),\nKirill Koncha [ctb] (ORCID: ),\nMikhail Leonov [ctb],\nAnna Smirnova [ctb],\nEkaterina Zalivina [ctb]", "Maintainer": "George Moroz ", "_user": "ropensci", "_type": "src", "_file": "lingtypology_1.1.26.tar.gz", "_fileid": "https://r2.ropensci.org/40e8222a48ab13207538a33ec84e8c7451fdc505e2048e6d85b5ffc480c2f121", "_filesize": 1986046, "_sha256": "40e8222a48ab13207538a33ec84e8c7451fdc505e2048e6d85b5ffc480c2f121", "_expires": "2027-01-23T09:17:42.000Z", "_created": "2026-10-15T08:56:35.000Z", "_published": "2026-10-15T09:17:44.584Z", "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/38708816910", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116336584697, "time": 185, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11959284215" }, { "job": 116336584851, "time": 145, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11959558288" }, { "job": 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"https://github.com/ropensci/lingtypology", "_commit": { "id": "24d5c48d4c35b95454f8eb4de331e5abd50b7baa", "author": "George Moroz ", "committer": "George Moroz ", "message": "update\n", "time": 1785054237 }, "_maintainer": { "name": "George Moroz", "email": "agricolamz@gmail.com", "login": "agricolamz", "orcid": "0000-0003-1990-6083", "twitter": "@aGricolaMZ", "description": "I'm teaching Linguistics and working on phonetics, linguistic mapping, statistics and indigenous language of the Caucasus", "uuid": 15956515 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "leaflet", "role": "Imports" }, { "package": "leaflet.minicharts", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stringdist", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "sp", "role": "Suggests" }, { "package": "sf", "role": "Suggests" }, { "package": "ape", "role": "Suggests" } ], "_owner": "ropensci", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-10", "n": 1 }, { "week": "2026-30", "n": 2 } ], "_tags": [ { "name": "v1.1.25", "date": "2026-03-02" }, { "name": "v1.1.26", "date": "2026-07-26" } ], "_topics": [ "abvd", "afbo", "atlas", "autotype", "bivaltyp", "glottolog-database", "grambank", "linguistic-maps", "linguistics", "phoible", "sails", "typology", "wals" ], "_stars": 54, "_contributors": [ { "user": "agricolamz", "count": 541, "uuid": 15956515 }, { "user": "forlinguistics", "count": 23, "uuid": 42992800 }, { "user": "kirillkoncha", "count": 12, "uuid": 42929201 }, { "user": "ustera", "count": 6, "uuid": 36166531 }, { "user": "suppukerr", "count": 3, "uuid": 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"1.1.1", "date": "2020-02-10" }, { "version": "1.1.2", "date": "2020-03-01" }, { "version": "1.1.3", "date": "2020-04-26" }, { "version": "1.1.4", "date": "2020-10-05" }, { "version": "1.1.5", "date": "2021-05-15" }, { "version": "1.1.6", "date": "2021-10-14" }, { "version": "1.1.7", "date": "2021-10-24" }, { "version": "1.1.8", "date": "2021-12-10" }, { "version": "1.1.9", "date": "2022-06-24" }, { "version": "1.1.10", "date": "2022-11-10" }, { "version": "1.1.11", "date": "2022-12-20" }, { "version": "1.1.12", "date": "2023-02-26" }, { "version": "1.1.13", "date": "2023-04-22" }, { "version": "1.1.14", "date": "2023-05-29" }, { "version": "1.1.15", "date": "2023-08-24" }, { "version": "1.1.16", "date": "2024-02-04" }, { "version": "1.1.17", "date": "2024-03-13" }, { "version": "1.1.18", "date": "2024-08-16" }, { "version": "1.1.19", "date": "2024-09-20" }, { "version": "1.1.20", "date": "2024-10-31" }, { "version": "1.1.21", "date": "2025-05-27" }, { "version": "1.1.22", "date": "2025-06-14" }, { "version": "1.1.23", "date": "2025-08-18" }, { "version": "1.1.24", "date": "2025-09-28" }, { "version": "1.1.25", "date": "2026-03-02" }, { "version": "1.1.26", "date": "2026-07-26" } ], "_exports": [ "abvd.feature", "afbo.feature", "aff.lang", "area.lang", "atlas.database", "autotyp.feature", "bantu.feature", "bivaltyp.feature", "country.lang", "eurasianphonology.feature", "frequency_list.feature", "gltc.iso", "gltc.lang", "grambank.feature", "is.glottolog", "iso.gltc", "iso.lang", "iso3.iso1", "lang.aff", "lang.country", "lang.gltc", "lang.iso", "lat.lang", "level.lang", "long.lang", "map.feature", "oto_mangueanIC.feature", "phoible.feature", "sails.feature", "soundcomparisons.feature", "subc.lang", "uralex.feature", "url.lang", "valpal.feature", "vanuatu.feature", "wals.feature" ], "_datasets": [ { "name": "abvd", "title": "ABVD's Language identifiers", "object": "abvd", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "id", "glottocode" ], "rows": 1468, "table": true, "tojson": true }, { "name": "autotyp", "title": "AUTOTYP's Language identifiers", "object": "autotyp", "class": [ "data.frame" ], "fields": [ "file", "path", "variable" ], "rows": 1342, "table": true, "tojson": true }, { "name": "bantu", "title": "BANTU's Language identifiers", "object": "bantu", "class": [ "data.frame" ], "fields": [ "id", "word" ], "rows": 430, "table": true, "tojson": true }, { "name": "circassian", "title": "Circassian villages in Russia", "object": "circassian", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "latitude", "longitude", "village", "district", "dialect", "language" ], "rows": 158, "table": true, "tojson": true }, { "name": "countries", "title": "Catalogue of countries", "object": "countries", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "alpha3", "alpha2", "country_name", "additional_names", "official_languages" ], "rows": 189, "table": true, "tojson": true }, { "name": "eurasianphonology", "title": "Eurasianphonology data", "object": "eurasianphonology", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "id", "name", "language", "iso", "glottocode", "type", "latitude", "longitude", "gen1", "gen2", "tones", "syllab", "cluster", "finals", "segments", "segment_type", "source", "comment", "contr" ], "rows": 19825, "table": true, "tojson": true }, { "name": "glottolog", "title": "Catalogue of languages of the world", "object": "glottolog", "class": [ "data.frame" ], "fields": [ "glottocode", "language", "iso", "level", "area", "latitude", "longitude", "countries", "affiliation", "subclassification" ], "rows": 27177, "table": true, "tojson": true }, { "name": "iso_639", "title": "ISO 639-3 is a set of codes that defines three-letter identifiers for all known human languages.", "object": "iso_639", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "ISO_639_3", "ISO_639_2_B", "ISO_639_2_T", "ISO_639_1", "Ref_Name" ], "rows": 183, "table": true, "tojson": true }, { "name": "oto_mangueanIC", "title": "Oto-Manguean Inflectional Class Database Language identifiers", "object": "oto_mangueanIC", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "Language.name", "language" ], "rows": 20, "table": true, "tojson": true }, { "name": "phoible", "title": "Phoible glottolog - language correspondencies", "object": "phoible", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "Glottocode", "language" ], "rows": 2185, "table": true, "tojson": true }, { "name": "phonological_profiles", "title": "Number of consonants and presence of ejectives", "object": "phonological_profiles", "class": [ "data.frame" ], "fields": [ "language", "tone", "long_vowels", "stress", "ejectives", "consonants", "vowels" ], "rows": 19, "table": true, "tojson": true }, { "name": "providers", "title": "Providers", "object": "providers", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "soundcomparisons", "title": "SOUNDCOMPARISONS's Language identifiers", "object": "soundcomparisons", "class": [ "data.frame" ], "fields": [ "LanguageName", "LanguageId", "glottocode" ], "rows": 556, "table": true, "tojson": true }, { "name": "uralex", "title": "UraLex's Language identifiers", "object": "uralex", "class": [ "data.frame" ], "fields": [ "uralex.name", "glottocode", "language" ], "rows": 27, "table": true, "tojson": true }, { "name": "wals", "title": "WALS's Language identifiers", "object": "wals", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "wals.code", "glottocode" ], "rows": 2678, "table": true, "tojson": true } ], "_help": [ { "page": "abvd", "title": "ABVD's Language identifiers", "topics": [ "abvd" ] }, { "page": "abvd.feature", "title": "Download ABVD data", "topics": [ "abvd.feature" ] }, { "page": "afbo.feature", "title": "Download AfBo data", "topics": [ "afbo.feature" ] }, { "page": "aff.lang", "title": "Get affiliation by language", "topics": [ "aff.lang" ] }, { "page": "area.lang", "title": "Get macro area by language", "topics": [ "area.lang" ] }, { "page": "atlas.database", "title": "Create an atlas", "topics": [ "atlas.database" ] }, { "page": "autotyp", "title": "AUTOTYP's Language identifiers", "topics": [ "autotyp" ] }, { "page": "autotyp.feature", "title": "Download AUTOTYP data", "topics": [ "autotyp.feature" ] }, { "page": "bantu", "title": "BANTU's Language identifiers", "topics": [ "bantu" ] }, { "page": "bantu.feature", "title": "Download BANTU data", "topics": [ "bantu.feature" ] }, { "page": "bivaltyp.feature", "title": "Download BivalTyp data", "topics": [ "bivaltyp.feature" ] }, { "page": "circassian", "title": "Circassian villages in Russia", "topics": [ "circassian" ] }, { "page": "countries", "title": "Catalogue of countries", "topics": [ "countries" ] }, { "page": "country.lang", "title": "Get country by language", "topics": [ "country.lang" ] }, { "page": "eurasianphonology", "title": "Eurasianphonology data", "topics": [ "eurasianphonology" ] }, { "page": "eurasianphonology.feature", "title": "Opens data from the database of Eurasian phonological inventories", "topics": [ "eurasianphonology.feature" ] }, { "page": "frequency_list.feature", "title": "Download frequency list", "topics": [ "frequency_list.feature" ] }, { "page": "glottolog", "title": "Catalogue of languages of the world", "topics": [ "glottolog" ] }, { "page": "gltc.iso", "title": "Get Glottocode by ISO 639-3 code", "topics": [ "gltc.iso" ] }, { "page": "gltc.lang", "title": "Get Glottocode by language", "topics": [ "gltc.lang" ] }, { "page": "grambank.feature", "title": "Download Grambank data", "topics": [ "grambank.feature" ] }, { "page": "imports", "title": "Objects imported from other packages", "topics": [ "%>%" ] }, { "page": "is.glottolog", "title": "Are these languages in glottolog?", "topics": [ "is.glottolog" ] }, { "page": "iso_639", "title": "ISO 639-3 is a set of codes that defines three-letter identifiers for all known human languages.", "topics": [ "iso_639" ] }, { "page": "iso.gltc", "title": "Get ISO 639-3 code by Glottocode", "topics": [ "iso.gltc" ] }, { "page": "iso.lang", "title": "Get ISO 639-3 code by language", "topics": [ "iso.lang" ] }, { "page": "iso3.iso1", "title": "Get ISO 639-3 code from ISO 639-1", "topics": [ "iso3.iso1" ] }, { "page": "lang.aff", "title": "Get languages by affiliation", "topics": [ "lang.aff" ] }, { "page": "lang.country", "title": "Get language by country", "topics": [ "lang.country" ] }, { "page": "lang.gltc", "title": "Get language by Glottocode", "topics": [ "lang.gltc" ] }, { "page": "lang.iso", "title": "Get language by ISO 639-3 code", "topics": [ "lang.iso" ] }, { "page": "lat.lang", "title": "Get latitude by language", "topics": [ "lat.lang" ] }, { "page": "level.lang", "title": "Get a level of language by language", "topics": [ "level.lang" ] }, { "page": "long.lang", "title": "Get longitude by language", "topics": [ "long.lang" ] }, { "page": "map.feature", "title": "Create a map", "topics": [ "map.feature" ] }, { "page": "oto_mangueanIC", "title": "Oto-Manguean Inflectional Class Database Language identifiers", "topics": [ "oto_mangueanIC" ] }, { "page": "oto_mangueanIC.feature", "title": "Download Oto-Manguean Inflectional Class Database data", "topics": [ "oto_mangueanIC.feature" ] }, { "page": "phoible", "title": "Phoible glottolog - language correspondencies", "topics": [ "phoible" ] }, { "page": "phoible.feature", "title": "Download PHOIBLE data", "topics": [ "phoible.feature" ] }, { "page": "phonological_profiles", "title": "Number of consonants and presence of ejectives", "topics": [ "phonological_profiles" ] }, { "page": "polygon.points_fd", "title": "Get polygons from fixed distance circles around coordinates", "topics": [ "polygon.points_fd" ] }, { "page": "polygon.points_kde", "title": "Get kernel density estimation poligon from coordinates", "topics": [ "polygon.points_kde" ] }, { "page": "providers", "title": "Providers", "topics": [ "providers" ] }, { "page": "sails.feature", "title": "Download SAILS data", "topics": [ "sails.feature" ] }, { "page": "soundcomparisons", "title": "SOUNDCOMPARISONS's Language identifiers", "topics": [ "soundcomparisons" ] }, { "page": "soundcomparisons.feature", "title": "Download SOUNDCOMPARISONS data", "topics": [ "soundcomparisons.feature" ] }, { "page": "subc.lang", "title": "Get subclassification by language", "topics": [ "subc.lang" ] }, { "page": "uralex", "title": "UraLex's Language identifiers", "topics": [ "uralex" ] }, { "page": "uralex.feature", "title": "Download UraLex data", "topics": [ "uralex.feature" ] }, { "page": "url.lang", "title": "Make a url-link to glottolog page for a language", "topics": [ "url.lang" ] }, { "page": "valpal.feature", "title": "Download ValPaL data", "topics": [ "valpal.feature" ] }, { "page": "vanuatu.feature", "title": "Download Vanuatu Voices data", "topics": [ "vanuatu.feature" ] }, { "page": "wals", "title": "WALS's Language identifiers", "topics": [ "wals" ] }, { "page": "wals.feature", "title": "Download WALS data", "topics": [ "wals.feature" ] } ], "_readme": "https://github.com/ropensci/lingtypology/raw/master/README.md", "_rundeps": [ "base64enc", "bslib", "cachem", "class", "classInt", "cli", "crosstalk", "DBI", "digest", "e1071", "evaluate", "farver", "fastmap", "fontawesome", "fs", "glue", "highr", "htmltools", "htmlwidgets", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lattice", "lazyeval", "leaflet", "leaflet.minicharts", "leaflet.providers", "lifecycle", "magrittr", "memoise", "mime", "png", "proxy", "R6", "rappdirs", "raster", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "s2", "sass", "scales", "sf", "sp", "stringdist", "terra", "tinytex", "units", "viridisLite", "wk", "xfun", "yaml" ], "_vignettes": [ { "source": "lingtypology_dplyr.Rmd", "filename": "lingtypology_dplyr.html", "title": "lingtypology and other packages", "author": "George Moroz", "engine": "knitr::rmarkdown", "headings": [ "1. dplyr and pipe |>", "2. leaflet, leaflet.extras, mapview, mapedit", "3. Combining maps in a grid and facetisation with mapview", "4. Get data from OpenStreetMap with overpass", "5. Create your own atlas with rmarkdown", "6. Create .kml file using sp and rgdal" ], "created": "2017-12-03 12:48:48", "modified": "2024-07-29 17:03:58", "commits": 26 }, { "source": "lingtypology_creating_maps.Rmd", "filename": "lingtypology_creating_maps.html", "title": "lingtypology: creating maps", "author": "George Moroz", "engine": "knitr::rmarkdown", "headings": [ "1. Base map", "2. Set features", "3. Set pop-up boxes", "4. Set labels", "5. Set coordinates", "6. Set colors", "7. Set shapes", "8. Set control box", "9. Set an additional set of features using strokes", "10. Set width and an opacity feature", "11. Customizing legends", "12. Set scale bar", "13. Set layouts", "14. Add a minimap to a map", "15. Add minicharts instead of points", "16. Add a rectangle to a map", "17. Add a density contourplot to a map", "18. Add isoglosses", "19. 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c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-5069-7964\")),\nperson(\"Pueyo-Ros\", \"Josep\", role = \"rev\",\ncomment = \"Josep reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/623#issuecomment-1951446662\"),\nperson(\"Le Meur\", \"Nolwenn\", role = \"rev\",\ncomment = \"Nolwenn reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/623#issuecomment-1961501137\"),\nperson(\"Filipe\", \"Batista e Silva\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-8752-6464\")),\nperson(\"Carmelo\", \"Attardo\", role = \"aut\"),\nperson(\"Cristian\", \"Pigaiani\", role = \"aut\"),\nperson(\"Michele\", \"Tucci\", role = \"aut\")\n)", "Description": "Motivated by changing administrative boundaries over time,\nthe 'nuts' package can convert European regional data with NUTS\ncodes between versions (2006, 2010, 2013, 2016, 2021 and 2024)\nand levels (NUTS 1, NUTS 2 and NUTS 3). The package uses\nspatial interpolation as in Lam (1983)\n based on granular (100m x\n100m) area, population and land use data provided by the\nEuropean Commission's Joint Research Center.", "License": "MIT + file LICENSE", "URL": "https://docs.ropensci.org/nuts/, https://github.com/ropensci/nuts", "BugReports": "https://github.com/ropensci/nuts", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.0.0", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-06-29 13:29:48 UTC", "RemoteUrl": "https://github.com/ropensci/nuts", "RemoteRef": "main", "RemoteSha": "8c9ec36261e42c86e4868a6c0275170096e16af5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-08 12:11:56 UTC", "User": "root" }, "Author": "Moritz Hennicke [aut, cre, cph] (ORCID:\n),\nWerner Krause [aut, cph] (ORCID:\n),\nPueyo-Ros Josep [rev] (Josep reviewed the package for rOpenSci, 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more details,\nsee Ariza-López et al. (2019) )\nand rivers (for more details, see Cohen et al. (2018)\n). It can use local Digital\nElevation Model (DEM) data or download DEM data via the\n'ceramic' package. 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Factors follow a\nstationary VAR process of order p. Estimation options include:\nrunning the Kalman Filter and Smoother once with PCA initial\nvalues (2S) as in Doz, Giannone and Reichlin (2011)\n; iterated Kalman Filtering\nand Smoothing until EM convergence as in Doz, Giannone and\nReichlin (2012) ; or the adapted EM\nalgorithm of Banbura and Modugno (2014) ,\nallowing arbitrary missing-data patterns and monthly-quarterly\nmixed-frequency datasets. The implementation uses the\n'Armadillo' 'C++' library and the 'collapse' package for fast\nestimation. A comprehensive set of methods supports\ninterpretation and visualization, forecasting, and\ndecomposition of the 'news' content of macroeconomic data\nreleases following Banbura and Modugno (2014). 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Currently, the package enables extraction from\nnine datasets: The National Elevation Dataset digital elevation\nmodels ( 1 and 1/3\narc-second; USGS); The National Hydrography Dataset\n(;\nUSGS); The Soil Survey Geographic (SSURGO) database from the\nNational Cooperative Soil Survey\n(; NCSS), which is led\nby the Natural Resources Conservation Service (NRCS) under the\nUSDA; the Global Historical Climatology Network\n(;\nGHCN), coordinated by National Climatic Data Center at NOAA;\nthe Daymet gridded estimates of daily weather parameters for\nNorth America, version 4, available from the Oak Ridge National\nLaboratory's Distributed Active Archive Center\n(; DAAC; currently deprecated, as the\ndata now require authentication to download); the International\nTree Ring Data Bank; the National Land Cover Database\n(; NLCD); the Cropland Data Layer from\nthe National Agricultural Statistics Service\n(;\nNASS); and the PAD-US dataset of protected area boundaries\n(;\nUSGS).", "License": "MIT + file LICENSE", "URL": "https://docs.ropensci.org/FedData/,\nhttps://github.com/ropensci/FedData", "BugReports": "https://github.com/ropensci/FedData/issues", "SystemRequirements": "GDAL (>= 3.1.0)", "Encoding": "UTF-8", "LazyData": "true", "NeedsCompilation": "no", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibglpk-dev libicu-dev libxml2-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev libx11-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-06-12 15:13:41 UTC", "RemoteUrl": "https://github.com/ropensci/FedData", "RemoteRef": "main", "RemoteSha": "b0c3f42c3f6efd41c96bb395936d083dd2acd04b", "Packaged": { "Date": "2026-10-17 11:06:36 UTC", "User": "root" }, "Author": "R. 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Wiki taxon", "concept": [ "taxonomic-ids" ], "topics": [ "as.data.frame.wiki", "as.wiki", "as.wiki.character", "as.wiki.data.frame", "as.wiki.list", "as.wiki.numeric", "as.wiki.wiki", "get_wiki", "get_wiki_" ] }, { "page": "get_wormsid", "title": "Get Worms ID for a taxon name", "concept": [ "taxonomic-ids" ], "topics": [ "as.data.frame.wormsid", "as.wormsid", "as.wormsid.character", "as.wormsid.data.frame", "as.wormsid.list", "as.wormsid.numeric", "as.wormsid.wormsid", "get_wormsid", "get_wormsid_" ] }, { "page": "getkey", "title": "Function to get API key.", "topics": [ "getkey" ] }, { "page": "gna_data_sources", "title": "Get metadata about GNA data sources", "topics": [ "gna_data_sources" ] }, { "page": "gna_parse", "title": "Parse scientific names using Global Names Parser", "topics": [ "gna_parse" ] }, { "page": "gna_search", "title": "Search for taxonomic names using the Global Names Architecture", "topics": [ "gna_search" ] }, { "page": "gna_verifier", "title": "Verify a list 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"title": "Retrieve accepted TSN and name", "topics": [ "itis_acceptname" ] }, { "page": "itis_downstream", "title": "Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.", "topics": [ "itis_downstream" ] }, { "page": "itis_getrecord", "title": "Get full ITIS record for one or more ITIS TSN's or lsid's.", "topics": [ "itis_getrecord" ] }, { "page": "itis_hierarchy", "title": "ITIS hierarchy", "topics": [ "itis_hierarchy" ] }, { "page": "itis_kingdomnames", "title": "Get kingdom names", "topics": [ "itis_kingdomnames" ] }, { "page": "itis_lsid", "title": "Get TSN from LSID", "topics": [ "itis_lsid" ] }, { "page": "itis_name-deprecated", "title": "Get taxonomic names for a given taxonomic name query.", "topics": [ "itis_name" ] }, { "page": "itis_native", "title": "Get jurisdiction data, i.e., native or not native in a region.", "topics": [ "itis_native" ] }, { "page": "itis_refs", "title": "Get references related to a ITIS TSN.", "topics": [ "itis_refs" ] }, { "page": "itis_taxrank", "title": "Retrieve taxonomic rank name from given TSN.", "topics": [ "itis_taxrank" ] }, { "page": "itis_terms", "title": "Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.", "topics": [ "itis_terms" ] }, { "page": "iucn_getname", "title": "Get any matching IUCN species names", "topics": [ "iucn_getname" ] }, { "page": "iucn_id", "title": "Get an ID for a IUCN listed taxon", "topics": [ "iucn_id" ] }, { "page": "iucn_status", "title": "Extractor functions for 'iucn'-class.", "topics": [ "iucn_status" ] }, { "page": "iucn_summary", "title": "Get a summary from the IUCN Red List", "topics": [ "iucn_summary" ] }, { "page": "key_helpers", "title": "Helpers to set up authentication for the different providers.", "topics": [ "key_helpers", "use_entrez", "use_iucn", "use_tropicos" ] }, { "page": "lowest_common", "title": "Retrieve the lowest common taxon and rank for a given taxon name or ID", "topics": [ "lowest_common", "lowest_common.default", "lowest_common.gbifid", "lowest_common.tolid", "lowest_common.tsn", "lowest_common.uid" ] }, { "page": "names_list", "title": "Get a random vector of species names.", "topics": [ "names_list" ] }, { "page": "nbn_classification", "title": "Search UK National Biodiversity Network database for taxonomic classification", "concept": [ "nbn" ], "topics": [ "nbn_classification" ] }, { "page": "nbn_search", "title": "Search UK National Biodiversity Network", "concept": [ "nbn" ], "topics": [ "nbn_search" ] }, { "page": "nbn_synonyms", "title": "Return all synonyms for a taxon name with a given id from NBN", "concept": [ "nbn" ], "topics": [ "nbn_synonyms" ] }, { "page": "ncbi_children", "title": "Search NCBI for children of a taxon", "topics": [ "ncbi_children" ] }, { "page": "ncbi_downstream", "title": "Retrieve all taxa names downstream in hierarchy for NCBI", "topics": [ "ncbi_downstream" ] }, { "page": "ncbi_get_taxon_summary", "title": "NCBI taxon information from uids", "topics": [ 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"pow" ], "topics": [ "pow_synonyms" ] }, { "page": "rank_ref", "title": "Lookup-table for IDs of taxonomic ranks", "topics": [ "rank_ref" ] }, { "page": "rank_ref_zoo", "title": "Lookup-table for IDs of taxonomic ranks (WoRMS)", "topics": [ "rank_ref_zoo" ] }, { "page": "rankagg", "title": "Aggregate data by given taxonomic rank", "topics": [ "rankagg" ] }, { "page": "resolve", "title": "Resolve names from different data sources", "topics": [ "resolve" ] }, { "page": "sci2comm", "title": "Get common names from scientific names.", "topics": [ "sci2comm", "sci2comm.default", "sci2comm.iucn", "sci2comm.tsn", "sci2comm.uid", "sci2comm.wormsid" ] }, { "page": "scrapenames", "title": "Find taxon names using Global Names Recognition and Discovery", "topics": [ "scrapenames" ] }, { "page": "species_plantarum_binomials", "title": "Species names from Species Plantarum", "topics": [ "species_plantarum_binomials" ] }, { "page": "status_codes", "title": "Get HTTP status codes", "topics": [ 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Although we envisioned git2rdata with a git\nworkflow in mind, you can use it in combination with other\nversion control systems like subversion or mercurial. 3)\ngit2rdata is a useful tool in a reproducible and traceable\nworkflow. vignette(\"workflow\", package = \"git2rdata\") gives a\ntoy example. 4) vignette(\"efficiency\", package = \"git2rdata\")\nprovides some insight into the efficiency of file storage, git\nrepository size and speed for writing and reading.", "License": "GPL-3", "URL": "https://ropensci.github.io/git2rdata/,\nhttps://github.com/ropensci/git2rdata/,\nhttps://doi.org/10.5281/zenodo.1485309", "BugReports": "https://github.com/ropensci/git2rdata/issues", "VignetteBuilder": "knitr", "Config/checklist/communities": "inbo", "Config/checklist/keywords": "git; version control; plain text data", "Encoding": "UTF-8", "Language": "en-GB", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Collate": "'clean_data_path.R' 'data_package.R' 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,\naffiliation: Research Institute for Nature and Forest (INBO)),\nResearch Institute for Nature and Forest (INBO) [cph, fnd] (ROR:\n)", "Maintainer": "Thierry Onkelinx ", "_user": "ropensci", "_type": "src", "_file": "git2rdata_0.5.2.tar.gz", "_fileid": "https://r2.ropensci.org/aaf14233fec84ac1352607261547167a42ca32f30e61ca9ed6f70320779fe65e", "_filesize": 1298680, "_sha256": "aaf14233fec84ac1352607261547167a42ca32f30e61ca9ed6f70320779fe65e", "_expires": "2027-02-06T07:48:39.000Z", "_created": "2026-10-29T07:45:07.000Z", "_published": "2026-10-29T07:48:41.215Z", "_upstream": "https://github.com/ropensci/git2rdata", "_status": "success", "_maintainer": { "name": "Thierry Onkelinx", "email": "thierry.onkelinx@inbo.be", "login": "thierryo", "mastodon": "@ThierryO@fosstodon.org", "orcid": "0000-0001-8804-4216", "description": "", "uuid": 446636 }, "_jobs": [ { "job": 123325561366, "time": 124, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12881805428" }, { 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"display_metadata" ] }, { "page": "is_git2rdata", "title": "Check Whether a Git2rdata Object is Valid.", "concept": [ "internal" ], "topics": [ "is_git2rdata" ] }, { "page": "is_git2rmeta", "title": "Check Whether a Git2rdata Object Has Valid Metadata.", "concept": [ "internal" ], "topics": [ "is_git2rmeta" ] }, { "page": "list_data", "title": "List Available Git2rdata Files Containing Data", "concept": [ "storage" ], "topics": [ "list_data" ] }, { "page": "meta", "title": "Optimize an Object for Storage as Plain Text and Add Metadata", "concept": [ "internal" ], "topics": [ "meta", "meta.character", "meta.data.frame", "meta.Date", "meta.factor", "meta.logical", "meta.POSIXct" ] }, { "page": "print.git2rdata", "title": "Print method for 'git2rdata' objects.", "concept": [ "internal" ], "topics": [ "print.git2rdata" ] }, { "page": "prune_meta", "title": "Prune Metadata Files", "concept": [ "storage" ], "topics": [ "prune_meta", "prune_meta.git_repository" ] }, { "page": "pull", "title": "Re-exported Function From 'git2r'", "concept": [ "version_control" ], "topics": [ "pull" ] }, { "page": "push", "title": "Re-exported Function From 'git2r'", "concept": [ "version_control" ], "topics": [ "push" ] }, { "page": "read_vc", "title": "Read a Git2rdata Object from Disk", "concept": [ "storage" ], "topics": [ "read_vc" ] }, { "page": "recent_commit", "title": "Retrieve the Most Recent File Change", "concept": [ "version_control" ], "topics": [ "recent_commit" ] }, { "page": "relabel", "title": "Relabel Factor Levels by Updating the Metadata", "concept": [ "storage" ], "topics": [ "relabel" ] }, { "page": "rename_variable", "title": "Rename a Variable", "concept": [ "storage" ], "topics": [ "rename_variable", "rename_variable.character", "rename_variable.default", "rename_variable.git_repository" ] }, { "page": "repository", "title": "Re-exported Function From 'git2r'", "concept": [ "version_control" ], "topics": [ "repository" ] }, { "page": "rm_data", "title": "Remove Data Files From Git2rdata Objects", "concept": [ "storage" ], "topics": [ "rm_data", "rm_data.git_repository" ] }, { "page": "status", "title": "Re-exported Function From 'git2r'", "concept": [ "version_control" ], "topics": [ "status" ] }, { "page": "summary.git2rdata", "title": "Summary method for 'git2rdata' objects.", "concept": [ "internal" ], "topics": [ "summary.git2rdata" ] }, { "page": "update_metadata", "title": "Update the description of a 'git2rdata' object", "concept": [ "storage" ], "topics": [ "update_metadata" ] }, { "page": "upgrade_data", "title": "Upgrade Files to the New Version", "concept": [ "internal" ], "topics": [ "upgrade_data", "upgrade_data.git_repository" ] }, { "page": "verify_vc", "title": "Read a file an verify the presence of variables", "concept": [ "storage" ], "topics": [ "verify_vc" ] }, { "page": "write_vc", "title": "Store a Data.Frame as a Git2rdata Object on Disk", "concept": [ "storage" ], "topics": [ "write_vc", "write_vc.character", 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"Package": "mbquartR", "Title": "Finding Manitoba Quarter Sections", "Version": "0.1.1", "Authors@R": "c(\nperson(\"Alex\", \"Koiter\", , \"koitera@brandonu.ca\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-9355-9561\", \"Associate Professor,\nDepartment of Geography and Environment, Brandon University\n\")),\nperson(\"Emily H\", \"Markowitz\", role = \"rev\",\ncomment = \"Research Fisheries Biologist, Alaska Fisheries Science Center\nNOAA Fisheries | U.S. Department of Commerce.\n\nEmily reviewed the package for rOpenSci, see\n\"),\nperson(\"Sheila M\", \"Saia\", role = \"rev\",\ncomment = \"Environmental Data Scientist, Tetra Tech.\n\nSheila reviewed the package for rOpenSci, see\n\")\n)", "Description": "This package has four main functions: 1) download the\nManitoba Original Survey Legal Descriptions data set; 2) find\nthe coordinates of a quarter sections given the legal land\ndescription (e.g., \"NE-11-33-29W\"); 3) find the legal land\ndescription using 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"object": "samples_l8_rondonia_2bands", "class": [ "sits", "tbl_df", "tbl", "data.frame" ], "fields": [ "longitude", "latitude", "start_date", "end_date", "label", "cube", "time_series" ], "rows": 160, "table": false, "tojson": true }, { "name": "samples_modis_ndvi", "title": "Samples of nine classes for the state of Mato Grosso", "object": "samples_modis_ndvi", "class": [ "sits", "tbl_df", "tbl", "data.frame" ], "fields": [ "longitude", "latitude", "start_date", "end_date", "label", "cube", "time_series" ], "rows": 1218, "table": false, "tojson": true } ], "_help": [ { "page": "sits-package", "title": "sits", "topics": [ "sits-package", "sits" ] }, { "page": "cerrado_2classes", "title": "Samples of classes Cerrado and Pasture", "topics": [ "cerrado_2classes" ] }, { "page": "hist.probs_cube", "title": "histogram of prob cubes", "topics": [ "hist.probs_cube" ] }, { "page": "hist.raster_cube", "title": "histogram of data cubes", "topics": [ "hist.raster_cube" ] }, { "page": "hist.sits", "title": "Histogram", "topics": [ "hist.sits" ] }, { "page": "hist.uncertainty_cube", "title": "Histogram uncertainty cubes", "topics": [ "hist.uncertainty_cube" ] }, { "page": "impute_linear", "title": "Replace NA values by linear interpolation", "topics": [ "impute_linear" ] }, { "page": "impute_mean", "title": "Remove NA using mean", "topics": [ "impute_mean" ] }, { "page": "impute_mean_window", "title": "Remove NA using weighted moving average", "topics": [ "impute_mean_window" ] }, { "page": "impute_median", "title": "Remove NA using median", "topics": [ "impute_median" ] }, { "page": "plot", "title": "Plot time series and data cubes", "topics": [ "plot", "plot.sits" ] }, { "page": "plot.class_cube", "title": "Plot classified images", "topics": [ "plot.class_cube" ] }, { "page": "plot.class_vector_cube", "title": "Plot Segments", "topics": [ "plot.class_vector_cube" ] }, { "page": "plot.dem_cube", "title": "Plot DEM cubes", "topics": [ "plot.dem_cube" ] }, { "page": "plot.geo_distances", "title": "Make a kernel density plot of samples distances.", "topics": [ "plot.geo_distances" ] }, { "page": "plot.patterns", "title": "Plot patterns that describe classes", "topics": [ "plot.patterns" ] }, { "page": "plot.predicted", "title": "Plot time series predictions", "topics": [ "plot.predicted" ] }, { "page": "plot.probs_cube", "title": "Plot probability cubes", "topics": [ "plot.probs_cube" ] }, { "page": "plot.probs_vector_cube", "title": "Plot probability vector cubes", "topics": [ "plot.probs_vector_cube" ] }, { "page": "plot.raster_cube", "title": "Plot RGB data cubes", "topics": [ "plot.raster_cube" ] }, { "page": "plot.rfor_model", "title": "Plot Random Forest model", "topics": [ "plot.rfor_model" ] }, { "page": "plot.sar_cube", "title": "Plot SAR data cubes", "topics": [ "plot.sar_cube" ] }, { "page": "plot.sits_accuracy", "title": "Plot confusion matrix", "topics": [ "plot.sits_accuracy" ] }, { "page": "plot.sits_cluster", "title": "Plot a dendrogram cluster", "topics": [ "plot.sits_cluster" ] }, { "page": "plot.sits_model", "title": "Message for models whose plots are not available", "topics": [ "plot.sits_model" ] }, { "page": "plot.som_clean_samples", "title": "Plot SOM samples evaluated", "topics": [ "plot.som_clean_samples" ] }, { "page": "plot.som_evaluate_cluster", "title": "Plot confusion between clusters", "topics": [ "plot.som_evaluate_cluster" ] }, { "page": "plot.som_map", "title": "Plot a SOM map", "topics": [ "plot.som_map" ] }, { "page": "plot.torch_model", "title": "Plot Torch (deep learning) model", "topics": [ "plot.torch_model" ] }, { "page": "plot.uncertainty_cube", "title": "Plot uncertainty cubes", "topics": [ "plot.uncertainty_cube" ] }, { "page": "plot.uncertainty_vector_cube", "title": "Plot uncertainty vector cubes", "topics": [ "plot.uncertainty_vector_cube" ] }, { "page": "plot.variance_cube", "title": "Plot variance cubes", "topics": [ "plot.variance_cube" ] }, { "page": "plot.vector_cube", "title": "Plot RGB vector data cubes", "topics": [ "plot.vector_cube" ] }, { "page": "plot.xgb_model", "title": "Plot XGB model", "topics": [ "plot.xgb_model" ] }, { "page": "point_mt_6bands", "title": "A time series sample with data from 2000 to 2016", "topics": [ "point_mt_6bands" ] }, { "page": "samples_l8_rondonia_2bands", "title": "Samples of Amazon tropical forest biome for deforestation analysis", "topics": [ "samples_l8_rondonia_2bands" ] }, { "page": "samples_modis_ndvi", "title": "Samples of nine classes for the state of Mato Grosso", "topics": [ "samples_modis_ndvi" ] }, { "page": "sits_accuracy", "title": "Assess classification accuracy", "topics": [ "sits_accuracy", "sits_accuracy.class_cube", "sits_accuracy.class_vector_cube", "sits_accuracy.default", "sits_accuracy.derived_cube", "sits_accuracy.raster_cube", "sits_accuracy.sits", "sits_accuracy.tbl_df" ] }, { "page": "sits_add_base_cube", "title": "Add base maps to a time series data cube", "topics": [ "sits_add_base_cube" ] }, { "page": "sits_apply", "title": "Apply a function on a set of time series", "topics": [ "sits_apply", "sits_apply.default", "sits_apply.derived_cube", "sits_apply.raster_cube", "sits_apply.sits" ] }, { "page": "sits_as_sf", "title": "Return a sits_tibble or raster_cube as an sf object.", "topics": [ "sits_as_sf", "sits_as_sf.default", "sits_as_sf.raster_cube", "sits_as_sf.sits", "sits_as_sf.vector_cube" ] }, { "page": "sits_as_stars", "title": "Convert a data cube into a stars object", "topics": [ "sits_as_stars" ] }, { "page": "sits_as_terra", "title": "Convert a data cube into a Spatial Raster object from terra", "topics": [ "sits_as_terra", "sits_as_terra.class_cube", "sits_as_terra.probs_cube", "sits_as_terra.raster_cube", "sits_as_terra.uncertainty_cube", "sits_as_terra.variance_cube" ] }, { "page": "sits_bands", "title": "Get the names of the bands", "topics": [ "sits_bands", "sits_bands.default", "sits_bands.patterns", "sits_bands.raster_cube", "sits_bands.sits", "sits_bands.sits_model", "sits_bands<-", "sits_bands<-.default", "sits_bands<-.raster_cube", "sits_bands<-.sits" ] }, { "page": "sits_bbox", "title": "Get the bounding box of the data", "topics": [ "sits_bbox", "sits_bbox.default", "sits_bbox.raster_cube", "sits_bbox.sits", "sits_bbox.tbl_df" ] }, { "page": "sits_classify", "title": "Classify time series or data cubes", "topics": [ "sits_classify", "sits_classify.default", "sits_classify.derived_cube", "sits_classify.tbl_df" ] }, { "page": "sits_classify.raster_cube", "title": "Classify a regular raster cube", "topics": [ "sits_classify.raster_cube" ] }, { "page": "sits_classify.sits", "title": "Classify a set of time series", "topics": [ "sits_classify.sits" ] }, { "page": "sits_classify.vector_cube", "title": "Classify a segmented data cube", "topics": [ "sits_classify.vector_cube" ] }, { "page": "sits_clean", "title": "Cleans a classified map using a local window", "topics": [ "sits_clean", "sits_clean.class_cube", "sits_clean.default", "sits_clean.derived_cube", "sits_clean.raster_cube" ] }, { "page": "sits_cluster_clean", "title": "Removes labels that are minority in each cluster.", "topics": [ "sits_cluster_clean" ] }, { "page": "sits_cluster_dendro", "title": "Find clusters in time series samples", "topics": [ "sits_cluster_dendro" ] }, { "page": "sits_cluster_frequency", "title": "Show label frequency in each cluster produced by dendrogram analysis", "topics": [ "sits_cluster_frequency" ] }, { "page": "sits_colors", "title": "Function to retrieve sits color table", "topics": [ "sits_colors" ] }, { "page": "sits_colors_qgis", "title": "Function to save color table as QML style for data cube", "topics": [ "sits_colors_qgis", "sits_colors_qgis.class_cube", "sits_colors_qgis.class_vector_cube" ] }, { "page": "sits_colors_reset", "title": "Function to reset sits color table", "topics": [ "sits_colors_reset" ] }, { "page": "sits_colors_set", "title": "Function to set sits color table", "topics": [ "sits_colors_set" ] }, { "page": "sits_colors_show", "title": "Function to show colors in SITS", "topics": [ "sits_colors_show" ] }, { "page": "sits_combine_predictions", "title": "Estimate ensemble prediction based on list of probs cubes", "topics": [ "sits_combine_predictions", "sits_combine_predictions.average", "sits_combine_predictions.default", "sits_combine_predictions.uncertainty" ] }, { "page": "sits_confidence_sampling", "title": "Suggest high confidence samples to increase the training set.", "topics": [ "sits_confidence_sampling" ] }, { "page": "sits_config", "title": "Configure parameters for sits package", "topics": [ "sits_config" ] }, { "page": "sits_config_show", "title": "Show current sits configuration", "topics": [ "sits_config_show" ] }, { "page": "sits_config_user_file", "title": "Create a user configuration file.", "topics": [ "sits_config_user_file" ] }, { "page": "sits_cube", "title": "Create data cubes from image collections", "topics": [ "sits_cube" ] }, { "page": "sits_cube_copy", "title": "Copy the images of a cube to a local directory", "topics": [ "sits_cube_copy" ] }, { "page": "sits_cube.local_cube", "title": "Create sits cubes from cubes in flat files in a local", "topics": [ "sits_cube.local_cube" ] }, { "page": "sits_cube.results_cube", "title": "Create a results cube from local files", "topics": [ "sits_cube.results_cube" ] }, { "page": "sits_cube.stac_cube", "title": "Create data cubes from image collections accessible by STAC", "topics": [ "sits_cube.stac_cube" ] }, { "page": "sits_cube.vector_cube", "title": "Create a vector cube from local files", "topics": [ "sits_cube.vector_cube" ] }, { "page": "sits_factory_function", "title": "Create a closure for calling functions with and without data", "topics": [ "sits_factory_function" ] }, { "page": "sits_filter", "title": "Filter time series with smoothing filter", "topics": [ "sits_filter" ] }, { "page": "sits_formula_linear", "title": "Define a linear formula for classification models", "topics": [ "sits_formula_linear" ] }, { "page": "sits_formula_logref", "title": "Define a loglinear formula for classification models", "topics": [ "sits_formula_logref" ] }, { "page": "sits_geo_dist", "title": "Compute the minimum distances among samples and prediction points.", "topics": [ "sits_geo_dist" ] }, { "page": "sits_get_class", "title": "Get values from classified maps", "topics": [ "sits_get_class", "sits_get_class.csv", "sits_get_class.data.frame", "sits_get_class.default", "sits_get_class.sf", "sits_get_class.shp", "sits_get_class.sits" ] }, { "page": "sits_get_data", "title": "Get time series from data cubes and cloud services", "topics": [ "sits_get_data", "sits_get_data.default" ] }, { "page": "sits_get_data.csv", "title": "Get time series using CSV files", "topics": [ "sits_get_data.csv" ] }, { "page": "sits_get_data.data.frame", "title": "Get time series using sits objects", "topics": [ "sits_get_data.data.frame" ] }, { "page": "sits_get_data.sf", "title": "Get time series using sf objects", "topics": [ "sits_get_data.sf" ] }, { "page": "sits_get_data.shp", "title": "Get time series using shapefiles", "topics": [ "sits_get_data.shp" ] }, { "page": "sits_get_data.sits", "title": "Get time series using sits objects", "topics": [ "sits_get_data.sits" ] }, { "page": "sits_get_probs", "title": "Get values from probability maps", "topics": [ "sits_get_probs", "sits_get_probs.csv", "sits_get_probs.data.frame", "sits_get_probs.default", "sits_get_probs.sf", "sits_get_probs.shp", "sits_get_probs.sits" ] }, { "page": "sits_impute", "title": "Replace NA values in time series with imputation function", "topics": [ "sits_impute" ] }, { "page": "sits_kfold_validate", "title": "Cross-validate time series samples", "topics": [ "sits_kfold_validate" ] }, { "page": "sits_label_classification", "title": "Build a labelled image from a probability cube", "topics": [ "sits_label_classification", "sits_label_classification.default", "sits_label_classification.derived_cube", "sits_label_classification.probs_cube", "sits_label_classification.probs_vector_cube", "sits_label_classification.raster_cube" ] }, { "page": "sits_labels", "title": "Get labels associated to a data set", "topics": [ "sits_labels", "sits_labels.default", "sits_labels.derived_cube", "sits_labels.derived_vector_cube", "sits_labels.patterns", "sits_labels.raster_cube", "sits_labels.sits", "sits_labels.sits_model" ] }, { "page": "sits_labels_summary", "title": "Inform label distribution of a set of time series", "topics": [ "sits_labels_summary", "sits_labels_summary.sits" ] }, { "page": "sits_labels-set", "title": "Change the labels of a set of time series", "topics": [ "sits_labels<-" ] }, { "page": "sits_labels-set-.class_cube", "title": "Change the labels of a classified raster cube", "topics": [ "sits_labels<-.class_cube" ] }, { "page": "sits_labels-set-.class_vector_cube", "title": "Change the labels of a class vector data cube", "topics": [ "sits_labels<-.class_vector_cube" ] }, { "page": "sits_labels-set-.default", "title": "Change the labels of other data structures", "topics": [ "sits_labels<-.default" ] }, { "page": "sits_labels-set-.probs_cube", "title": "Change the labels of a probs raster cube", "topics": [ "sits_labels<-.probs_cube" ] }, { "page": "sits_labels-set-.probs_vector_cube", "title": "Change the labels of a probs vector data cube", "topics": [ "sits_labels<-.probs_vector_cube" ] }, { "page": "sits_labels-set-.sits", "title": "Change the labels of a set of time series", "topics": [ "sits_labels<-.sits" ] }, { "page": "sits_lightgbm", "title": "Train light gradient boosting model", "topics": [ "sits_lightgbm" ] }, { "page": "sits_lighttae", "title": "Train a model using Lightweight Temporal Self-Attention Encoder", "topics": [ "sits_lighttae" ] }, { "page": "sits_list_collections", "title": "List the cloud collections supported by sits", "topics": [ "sits_list_collections" ] }, { "page": "sits_lstm_fcn", "title": "Train a Long Short Term Memory Fully Convolutional Network", "topics": [ "sits_lstm_fcn" ] }, { "page": "sits_merge", "title": "Merge two data sets (time series or cubes)", "topics": [ "sits_merge", "sits_merge.default", "sits_merge.raster_cube", "sits_merge.sits" ] }, { "page": "sits_mgrs_to_roi", "title": "Convert MGRS tile information to ROI in WGS84", "topics": [ "sits_mgrs_to_roi" ] }, { "page": "sits_mixture_model", "title": "Multiple endmember spectral mixture analysis", "topics": [ "sits_mixture_model", "sits_mixture_model.default", "sits_mixture_model.derived_cube", "sits_mixture_model.raster_cube", "sits_mixture_model.sits", "sits_mixture_model.tbl_df" ] }, { "page": "sits_mlp", "title": "Train multi-layer perceptron models using torch", "topics": [ "sits_mlp" ] }, { "page": "sits_model_export", "title": "Export classification models", "topics": [ "sits_model_export", "sits_model_export.sits_model" ] }, { "page": "sits_mosaic", "title": "Mosaic classified cubes", "topics": [ "sits_mosaic" ] }, { "page": "sits_patterns", "title": "Find temporal patterns associated to a set of time series", "topics": [ "sits_patterns" ] }, { "page": "sits_pred_features", "title": "Obtain numerical values of predictors for time series samples", "topics": [ "sits_pred_features" ] }, { "page": "sits_pred_normalize", "title": "Normalize predictor values", "topics": [ "sits_pred_normalize" ] }, { "page": "sits_pred_references", "title": "Obtain categorical id and predictor labels for time series samples", "topics": [ "sits_pred_references" ] }, { "page": "sits_pred_sample", "title": "Obtain a fraction of the predictors data frame", "topics": [ "sits_pred_sample" ] }, { "page": "sits_predictors", "title": "Obtain predictors for time series samples", "topics": [ "sits_predictors" ] }, { "page": "sits_reclassify", "title": "Reclassify a classified cube", "topics": [ "sits_reclassify", "sits_reclassify.class_cube", "sits_reclassify.default" ] }, { "page": "sits_reduce", "title": "Reduces a cube or samples from a summarization function", "topics": [ "sits_reduce", "sits_reduce.raster_cube", "sits_reduce.sits" ] }, { "page": "sits_reduce_imbalance", "title": "Reduce imbalance in a set of samples", "topics": [ "sits_reduce_imbalance" ] }, { "page": "sits_regularize", "title": "Build a regular data cube from an irregular one", "topics": [ "sits_regularize", "sits_regularize.combined_cube", "sits_regularize.default", "sits_regularize.dem_cube", "sits_regularize.derived_cube", "sits_regularize.ogh_cube", "sits_regularize.rainfall_cube", "sits_regularize.raster_cube", "sits_regularize.sar_cube" ] }, { "page": "sits_resnet", "title": "Train ResNet classification models", "topics": [ "sits_resnet" ] }, { "page": "sits_rfor", "title": "Train random forest models", "topics": [ "sits_rfor" ] }, { "page": "sits_roi_to_mgrs", "title": "Given a ROI, find MGRS tiles intersecting it.", "topics": [ "sits_roi_to_mgrs" ] }, { "page": "sits_roi_to_tiles", "title": "Find tiles of a given ROI and Grid System", "topics": [ "sits_roi_to_tiles" ] }, { "page": "sits_run_examples", "title": "Informs if sits examples should run", "topics": [ "sits_run_examples" ] }, { "page": "sits_run_tests", "title": "Informs if sits tests should run", "topics": [ "sits_run_tests" ] }, { "page": "sits_sample", "title": "Sample a percentage of a time series", "topics": [ "sits_sample" ] }, { "page": "sits_sampling_design", "title": "Allocation of sample size to strata", "topics": [ "sits_sampling_design" ] }, { "page": "sits_segment", "title": "Segment an image", "topics": [ "sits_segment" ] }, { "page": "sits_select", "title": "Filter a data set (tibble or cube) for bands, tiles, and dates", "topics": [ "sits_select", "sits_select.default", "sits_select.raster_cube", "sits_select.sits" ] }, { "page": "sits_sgolay", "title": "Filter time series with Savitzky-Golay filter", "topics": [ "sits_sgolay" ] }, { "page": "sits_slic", "title": "Segment an image using SLIC", "topics": [ "sits_slic" ] }, { "page": "sits_smooth", "title": "Smooth probability cubes with spatial predictors", "topics": [ "sits_smooth", "sits_smooth.default", "sits_smooth.derived_cube", "sits_smooth.probs_cube", "sits_smooth.probs_vector_cube", "sits_smooth.raster_cube" ] }, { "page": "sits_snic", "title": "Segment an image using SNIC", "topics": [ "sits_snic" ] }, { "page": "sits_som_clean_samples", "title": "Cleans the samples based on SOM map information", "topics": [ "sits_som_clean_samples" ] }, { "page": "sits_som_evaluate_cluster", "title": "Evaluate cluster", "topics": [ "sits_som_evaluate_cluster" ] }, { "page": "sits_som_map", "title": "Build a SOM for quality analysis of time series samples", "topics": [ "sits_som_map" ] }, { "page": "sits_som_remove_samples", "title": "Evaluate cluster", "topics": [ "sits_som_remove_samples" ] }, { "page": "sits_stats", "title": "Obtain statistics for all sample bands", "topics": [ "sits_stats" ] }, { "page": "sits_stratified_sampling", "title": "Allocation of sample size to strata", "topics": [ "sits_stratified_sampling" ] }, { "page": "sits_svm", "title": "Train support vector machine models", "topics": [ "sits_svm" ] }, { "page": "sits_tae", "title": "Train a model using Temporal Self-Attention Encoder", "topics": [ "sits_tae" ] }, { "page": "sits_tempcnn", "title": "Train temporal convolutional neural network models", "topics": [ "sits_tempcnn" ] }, { "page": "sits_texture", "title": "Apply a set of texture measures on a data cube.", "topics": [ "sits_texture", "sits_texture.default", "sits_texture.derived_cube", "sits_texture.raster_cube" ] }, { "page": "sits_tiles_to_roi", "title": "Convert MGRS tile information to ROI in WGS84", "topics": [ "sits_tiles_to_roi" ] }, { "page": "sits_timeline", "title": "Get timeline of a cube or a set of time series", "topics": [ "sits_timeline", "sits_timeline.default", "sits_timeline.derived_cube", "sits_timeline.raster_cube", "sits_timeline.sits", "sits_timeline.sits_model", "sits_timeline.tbl_df" ] }, { "page": "sits_timeseries_to_csv", "title": "Export a a full sits tibble to the CSV format", "topics": [ "sits_timeseries_to_csv" ] }, { "page": "sits_to_csv", "title": "Export a sits tibble metadata to the CSV format", "topics": [ "sits_to_csv", "sits_to_csv.default", "sits_to_csv.sits", "sits_to_csv.tbl_df" ] }, { "page": "sits_to_xlsx", "title": "Save accuracy assessments as Excel files", "topics": [ "sits_to_xlsx", "sits_to_xlsx.list", "sits_to_xlsx.sits_accuracy" ] }, { "page": "sits_train", "title": "Train classification models", "topics": [ "sits_train" ] }, { "page": "sits_tuning", "title": "Tuning machine learning models hyper-parameters", "topics": [ "sits_tuning" ] }, { "page": "sits_tuning_hparams", "title": "Tuning machine learning models hyper-parameters", "topics": [ "sits_tuning_hparams" ] }, { "page": "sits_uncertainty", "title": 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language models (LLMs) based on 'transformer'\narchitectures via integration with the 'Hugging Face' ecosystem\n. The package interfaces with\npre-trained neural networks and supports both\ncausal/auto-regressive LLMs (e.g., 'GPT-2') and\nmasked/bidirectional LLMs (e.g., 'BERT') to compute the\nprobability of words, phrases, or tokens given their linguistic\ncontext. For details on GPT-2 and causal models, see Radford et\nal. (2019)\n,\nfor details on BERT and masked models, see Devlin et al. (2019)\n. 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"librdf_model_context_remove_statement", "librdf_model_context_remove_statements", "librdf_model_find_statements", "librdf_model_find_statements_in_context", "librdf_model_get_arc", "librdf_model_get_arcs", "librdf_model_get_arcs_in", "librdf_model_get_arcs_out", "librdf_model_get_contexts", "librdf_model_get_feature", "librdf_model_get_source", "librdf_model_get_sources", "librdf_model_get_target", "librdf_model_get_targets", "librdf_model_has_arc_in", "librdf_model_has_arc_out", "librdf_model_load", "librdf_model_query_execute", "librdf_model_remove_statement", "librdf_model_set_feature", "librdf_model_size", "librdf_model_sync", "librdf_model_to_string", "librdf_model_transaction_commit", "librdf_model_transaction_rollback", "librdf_model_transaction_start", "librdf_new_digest", "librdf_new_hash", "librdf_new_hash_from_array_of_strings", "librdf_new_hash_from_string", "librdf_new_model", "librdf_new_model_from_model", "librdf_new_model_with_options", "librdf_new_node", "librdf_new_node_from_blank_identifier", "librdf_new_node_from_literal", "librdf_new_node_from_node", "librdf_new_node_from_normalised_uri_string", "librdf_new_node_from_typed_literal", "librdf_new_node_from_uri", "librdf_new_node_from_uri_local_name", "librdf_new_node_from_uri_string", "librdf_new_parser", "librdf_new_query", "librdf_new_query_from_query", "librdf_new_serializer", "librdf_new_statement", "librdf_new_statement_from_nodes", "librdf_new_statement_from_statement", "librdf_new_storage", "librdf_new_storage_from_storage", "librdf_new_uri", "librdf_new_uri_from_filename", "librdf_new_uri_from_uri", "librdf_new_world", "librdf_node_equals", "librdf_node_get_blank_identifier", "librdf_node_get_li_ordinal", "librdf_node_get_literal_value", "librdf_node_get_literal_value_as_latin1", "librdf_node_get_literal_value_datatype_uri", "librdf_node_get_literal_value_is_wf_xml", "librdf_node_get_literal_value_language", "librdf_node_get_type", "librdf_node_get_uri", "librdf_node_is_blank", "librdf_node_is_literal", "librdf_node_is_resource", "librdf_parser_check_name", "librdf_parser_get_accept_header", "librdf_parser_get_feature", "librdf_parser_get_namespaces_seen_count", "librdf_parser_get_namespaces_seen_prefix", "librdf_parser_get_namespaces_seen_uri", "librdf_parser_guess_name2", "librdf_parser_parse_as_stream", "librdf_parser_parse_counted_string_as_stream", "librdf_parser_parse_counted_string_into_model", "librdf_parser_parse_into_model", "librdf_parser_parse_string_as_stream", "librdf_parser_parse_string_into_model", "librdf_parser_set_feature", "librdf_query_execute", "librdf_query_get_limit", "librdf_query_get_offset", "librdf_query_results_as_stream", "librdf_query_results_finished", "librdf_query_results_get_binding_name", "librdf_query_results_get_binding_value", "librdf_query_results_get_binding_value_by_name", "librdf_query_results_get_bindings_count", "librdf_query_results_get_boolean", "librdf_query_results_get_count", "librdf_query_results_is_bindings", "librdf_query_results_is_boolean", "librdf_query_results_is_graph", "librdf_query_results_is_syntax", "librdf_query_results_next", "librdf_query_results_to_file2", "librdf_query_results_to_string2", "librdf_query_set_limit", "librdf_query_set_offset", "librdf_serializer_check_name", "librdf_serializer_get_feature", "librdf_serializer_serialize_model_to_file", "librdf_serializer_serialize_model_to_string", "librdf_serializer_serialize_stream_to_file", "librdf_serializer_serialize_stream_to_string", "librdf_serializer_set_feature", "librdf_serializer_set_namespace", "librdf_short_copyright_string", "librdf_short_copyright_string_get", "librdf_statement_equals", "librdf_statement_get_object", "librdf_statement_get_predicate", "librdf_statement_get_subject", "librdf_statement_is_complete", "librdf_statement_match", "librdf_statement_set_object", "librdf_statement_set_predicate", "librdf_statement_set_subject", "librdf_stream_end", "librdf_stream_get_object", "librdf_stream_next", "librdf_uri_compare", "librdf_uri_equals", "librdf_uri_to_string", "librdf_version_decimal", "librdf_version_decimal_get", "librdf_version_major", "librdf_version_major_get", "librdf_version_minor", "librdf_version_minor_get", "librdf_version_release", "librdf_version_release_get", "librdf_version_string", "librdf_version_string_get", "librdf_world_get_feature", "librdf_world_open", "librdf_world_set_feature", "librdf_world_set_logger", "mergeNamespace_roclet", "parseFileIntoModel", "raptor_locator_byte", "raptor_locator_column", "raptor_locator_file", "raptor_locator_line", "raptor_locator_uri", "raptor_version_decimal", "raptor_version_decimal_get", "raptor_version_major", "raptor_version_major_get", "raptor_version_minor", "raptor_version_minor_get", "raptor_version_release", "raptor_version_release_get", "raptor_version_string", "raptor_version_string_get", "rasqal_version_decimal", "rasqal_version_decimal_get", "rasqal_version_major", "rasqal_version_major_get", "rasqal_version_minor", "rasqal_version_minor_get", "rasqal_version_release", "rasqal_version_release_get", "rasqal_version_string", "rasqal_version_string_get", "serializeToCharacter", "serializeToFile", "setNameSpace", "setQueryResultLimit", "writeResults" ], "_help": [ { "page": "sub-ExternalReference-method", "title": "Subset a list of ExternalReferences", "topics": [ "[,ExternalReference-method" ] }, { "page": "subset-ExternalReference-method", "title": "Assign values in a list of ExternalReferences", "topics": [ "[<-,ExternalReference-method" ] }, { "page": "addStatement", "title": "Add a Statement object to the Model", "topics": [ "addStatement", "addStatement,Model,Statement-method" ] }, { "page": "executeQuery", "title": "Execute a query", "topics": [ "executeQuery", "executeQuery,Query-method" ] }, { "page": "freeModel", "title": "Free memory used by a librdf model.", "topics": [ "freeModel", "freeModel,Model-method" ] }, { "page": "freeParser", "title": "Free memory used by a librdf parser", "topics": [ "freeParser", "freeParser,Parser-method" ] }, { "page": "freeQuery", "title": "Free memory used by a librdf query", "topics": [ "freeQuery", "freeQuery,Query-method" ] }, { "page": "freeQueryResults", "title": "Free memory used by a librdf query results", "topics": [ "freeQueryResults", "freeQueryResults,QueryResults-method" ] }, { "page": "freeSerializer", "title": "Free memory used by a librdf serializer.", "topics": [ "freeSerializer", "freeSerializer,Serializer-method" ] }, { "page": "freeStatement", "title": "Free memory used by a librdf statement", "topics": [ "freeStatement", "freeStatement,Statement-method" ] }, { "page": "freeStorage", "title": "Free memory used by a librdf storage object", "topics": [ "freeStorage", "freeStorage,Storage-method" ] }, { "page": "freeWorld", "title": "Free memory used by a librdf world object", "topics": [ "freeWorld", "freeWorld,World-method" ] }, { "page": "getBlankNodeId", "title": "Get the blank identifier that has been assigned for a specified Node object", "topics": [ "getBlankNodeId", "getBlankNodeId,Node-method" ] }, { "page": "getNodeType", "title": "Determine the node type and return as a string", "topics": [ "getNodeType", "getNodeType,Node-method" ] }, { "page": "getNodeValue", "title": "Get the value of the node as a string", "topics": [ "getNodeValue", "getNodeValue,Node-method" ] }, { "page": "getQueryResultsLimit", "title": "Get the query result limit", "topics": [ "getQueryResultLimit", "getQueryResultLimit,Query-method" ] }, { "page": "getResults", "title": "Return all query results", "topics": [ "getResults", "getResults,Query-method" ] }, { "page": "getTermType", "title": "Return the redland node type for the specified RDF term in a statement", "topics": [ "getTermType", "getTermType,Statement,character-method" ] }, { "page": "Model-initialize", "title": "Constructor for a Model object.", "topics": [ "initialize,Model-method", "Model-initialize" ] }, { "page": "Node-initialize", "title": "Initialize a Node object.", "topics": [ "initialize,Node-method", "Node-initialize" ] }, { "page": "Parser-initialize", "title": "Initialize a Parser object.", "topics": [ "initialize,Parser-method", "Parser-initialize" ] }, { "page": "Query-initialize", "title": "Initialize the Query object.", "topics": [ "initialize,Query-method", "Query-initialize" ] }, { "page": "QueryResults-initialize", "title": "Initialize the QueryResults object.", "topics": [ "initialize,QueryResults-method", "QueryResults-initialize" ] }, { "page": "Serializer-initialize", "title": "Construct a Serializer object.", "topics": [ "initialize,Serializer-method", "Serializer-initialize" ] }, { "page": "Statement-initialize", "title": "Construct a Statement object.", "topics": [ "initialize,Statement-method", "Statement-initialize" ] }, { "page": "Storage-initialize", "title": "Initialize a Storage object", "topics": [ "initialize,Storage-method", "Storage-initialize" ] }, { "page": "World-initialize", "title": "Initialize the World object.", "topics": [ "initialize,World-method", "World-initialize" ] }, { "page": "is.null.externalptr", "title": "Determine whether an externalptr object is NULL.", "topics": [ "is.null.externalptr" ] }, { "page": "length-SWIGArray-method", "title": "Return length of a SWIGArray", "topics": [ "length,SWIGArray-method" ] }, { "page": "librdf_copyright_string", "title": "Copyright string (multiple lines).", "topics": [ "librdf_copyright_string" ] }, { "page": "librdf_copyright_string_get", "title": "Return Redland RDF copyright string", "topics": [ "librdf_copyright_string_get" ] }, { "page": "librdf_digest_final", "title": "Finish the digesting of data.", "topics": [ "librdf_digest_final" ] }, { "page": "librdf_digest_init", "title": "(Re)initialise the librdf_digest object.", "topics": [ "librdf_digest_init" ] }, { "page": "librdf_digest_to_string", "title": "Get a string representation of the digest object.", "topics": [ "librdf_digest_to_string" ] }, { "page": "librdf_digest_update", "title": "Add more data to the librdf_digest object.", "topics": [ "librdf_digest_update" ] }, { "page": "librdf_digest_update_string", "title": "Add a string to the librdf_digest object.", "topics": [ "librdf_digest_update_string" ] }, { "page": "librdf_free_digest", "title": "Destructor - destroy a librdf_digest object.", "topics": [ "librdf_free_digest" ] }, { "page": "librdf_free_hash", "title": "Destructor - destroy a librdf_hash object.", "topics": [ "librdf_free_hash" ] }, { "page": "librdf_free_iterator", "title": "Destructor - destroy a librdf_iterator object.", "topics": [ "librdf_free_iterator" ] }, { "page": "librdf_free_model", "title": "Destructor - Destroy a librdf_model object.", "topics": [ "librdf_free_model" ] }, { "page": "librdf_free_node", "title": "Destructor - destroy an librdf_node object.", "topics": [ "librdf_free_node" ] }, { "page": "librdf_free_parser", "title": "Destructor - destroys a librdf_parser object.", "topics": [ "librdf_free_parser" ] }, { "page": "librdf_free_query", "title": "Destructor - destroy a librdf_query object.", "topics": [ "librdf_free_query" ] }, { "page": "librdf_free_query_results", "title": "Destructor - destroy a librdf_query_results object.", "topics": [ "librdf_free_query_results" ] }, { "page": "librdf_free_serializer", "title": "Destructor - destroys a librdf_serializer object.", "topics": [ "librdf_free_serializer" ] }, { "page": "librdf_free_statement", "title": "Destructor - destroy a librdf_statement.", "topics": [ "librdf_free_statement" ] }, { "page": "librdf_free_storage", "title": "Destructor - destroy a librdf_storage object.", "topics": [ "librdf_free_storage" ] }, { "page": "librdf_free_stream", "title": "Destructor - destroy an libdf_stream object.", "topics": [ "librdf_free_stream" ] }, { "page": "librdf_free_uri", "title": "Destructor - destroy a librdf_uri object.", "topics": [ "librdf_free_uri" ] }, { "page": "librdf_free_world", "title": "Terminate the library and frees all allocated resources.", "topics": [ "librdf_free_world" ] }, { "page": "librdf_hash_to_string", "title": "Format the hash as a string, suitable for parsing by librdf_hash_from_string.", "topics": [ "librdf_hash_to_string" ] }, { "page": "librdf_internal_test_error", "title": "For internal testing, not part of public API", "topics": [ "librdf_internal_test_error" ] }, { "page": "librdf_internal_test_warning", "title": "For internal testing, not part of public API", "topics": [ "librdf_internal_test_warning" ] }, { "page": "librdf_iterator_end", "title": "Test if the iterator has finished.", "topics": [ "librdf_iterator_end" ] }, { "page": "librdf_iterator_get_context", "title": "Get the context of the current object on the iterator.", "topics": [ "librdf_iterator_get_context" ] }, { "page": "librdf_iterator_get_object", "title": "Get the current object from the iterator.", "topics": [ "librdf_iterator_get_object" ] }, { "page": "librdf_iterator_next", "title": "Move to the next iterator element.", "topics": [ "librdf_iterator_next" ] }, { "page": "librdf_log_message_code", "title": "Retrieve error code from log message.", "topics": [ "librdf_log_message_code" ] }, { "page": "librdf_log_message_facility", "title": "Retrieve facility that generated the message.", "topics": [ "librdf_log_message_facility" ] }, { "page": "librdf_log_message_level", "title": "Retrieve severity of log message.", "topics": [ "librdf_log_message_level" ] }, { "page": "librdf_log_message_locator", "title": "Retrieve locator of log entry.", "topics": [ "librdf_log_message_locator" ] }, { "page": "librdf_log_message_message", "title": "Retrieve text message from log entry.", "topics": [ "librdf_log_message_message" ] }, { "page": "librdf_model_add", "title": "Create and add a new statement about a resource to the model.", "topics": [ "librdf_model_add" ] }, { "page": "librdf_model_add_statement", "title": "Add a statement to the model.", "topics": [ "librdf_model_add_statement" ] }, { "page": "librdf_model_add_statements", "title": "Add a stream of statements to the model.", "topics": [ "librdf_model_add_statements" ] }, { "page": "librdf_model_add_string_literal_statement", "title": "Create and add a new statement about a literal to the model.", "topics": [ "librdf_model_add_string_literal_statement" ] }, { "page": "librdf_model_add_typed_literal_statement", "title": "Create and add a new statement about a typed literal to the model.", "topics": [ "librdf_model_add_typed_literal_statement" ] }, { "page": "librdf_model_as_stream", "title": "List the model contents as a stream of statements.", "topics": [ "librdf_model_as_stream" ] }, { "page": "librdf_model_contains_context", "title": "Check for a context in the model.", "topics": [ "librdf_model_contains_context" ] }, { "page": "librdf_model_contains_statement", "title": "Check for a statement in the model.", "topics": [ "librdf_model_contains_statement" ] }, { "page": "librdf_model_context_add_statement", "title": "Add a statement to a model with a context.", "topics": [ "librdf_model_context_add_statement" ] }, { "page": "librdf_model_context_add_statements", "title": "Add statements to a model with a context.", "topics": [ "librdf_model_context_add_statements" ] }, { "page": "librdf_model_context_as_stream", "title": "List all statements in a model context.", "topics": [ "librdf_model_context_as_stream" ] }, { "page": "librdf_model_context_remove_statement", "title": "Remove a statement from a model in a context.", "topics": [ "librdf_model_context_remove_statement" ] }, { "page": "librdf_model_context_remove_statements", "title": "Remove statements from a model with the given context.", "topics": [ "librdf_model_context_remove_statements" ] }, { "page": "librdf_model_find_statements", "title": "Find matching statements in the model.", "topics": [ "librdf_model_find_statements" ] }, { "page": "librdf_model_find_statements_in_context", "title": "Search the model for matching statements in a given context.", "topics": [ "librdf_model_find_statements_in_context" ] }, { "page": "librdf_model_get_arc", "title": "Return one arc (predicate) of an arc in an RDF graph given source (subject) and target (object).", "topics": [ "librdf_model_get_arc" ] }, { "page": "librdf_model_get_arcs", "title": "Return the arcs (predicates) of an arc in an RDF graph given source (subject) and target (object).", "topics": [ "librdf_model_get_arcs" ] }, { "page": "librdf_model_get_arcs_in", "title": "Return the properties pointing to the given resource.", "topics": [ "librdf_model_get_arcs_in" ] }, { "page": "librdf_model_get_arcs_out", "title": "Return the properties pointing from the given resource.", "topics": [ "librdf_model_get_arcs_out" ] }, { "page": "librdf_model_get_contexts", "title": "Return the list of contexts in the graph.", "topics": [ "librdf_model_get_contexts" ] }, { "page": "librdf_model_get_feature", "title": "Get the value of a graph feature .", "topics": [ "librdf_model_get_feature" ] }, { "page": "librdf_model_get_source", "title": "Return one source (subject) of arc in an RDF graph given arc (predicate) and target (object).", "topics": [ "librdf_model_get_source" ] }, { "page": "librdf_model_get_sources", "title": "Return the sources (subjects) of arc in an RDF graph given arc (predicate) and target (object).", "topics": [ "librdf_model_get_sources" ] }, { "page": "librdf_model_get_target", "title": "Return one target (object) of an arc in an RDF graph given source (subject) and arc (predicate).", "topics": [ "librdf_model_get_target" ] }, { "page": "librdf_model_get_targets", "title": "Return the targets (objects) of an arc in an RDF graph given source (subject) and arc (predicate).", "topics": [ "librdf_model_get_targets" ] }, { "page": "librdf_model_has_arc_in", "title": "Check if a node has a given property pointing to it.", "topics": [ "librdf_model_has_arc_in" ] }, { "page": "librdf_model_has_arc_out", "title": "Check if a node has a given property pointing from it.", "topics": [ "librdf_model_has_arc_out" ] }, { "page": "librdf_model_load", "title": "Load content from a URI into the model.", "topics": [ "librdf_model_load" ] }, { "page": "librdf_model_query_execute", "title": "Execute a query against the model.", "topics": [ "librdf_model_query_execute" ] }, { "page": "librdf_model_remove_statement", "title": "Remove a known statement from the model.", "topics": [ "librdf_model_remove_statement" ] }, { "page": "librdf_model_set_feature", "title": "Set the value of a graph feature.", "topics": [ "librdf_model_set_feature" ] }, { "page": "librdf_model_size", "title": "Get the number of statements in the model.", "topics": [ "librdf_model_size" ] }, { "page": "librdf_model_sync", "title": "Synchronise the model to the model implementation.", "topics": [ "librdf_model_sync" ] }, { "page": "librdf_model_to_string", "title": "Write serialized model to a string.", "topics": [ "librdf_model_to_string" ] }, { "page": "librdf_model_transaction_commit", "title": "Commit a transaction.", "topics": [ "librdf_model_transaction_commit" ] }, { "page": "librdf_model_transaction_rollback", "title": "Rollback a transaction.", "topics": [ "librdf_model_transaction_rollback" ] }, { "page": "librdf_model_transaction_start", "title": "Start a transaction", "topics": [ "librdf_model_transaction_start" ] }, { "page": "librdf_new_digest", "title": "Constructor - create a new librdf_digest object.", "topics": [ "librdf_new_digest" ] }, { "page": "librdf_new_hash", "title": "Constructor - create a new librdf_hash object.", "topics": [ "librdf_new_hash" ] }, { "page": "librdf_new_hash_from_array_of_strings", "title": "Constructor - create a new librdf_hash object from an array of strings.", "topics": [ "librdf_new_hash_from_array_of_strings" ] }, { "page": "librdf_new_hash_from_string", "title": "Constructor - create a new librdf_hash object from a string.", "topics": [ "librdf_new_hash_from_string" ] }, { "page": "librdf_new_model", "title": "Constructor - create a new storage librdf_model object.", "topics": [ "librdf_new_model" ] }, { "page": "librdf_new_model_from_model", "title": "Copy constructor - create a new librdf_model from an existing one.", "topics": [ "librdf_new_model_from_model" ] }, { "page": "librdf_new_model_with_options", "title": "Constructor - Create a new librdf_model with storage.", "topics": [ "librdf_new_model_with_options" ] }, { "page": "librdf_new_node", "title": "Constructor - create a new librdf_node object with a private identifier.", "topics": [ "librdf_new_node" ] }, { "page": "librdf_new_node_from_blank_identifier", "title": "Constructor - create a new blank node librdf_node object from a blank node identifier.", "topics": [ "librdf_new_node_from_blank_identifier" ] }, { "page": "librdf_new_node_from_literal", "title": "Constructor - create a new literal librdf_node object.", "topics": [ "librdf_new_node_from_literal" ] }, { "page": "librdf_new_node_from_node", "title": "Copy constructor - create a new librdf_node object from an existing librdf_node object.", "topics": [ "librdf_new_node_from_node" ] }, { "page": "librdf_new_node_from_normalised_uri_string", "title": "Constructor - create a new librdf_node object from a UTF-8 encoded URI string normalised to a new base URI.", "topics": [ "librdf_new_node_from_normalised_uri_string" ] }, { "page": "librdf_new_node_from_typed_literal", "title": "Constructor - create a new typed literal librdf_node object.", "topics": [ "librdf_new_node_from_typed_literal" ] }, { "page": "librdf_new_node_from_uri", "title": "Constructor - create a new resource librdf_node object with a given URI.", "topics": [ "librdf_new_node_from_uri" ] }, { "page": "librdf_new_node_from_uri_local_name", "title": "Constructor - create a new resource librdf_node object with a given URI and local name.", "topics": [ "librdf_new_node_from_uri_local_name" ] }, { "page": "librdf_new_node_from_uri_string", "title": "Constructor - create a new librdf_node object from a URI string.", "topics": [ "librdf_new_node_from_uri_string" ] }, { "page": "librdf_new_parser", "title": "Constructor - create a new librdf_parser object.", "topics": [ "librdf_new_parser" ] }, { "page": "librdf_new_query", "title": "Constructor - create a new librdf_query object.", "topics": [ "librdf_new_query" ] }, { "page": "librdf_new_query_from_query", "title": "Copy constructor - create a new librdf_query object from an existing one", "topics": [ "librdf_new_query_from_query" ] }, { "page": "librdf_new_serializer", "title": "Constructor - create a new librdf_serializer object.", "topics": [ "librdf_new_serializer" ] }, { "page": "librdf_new_statement", "title": "Constructor - create a new empty librdf_statement.", "topics": [ "librdf_new_statement" ] }, { "page": "librdf_new_statement_from_nodes", "title": "Constructor - create a new librdf_statement from existing librdf_node objects.", "topics": [ "librdf_new_statement_from_nodes" ] }, { "page": "librdf_new_statement_from_statement", "title": "Copy constructor - create a new librdf_statement from an existing librdf_statement. Creates a deep copy - changes to original statement nodes are not reflected in the copy.", "topics": [ "librdf_new_statement_from_statement" ] }, { "page": "librdf_new_storage", "title": "Constructor - create a new librdf_storage object.", "topics": [ "librdf_new_storage" ] }, { "page": "librdf_new_storage_from_storage", "title": "Copy constructor - create a new librdf_storage object from an existing one", "topics": [ "librdf_new_storage_from_storage" ] }, { "page": "librdf_new_uri", "title": "Constructor - create a new librdf_uri object from a URI string.", "topics": [ "librdf_new_uri" ] }, { "page": "librdf_new_uri_from_filename", "title": "Constructor - create a new librdf_uri object from a filename.", "topics": [ "librdf_new_uri_from_filename" ] }, { "page": "librdf_new_uri_from_uri", "title": "Copy constructor - create a new librdf_uri object from an existing librdf_uri object.", "topics": [ "librdf_new_uri_from_uri" ] }, { "page": "librdf_new_world", "title": "Create a new Redland execution environment.", "topics": [ "librdf_new_world" ] }, { "page": "librdf_node_equals", "title": "Compare two librdf_node objects for equality.", "topics": [ "librdf_node_equals" ] }, { "page": "librdf_node_get_blank_identifier", "title": "Get the blank node identifier as a UTF-8 encoded string.", "topics": [ "librdf_node_get_blank_identifier" ] }, { "page": "librdf_node_get_li_ordinal", "title": "Get the node li object ordinal value.", "topics": [ "librdf_node_get_li_ordinal" ] }, { "page": "librdf_node_get_literal_value", "title": "Get the literal value of the node as a UTF-8 encoded string.", "topics": [ "librdf_node_get_literal_value" ] }, { "page": "librdf_node_get_literal_value_as_latin1", "title": "Get the string literal value of the node as ISO Latin-1.", "topics": [ "librdf_node_get_literal_value_as_latin1" ] }, { "page": "librdf_node_get_literal_value_datatype_uri", "title": "Get the typed literal datatype URI of the literal node.", "topics": [ "librdf_node_get_literal_value_datatype_uri" ] }, { "page": "librdf_node_get_literal_value_is_wf_xml", "title": "Get the XML well-formness property of the node.", "topics": [ "librdf_node_get_literal_value_is_wf_xml" ] }, { "page": "librdf_node_get_literal_value_language", "title": "Get the XML language of the node.", "topics": [ "librdf_node_get_literal_value_language" ] }, { "page": "librdf_node_get_type", "title": "Get the type of the node.", "topics": [ "librdf_node_get_type" ] }, { "page": "librdf_node_get_uri", "title": "Get the URI for a node object.", "topics": [ "librdf_node_get_uri" ] }, { "page": "librdf_node_is_blank", "title": "Check node is a blank nodeID.", "topics": [ "librdf_node_is_blank" ] }, { "page": "librdf_node_is_literal", "title": "Check node is a literal.", "topics": [ "librdf_node_is_literal" ] }, { "page": "librdf_node_is_resource", "title": "Check node is a resource.", "topics": [ "librdf_node_is_resource" ] }, { "page": "librdf_parser_check_name", "title": "Check if a parser name is known", "topics": [ "librdf_parser_check_name" ] }, { "page": "librdf_parser_get_accept_header", "title": "Get an HTTP Accept value for the parser.", "topics": [ "librdf_parser_get_accept_header" ] }, { "page": "librdf_parser_get_feature", "title": "Get the value of a parser feature.", "topics": [ "librdf_parser_get_feature" ] }, { "page": "librdf_parser_get_namespaces_seen_count", "title": "Get the number of namespaces seen during parsing", "topics": [ "librdf_parser_get_namespaces_seen_count" ] }, { "page": "librdf_parser_get_namespaces_seen_prefix", "title": "Get the prefix of namespaces seen during parsing", "topics": [ "librdf_parser_get_namespaces_seen_prefix" ] }, { "page": "librdf_parser_get_namespaces_seen_uri", "title": "Get the uri of namespaces seen during parsing", "topics": [ "librdf_parser_get_namespaces_seen_uri" ] }, { "page": "librdf_parser_guess_name2", "title": "Get a parser name for content with type or identifier", "topics": [ "librdf_parser_guess_name2" ] }, { "page": "librdf_parser_parse_as_stream", "title": "Parse a URI to a librdf_stream of statements.", "topics": [ "librdf_parser_parse_as_stream" ] }, { "page": "librdf_parser_parse_counted_string_as_stream", "title": "Parse a counted string of content to a librdf_stream of statements.", "topics": [ "librdf_parser_parse_counted_string_as_stream" ] }, { "page": "librdf_parser_parse_counted_string_into_model", "title": "Parse a counted string of content into an librdf_model.", "topics": [ "librdf_parser_parse_counted_string_into_model" ] }, { "page": "librdf_parser_parse_into_model", "title": "Parse a URI of content into an librdf_model.", "topics": [ "librdf_parser_parse_into_model" ] }, { "page": "librdf_parser_parse_string_as_stream", "title": "Parse a string of content to a librdf_stream of statements.", "topics": [ "librdf_parser_parse_string_as_stream" ] }, { "page": "librdf_parser_parse_string_into_model", "title": "Parse a string of content into an librdf_model.", "topics": [ "librdf_parser_parse_string_into_model" ] }, { "page": "librdf_parser_set_feature", "title": "Set the value of a parser feature.", "topics": [ "librdf_parser_set_feature" ] }, { "page": "librdf_query_execute", "title": "Run the query on a model.", "topics": [ "librdf_query_execute" ] }, { "page": "librdf_query_get_limit", "title": "Get the query-specified limit on results.", "topics": [ "librdf_query_get_limit" ] }, { "page": "librdf_query_get_offset", "title": "Get the query-specified offset on results.", "topics": [ "librdf_query_get_offset" ] }, { "page": "librdf_query_results_as_stream", "title": "Get a query result as an RDF graph in librdf_stream form", "topics": [ "librdf_query_results_as_stream" ] }, { "page": "librdf_query_results_finished", "title": "Find out if binding results are exhausted.", "topics": [ "librdf_query_results_finished" ] }, { "page": "librdf_query_results_get_binding_name", "title": "Get binding name for the current result.", "topics": [ "librdf_query_results_get_binding_name" ] }, { "page": "librdf_query_results_get_binding_value", "title": "Get one binding value for the current result.", "topics": [ "librdf_query_results_get_binding_value" ] }, { "page": "librdf_query_results_get_binding_value_by_name", "title": "Get one binding value for a given name in the current result.", "topics": [ "librdf_query_results_get_binding_value_by_name" ] }, { "page": "librdf_query_results_get_bindings_count", "title": "Get the number of bound variables in the result.", "topics": [ "librdf_query_results_get_bindings_count" ] }, { "page": "librdf_query_results_get_boolean", "title": "Get boolean query result.", "topics": [ "librdf_query_results_get_boolean" ] }, { "page": "librdf_query_results_get_count", "title": "Get number of bindings so far.", "topics": [ "librdf_query_results_get_count" ] }, { "page": "librdf_query_results_is_bindings", "title": "Test if librdf_query_results is variable bindings format.", "topics": [ "librdf_query_results_is_bindings" ] }, { "page": "librdf_query_results_is_boolean", "title": "Test if librdf_query_results is boolean format.", "topics": [ "librdf_query_results_is_boolean" ] }, { "page": "librdf_query_results_is_graph", "title": "Test if librdf_query_results is RDF graph format.", "topics": [ "librdf_query_results_is_graph" ] }, { "page": "librdf_query_results_is_syntax", "title": "Test if librdf_query_results is a syntax.", "topics": [ "librdf_query_results_is_syntax" ] }, { "page": "librdf_query_results_next", "title": "Move to the next result.", "topics": [ "librdf_query_results_next" ] }, { "page": "librdf_query_results_to_file2", "title": "Write a query results to a file.", "topics": [ "librdf_query_results_to_file2" ] }, { "page": "librdf_query_results_to_string2", "title": "Turn a query results into a string.", "topics": [ "librdf_query_results_to_string2" ] }, { "page": "librdf_query_set_limit", "title": "Set the query-specified limit on results.", "topics": [ "librdf_query_set_limit" ] }, { "page": "librdf_query_set_offset", "title": "Set the query-specified offset on results.", "topics": [ "librdf_query_set_offset" ] }, { "page": "librdf_serializer_check_name", "title": "Check if a serializer name is known", "topics": [ "librdf_serializer_check_name" ] }, { "page": "librdf_serializer_get_feature", "title": "Get the value of a serializer feature.", "topics": [ "librdf_serializer_get_feature" ] }, { "page": "librdf_serializer_serialize_model_to_file", "title": "Write a serialized librdf_model to a file.", "topics": [ "librdf_serializer_serialize_model_to_file" ] }, { "page": "librdf_serializer_serialize_model_to_string", "title": "Write a serialized librdf_model to a string. The returned string must be freed by the caller using librdf_free_memory().", "topics": [ "librdf_serializer_serialize_model_to_string" ] }, { "page": "librdf_serializer_serialize_stream_to_file", "title": "Write a librdf_stream to a file.", "topics": [ "librdf_serializer_serialize_stream_to_file" ] }, { "page": "librdf_serializer_serialize_stream_to_string", "title": "Write a librdf_stream to a string.", "topics": [ "librdf_serializer_serialize_stream_to_string" ] }, { "page": "librdf_serializer_set_feature", "title": "Set the value of a serializer feature.", "topics": [ "librdf_serializer_set_feature" ] }, { "page": "librdf_serializer_set_namespace", "title": "Set a namespace URI/prefix mapping.", "topics": [ "librdf_serializer_set_namespace" ] }, { "page": "librdf_short_copyright_string", "title": "Short copyright string (one line).", "topics": [ "librdf_short_copyright_string" ] }, { "page": "librdf_short_copyright_string_get", "title": "Return Redland librdf copyright string", "topics": [ "librdf_short_copyright_string_get" ] }, { "page": "librdf_statement_equals", "title": "Check if two statements are equal.", "topics": [ "librdf_statement_equals" ] }, { "page": "librdf_statement_get_object", "title": "Get the statement object.", "topics": [ "librdf_statement_get_object" ] }, { "page": "librdf_statement_get_predicate", "title": "Get the statement predicate.", "topics": [ "librdf_statement_get_predicate" ] }, { "page": "librdf_statement_get_subject", "title": "Get the statement subject.", "topics": [ "librdf_statement_get_subject" ] }, { "page": "librdf_statement_is_complete", "title": "Check if statement is a complete and legal RDF triple.", "topics": [ "librdf_statement_is_complete" ] }, { "page": "librdf_statement_match", "title": "Match a statement against a 'partial' statement.", "topics": [ "librdf_statement_match" ] }, { "page": "librdf_statement_set_object", "title": "Set the statement object.", "topics": [ "librdf_statement_set_object" ] }, { "page": "librdf_statement_set_predicate", "title": "Set the statement predicate.", "topics": [ "librdf_statement_set_predicate" ] }, { "page": "librdf_statement_set_subject", "title": "Set the statement subject.", "topics": [ "librdf_statement_set_subject" ] }, { "page": "librdf_stream_end", "title": "Test if the stream has ended.", "topics": [ "librdf_stream_end" ] }, { "page": "librdf_stream_get_object", "title": "Get the current librdf_statement in the stream.", "topics": [ "librdf_stream_get_object" ] }, { "page": "librdf_stream_next", "title": "Move to the next librdf_statement in the stream.", "topics": [ "librdf_stream_next" ] }, { "page": "librdf_uri_compare", "title": "Compare two librdf_uri objects lexicographically.", "topics": [ "librdf_uri_compare" ] }, { "page": "librdf_uri_equals", "title": "Compare two librdf_uri objects for equality.", "topics": [ "librdf_uri_equals" ] }, { "page": "librdf_uri_to_string", "title": "Format the URI as a string.", "topics": [ "librdf_uri_to_string" ] }, { "page": "librdf_version_decimal", "title": "Library full version as a decimal integer.", "topics": [ "librdf_version_decimal" ] }, { "page": "librdf_version_decimal_get", "title": "Return Redland librdf copyright", "topics": [ "librdf_version_decimal_get" ] }, { "page": "librdf_version_major", "title": "Library major version number as a decimal integer.", "topics": [ "librdf_version_major" ] }, { "page": "librdf_version_major_get", "title": "Return the Redland librdf major version number", "topics": [ "librdf_version_major_get" ] }, { "page": "librdf_version_minor", "title": "Library minor version number as a decimal integer.", "topics": [ "librdf_version_minor" ] }, { "page": "librdf_version_minor_get", "title": "Return the Redland librdf minor version number", "topics": [ "librdf_version_minor_get" ] }, { "page": "librdf_version_release", "title": "Library release version number as a decimal integer.", "topics": [ "librdf_version_release" ] }, { "page": "librdf_version_release_get", "title": "Return the Redland librdf release version number", "topics": [ "librdf_version_release_get" ] }, { "page": "librdf_version_string", "title": "Library full version as a string.", "topics": [ "librdf_version_string" ] }, { "page": "librdf_version_string_get", "title": "Return the Redland librdf version as a string.", "topics": [ "librdf_version_string_get" ] }, { "page": "librdf_world_get_feature", "title": "Get the value of a world feature.", "topics": [ "librdf_world_get_feature" ] }, { "page": "librdf_world_open", "title": "Open a created redland world environment.", "topics": [ "librdf_world_open" ] }, { "page": "librdf_world_set_feature", "title": "Set the value of a world feature.", "topics": [ "librdf_world_set_feature" ] }, { "page": "librdf_world_set_logger", "title": "Set the world log handling function.", "topics": [ "librdf_world_set_logger" ] }, { "page": "mergeNamespace_roclet", "title": "A custom Roxygen roclet that adds Redland RDF functions to NAMESPACE file generated by Roxygen.", "topics": [ "mergeNamespace_roclet" ] }, { "page": "Model-class", "title": "A Redland Model object", "topics": [ "Model", "Model-class" ] }, { "page": "Node-class", "title": "A Redland Node, used to store one node in an RDF triple statement.", "topics": [ "Node", "Node-class" ] }, { "page": "parseFileIntoModel", "title": "Parse the contents of a file into a model", "topics": [ "parseFileIntoModel", "parseFileIntoModel,Parser,World,character,Model-method" ] }, { "page": "Parser-class", "title": "An RDF Parser object", "topics": [ "Parser", "Parser-class" ] }, { "page": "Query-class", "title": "Query an RDF model", "topics": [ "Query", "Query-class" ] }, { "page": "QueryResults-class", "title": "A Redland QueryResults object is used to inspect query results from a Query object.", "topics": [ "QueryResults", "QueryResults-class" ] }, { "page": "raptor_locator_byte", "title": "Get the locator byte offset from locator.", "topics": [ 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'BEAUti 2' (which is part of\n'BEAST2') is a GUI tool that allows users to specify the many\npossible setups and generates the XML file 'BEAST2' needs to\nrun. This package provides a way to create 'BEAST2' input files\nwithout active user input, but using R function calls instead.", "License": "GPL-3", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "URL": "https://docs.ropensci.org/beautier/,\nhttps://github.com/ropensci/beautier", "BugReports": "https://github.com/ropensci/beautier/issues", "Language": "en-US", "Encoding": "UTF-8", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-12-08 18:28:22 UTC", "RemoteUrl": "https://github.com/ropensci/beautier", "RemoteRef": "main", "RemoteSha": "e2184775ea9b577a76b7a5935ed632723abb2bd5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-08 12:11:59 UTC", "User": "root" }, "Author": "Richèl J.C. 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"create_jc69_subst_model_xml", "create_kappa_1_param", "create_kappa_2_param", "create_kappa_param", "create_lambda_param", "create_laplace_distr", "create_log_normal_distr", "create_loggers_xml", "create_m_param", "create_mcmc", "create_mcmc_nested_sampling", "create_mean_param", "create_mrca_prior", "create_mu_param", "create_normal_distr", "create_ns_inference_model", "create_ns_mcmc", "create_one_div_x_distr", "create_param", "create_param_alpha", "create_param_b_pop_sizes", "create_param_beta", "create_param_clock_rate", "create_param_freq", "create_param_kappa", "create_param_kappa_1", "create_param_kappa_2", "create_param_lambda", "create_param_m", "create_param_mean", "create_param_mu", "create_param_rate_ac", "create_param_rate_ag", "create_param_rate_at", "create_param_rate_cg", "create_param_rate_ct", "create_param_rate_gt", "create_param_s", "create_param_scale", "create_param_sigma", "create_poisson_distr", "create_rate_ac_param", "create_rate_ag_param", "create_rate_at_param", "create_rate_categories_state_node_xml", "create_rate_cg_param", "create_rate_ct_param", "create_rate_gt_param", "create_rln_clock_branch_rate_model_xml", "create_rln_clock_model", "create_s_param", "create_scale_param", "create_screenlog", "create_screenlog_xml", "create_sigma_param", "create_site_model", "create_site_model_from_name", "create_site_model_gtr", "create_site_model_hky", "create_site_model_jc69", "create_site_model_parameters_xml", "create_site_model_tn93", "create_site_model_xml", "create_site_models", "create_site_models_from_names", "create_strict_clock_branch_rate_model_xml", "create_strict_clock_model", "create_strict_clock_rate_scaler_operator_xml", "create_subst_model_xml", "create_temp_screenlog_filename", "create_temp_tracelog_filename", "create_temp_treelog_filename", "create_test_inference_model", "create_test_mcmc", "create_test_ns_inference_model", "create_test_ns_mcmc", "create_test_screenlog", "create_test_tracelog", "create_test_treelog", "create_tn93_site_model", "create_tn93_subst_model_xml", "create_tracelog", "create_tracelog_xml", "create_trait_set_string", "create_tree_likelihood_distr_xml", "create_tree_prior", "create_tree_prior_bd", "create_tree_prior_cbs", "create_tree_prior_ccp", "create_tree_prior_cep", "create_tree_prior_yule", "create_tree_priors", "create_treelog", "create_treelog_xml", "create_ucld_mean_state_node_param_xml", "create_ucld_stdev_state_node_param_xml", "create_uniform_distr", "create_xml_declaration", "create_yule_tree_prior", "distr_to_xml", "distr_to_xml_beta", "distr_to_xml_exp", "distr_to_xml_inv_gamma", "distr_to_xml_laplace", "distr_to_xml_log_normal", "distr_to_xml_normal", "distr_to_xml_one_div_x", "distr_to_xml_poisson", "distr_to_xml_uniform", "extract_xml_loggers_from_lines", "extract_xml_operators_from_lines", "extract_xml_section_from_lines", "fasta_file_to_sequences", "find_clock_model", "find_first_regex_line", "find_first_xml_opening_tag_line", "find_last_regex_line", "find_last_xml_closing_tag_line", "freq_equilibrium_to_xml", "freq_param_to_xml", "gamma_distr_to_xml", "gamma_site_model_to_xml_prior_distr", "gamma_site_model_to_xml_state", "gamma_site_models_to_xml_prior_distr", "get_alignment_id", "get_alignment_ids", "get_alignment_ids_from_fasta_filenames", "get_beautier_folder", "get_beautier_path", "get_beautier_paths", "get_beautier_tempfilename", "get_clock_model_name", "get_clock_model_names", "get_clock_models_ids", "get_crown_age", "get_default_beast_namespace", "get_default_beast_namespace_v2_4", "get_default_beast_namespace_v2_6", "get_distr_n_params", "get_distr_names", "get_fasta_filename", "get_file_base_sans_ext", "get_freq_equilibrium_names", "get_gamma_site_model_n_distrs", "get_gamma_site_model_n_params", "get_has_non_strict_clock_model", "get_inference_model_filenames", "get_log_modes", "get_log_sorts", "get_mcmc_filenames", "get_n_taxa", "get_operator_id_pre", "get_param_names", "get_remove_dir_fun", "get_remove_hex_fun", "get_replace_dir_fun", "get_site_model_n_distrs", "get_site_model_n_params", "get_site_model_names", "get_site_models_n_distrs", "get_site_models_n_params", "get_taxa_names", "get_tree_prior_n_distrs", "get_tree_prior_n_params", "get_tree_prior_names", "get_tree_priors_n_distrs", "get_tree_priors_n_params", "get_xml_closing_tag", "get_xml_opening_tag", "gtr_site_model_to_xml_prior_distr", "gtr_site_model_to_xml_state", "has_mrca_prior", "has_mrca_prior_with_distr", "has_rln_clock_model", "has_strict_clock_model", "has_tip_dating", "has_xml_closing_tag", "has_xml_opening_tag", "has_xml_short_closing_tag", "hky_site_model_to_xml_prior_distr", "hky_site_model_to_xml_state", "indent", "init_bd_tree_prior", "init_beta_distr", "init_ccp_tree_prior", "init_cep_tree_prior", "init_clock_models", "init_distr", "init_exp_distr", "init_gamma_distr", "init_gamma_site_model", "init_gtr_site_model", "init_hky_site_model", "init_inference_model", "init_inv_gamma_distr", "init_jc69_site_model", "init_laplace_distr", "init_log_normal_distr", "init_mrca_prior", "init_mrca_priors", "init_normal_distr", "init_one_div_x_distr", "init_param", "init_poisson_distr", "init_rln_clock_model", "init_site_models", "init_strict_clock_model", "init_tn93_site_model", "init_tree_priors", "init_uniform_distr", "init_yule_tree_prior", "interspace", "is_alpha_param", "is_b_pop_sizes_param", "is_bd_tree_prior", "is_beast2_input_file_with_tipdates", "is_beauti_options", "is_beta_distr", "is_beta_param", "is_cbs_tree_prior", "is_ccp_tree_prior", "is_cep_tree_prior", "is_clock_model", "is_clock_model_name", "is_clock_rate_param", "is_default_mcmc", "is_distr", "is_distr_name", "is_exp_distr", "is_freq_equilibrium_name", "is_freq_param", "is_gamma_distr", "is_gamma_site_model", "is_gtr_site_model", "is_hky_site_model", "is_id", "is_in_patterns", "is_inference_model", "is_init_bd_tree_prior", "is_init_beta_distr", "is_init_cbs_tree_prior", "is_init_ccp_tree_prior", "is_init_cep_tree_prior", "is_init_clock_model", "is_init_distr", "is_init_exp_distr", "is_init_gamma_distr", "is_init_gamma_site_model", "is_init_gtr_site_model", "is_init_hky_site_model", "is_init_inv_gamma_distr", "is_init_jc69_site_model", "is_init_laplace_distr", "is_init_log_normal_distr", "is_init_mrca_prior", "is_init_normal_distr", "is_init_one_div_x_distr", "is_init_param", "is_init_poisson_distr", "is_init_rln_clock_model", "is_init_site_model", "is_init_strict_clock_model", "is_init_tn93_site_model", "is_init_tree_prior", "is_init_uniform_distr", "is_init_yule_tree_prior", "is_inv_gamma_distr", "is_jc69_site_model", "is_kappa_1_param", "is_kappa_2_param", "is_kappa_param", "is_lambda_param", "is_laplace_distr", "is_log_normal_distr", "is_m_param", "is_mcmc", "is_mcmc_nested_sampling", "is_mean_param", "is_mrca_align_id_in_fasta", "is_mrca_align_ids_in_fastas", "is_mrca_prior", "is_mrca_prior_with_distr", "is_mu_param", "is_nested_sampling_mcmc", "is_normal_distr", "is_on_appveyor", "is_on_ci", "is_on_github_actions", "is_on_travis", "is_one_bool", "is_one_div_x_distr", "is_one_double", "is_one_empty_string", "is_one_int", "is_one_na", "is_one_string", "is_one_string_that_is_a_number", "is_param", "is_param_name", "is_phylo", "is_poisson_distr", "is_rate_ac_param", "is_rate_ag_param", "is_rate_at_param", "is_rate_cg_param", "is_rate_ct_param", "is_rate_gt_param", "is_rln_clock_model", "is_s_param", "is_scale_param", "is_sigma_param", "is_site_model", "is_site_model_name", "is_strict_clock_model", "is_tn93_site_model", "is_tree_prior", "is_tree_prior_name", "is_uniform_distr", "is_xml", "is_yule_tree_prior", "jc69_site_model_to_xml_state", "kappa_param_to_xml", "m_param_to_xml", "mcmc_to_xml_run", "mcmc_to_xml_run_default", "mcmc_to_xml_run_nested_sampling", "mrca_prior_to_xml_prior_distr", "mrca_prior_to_xml_state", "mrca_prior_to_xml_taxonset", "mrca_prior_to_xml_tracelog", "mrca_priors_to_xml_prior_distr", "needs_trait_set_str", "no_taxa_to_xml_tree", "obj_type_friendly", "parameter_to_xml", "parameter_to_xml_kappa_1", "parameter_to_xml_kappa_2", "parameter_to_xml_lambda", "parameter_to_xml_mean", "parameter_to_xml_mu", "parameter_to_xml_rate_ac", "parameter_to_xml_rate_ag", "parameter_to_xml_rate_at", "parameter_to_xml_rate_cg", "parameter_to_xml_rate_ct", "parameter_to_xml_rate_gt", "parameter_to_xml_scale", "parameter_to_xml_sigma", "read_tipdates_file", "remove_beautier_folder", "remove_empty_lines", "remove_multiline", "rename_inference_model_filenames", "rename_mcmc_filenames", "rln_clock_model_to_xml_mean_rate_prior", "rln_clock_model_to_xml_operators", "rln_clock_model_to_xml_prior_distr", "rln_clock_model_to_xml_state", "rln_clock_model_to_xml_tracelog", "rnd_phylo_to_xml_init", "s_parameter_to_xml", "site_model_to_xml_operators", "site_model_to_xml_prior_distr", "site_model_to_xml_state", "site_model_to_xml_tracelog", "site_models_to_xml_operators", "site_models_to_xml_prior_distr", "site_models_to_xml_tracelog", "stop_input_type", "strict_clock_model_to_xml_operators", "strict_clock_model_to_xml_prior_distr", "strict_clock_model_to_xml_state", "strict_clock_model_to_xml_tracelog", "taxa_to_xml_tree", "tipdate_taxa_to_xml_trait", "tipdate_taxa_to_xml_tree", "tn93_site_model_to_xml_prior_distr", "tn93_site_model_to_xml_state", "tree_model_to_tracelog_xml", "tree_prior_to_xml_operators", "tree_prior_to_xml_prior_distr", "tree_prior_to_xml_state", "tree_prior_to_xml_tracelog", "tree_priors_to_xml_prior_distr", "tree_priors_to_xml_tracelog", "unindent", "yule_tree_prior_to_xml_operators", "yule_tree_prior_to_xml_prior_distr" ], "_help": [ { "page": "alpha_parameter_to_xml", "title": "Internal function", "topics": [ "alpha_parameter_to_xml" ] }, { "page": "are_clock_models", "title": "Determine if x consists out of clock_models objects", "topics": [ "are_clock_models" ] }, { "page": "are_equal_mcmcs", "title": "Determine if two MCMCs are equal.", "topics": [ "are_equal_mcmcs" ] }, { "page": "are_equal_screenlogs", "title": "Determine if two screenlogs are equal.", "topics": [ "are_equal_screenlogs" ] }, { "page": "are_equal_tracelogs", "title": "Determine if two tracelogs are equal.", "topics": [ "are_equal_tracelogs" ] }, { "page": "are_equal_treelogs", "title": "Determine if two treelogs are equal.", "topics": [ "are_equal_treelogs" ] }, { "page": "are_equal_xml_files", "title": "Determine if XML files result in equal trees", "topics": [ "are_equal_xml_files" ] }, { "page": "are_equal_xml_lines", "title": "Determine if XML lines result in equal trees", "topics": [ "are_equal_xml_lines" ] }, { "page": "are_equivalent_xml_files", "title": "Internal function", "topics": [ "are_equivalent_xml_files" ] }, { "page": "are_equivalent_xml_lines", "title": "Determine if XML lines result in equivalent trees", "topics": [ "are_equivalent_xml_lines" ] }, { "page": "are_equivalent_xml_lines_all", "title": "Determine if XML lines result in equivalent trees", "topics": [ "are_equivalent_xml_lines_all" ] }, { "page": "are_equivalent_xml_lines_loggers", "title": "Determine if XML operator lines result in equivalent trees", "topics": [ "are_equivalent_xml_lines_loggers" ] }, { "page": "are_equivalent_xml_lines_operators", "title": "Determine if XML operator lines result in equivalent trees", "topics": [ "are_equivalent_xml_lines_operators" ] }, { "page": "are_equivalent_xml_lines_section", "title": "Determine if XML lines result in equivalent trees", "topics": [ "are_equivalent_xml_lines_section" ] }, { "page": "are_fasta_filenames", "title": "Checks if all filenames have a FASTA filename extension", "topics": [ "are_fasta_filenames" ] }, { "page": "are_ids", "title": "Determine if x consists out of IDs", "topics": [ "are_ids" ] }, { "page": "are_init_clock_models", "title": "Determine if x consists out of initialized clock_models objects", "topics": [ "are_init_clock_models" ] }, { "page": "are_init_mrca_priors", "title": "Determine if x consists out of initialized MRCA priors", "topics": [ "are_init_mrca_priors" ] }, { "page": "are_init_site_models", "title": "Determine if x consists out of initialized site_models objects", "topics": [ "are_init_site_models" ] }, { "page": "are_init_tree_priors", "title": "Determine if x consists out of initialized tree_priors objects", "topics": [ "are_init_tree_priors" ] }, { "page": "are_mrca_align_ids_in_fasta", "title": "Determine if the MRCA priors' alignment IDs are present in the FASTA files", "topics": [ "are_mrca_align_ids_in_fasta" ] }, { "page": "are_mrca_priors", "title": "Determine if x consists out of MRCA priors", "topics": [ "are_mrca_priors" ] }, { "page": "are_mrca_taxon_names_in_fasta", "title": "Determine if the MRCA priors' taxa names are present in the FASTA files", "topics": [ "are_mrca_taxon_names_in_fasta" ] }, { "page": "are_rln_clock_models", "title": "Are the clock models Relaxed Log-Normal clock models?", "topics": [ "are_rln_clock_models" ] }, { "page": "are_site_models", "title": "Determine if x consists out of site_models objects", "topics": [ "are_site_models" ] }, { "page": "are_tree_priors", "title": "Determine if x consists out of tree_priors objects", "topics": [ "are_tree_priors" ] }, { "page": "b_pop_sizes_param_to_xml", "title": "Internal function", "topics": [ "b_pop_sizes_param_to_xml" ] }, { "page": "b_pop_sizes_parameter_to_xml", "title": "Internal function", "topics": [ "b_pop_sizes_parameter_to_xml" ] }, { "page": "bd_tree_prior_to_xml_prior_distr", "title": "Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Birth-Death tree prior", "topics": [ "bd_tree_prior_to_xml_prior_distr" ] }, { "page": "beta_parameter_to_xml", "title": "Internal function", "topics": [ "beta_parameter_to_xml" ] }, { "page": "cbs_tree_prior_to_xml_prior_distr", "title": "Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Birth-Death tree prior", "topics": [ "cbs_tree_prior_to_xml_prior_distr" ] }, { "page": "ccp_tree_prior_to_xml_prior_distr", "title": "Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Coalescent Constant Population tree prior", "topics": [ "ccp_tree_prior_to_xml_prior_distr" ] }, { "page": "ccp_tree_prior_to_xml_state", "title": "Convert a CCP tree prior to the XML as part of the 'state' section", "topics": [ "ccp_tree_prior_to_xml_state" ] }, { "page": "cep_tree_prior_to_xml_prior_distr", "title": "Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Coalescent Exponential Population tree prior", "topics": [ "cep_tree_prior_to_xml_prior_distr" ] }, { "page": "check_alignment_id", "title": "Check if the 'alignment_id' is valid.", "topics": [ "check_alignment_id" ] }, { "page": "check_beauti_options", "title": "Check if the 'beauti_options' is a valid 'beauti_options' object.", "topics": [ "check_beauti_options" ] }, { "page": "check_bool", "title": "Determine if `x` is one boolean", "topics": [ "check_bool" ] }, { "page": "check_clock_model", "title": "Check if the clock model is a valid clock model.", "topics": [ "check_clock_model" ] }, { "page": "check_clock_models", "title": "Check if the object is a list of one or more clock models.", "topics": [ "check_clock_models" ] }, { "page": "check_empty_beautier_folder", "title": "Internal function", "topics": [ "check_empty_beautier_folder" ] }, { "page": "check_false", "title": "Determine if `x` is one FALSE", "topics": [ "check_false" ] }, { "page": "check_file_and_model_agree", "title": "Checks if the input FASTA file and the inference model agree.", "topics": [ "check_file_and_model_agree" ] }, { "page": "check_file_exists", "title": "Function to check if a file exists. Calls 'stop' if the file is absent", "topics": [ "check_file_exists" ] }, { "page": "check_filename", "title": "Check if the `filename` is valid", "topics": [ "check_filename" ] }, { "page": "check_gamma_site_model", "title": "Checks if the parameter is a valid gamma site model", "topics": [ "check_gamma_site_model" ] }, { "page": "check_gamma_site_model_names", "title": "Checks if the gamma site model has the right list elements' names", "topics": [ "check_gamma_site_model_names" ] }, { "page": "check_gtr_site_model", "title": "Check if the 'gtr_site_model' is a valid GTR nucleotide substitution model.", "topics": [ "check_gtr_site_model" ] }, { "page": "check_gtr_site_model_names", "title": "Check if the 'gtr_site_model' has the list elements of a valid 'gtr_site_model' object.", "topics": [ "check_gtr_site_model_names" ] }, { "page": "check_inference_model", "title": "Check if the supplied object is a valid Bayesian phylogenetic inference model.", "topics": [ "check_inference_model" ] }, { "page": "check_inference_models", "title": "Check if the 'inference_model' is a valid BEAUti inference model.", "topics": [ "check_inference_models" ] }, { "page": "check_is_monophyletic", "title": "Check if 'is_monophyletic' has a valid value.", "topics": [ "check_is_monophyletic" ] }, { "page": "check_log_mode", "title": "Check if the supplied 'mode' is a valid logging mode.", "topics": [ "check_log_mode" ] }, { "page": "check_log_sort", "title": "Check if the supplied 'sort' is a valid logging sorting option.", "topics": [ "check_log_sort" ] }, { "page": "check_logical", "title": "Determine if `x` is one logical value", "topics": [ "check_logical" ] }, { "page": "check_mcmc", "title": "Check if the MCMC is a valid MCMC object.", "topics": [ "check_mcmc" ] }, { "page": "check_mcmc_list_element_names", "title": "Check if the MCMC has the list elements of a valid MCMC object.", "topics": [ "check_mcmc_list_element_names" ] }, { "page": "check_mcmc_values", "title": "Check if the MCMC has the list elements with valid values for being a valid MCMC object.", "topics": [ "check_mcmc_values" ] }, { "page": "check_mrca_prior", "title": "Check if the MRCA prior is a valid MRCA prior.", "topics": [ "check_mrca_prior" ] }, { "page": "check_mrca_prior_name", "title": "Check if 'mrca_prior_name' is a valid MRCA prior name.", "topics": [ "check_mrca_prior_name" ] }, { "page": "check_mrca_prior_names", "title": "Check if the MRCA prior, which is a list, has all the named elements.", "topics": [ "check_mrca_prior_names" ] }, { "page": "check_mrca_prior_taxa_names", "title": "Check the MRCA prior's taxon names are valid.", "topics": [ "check_mrca_prior_taxa_names" ] }, { "page": "check_ns_mcmc", "title": "Check if this an MCMC that uses Nested Sampling to estimate a marginal likelihood.", "topics": [ "check_mcmc_nested_sampling", "check_nested_sampling_mcmc", "check_ns_mcmc" ] }, { "page": "check_number_whole", "title": "Determine if `x` is one whole number", "topics": [ "check_number_whole" ] }, { "page": "check_param", "title": "Check if the parameter is a valid parameter", "topics": [ "check_param" ] }, { "page": "check_param_names", "title": "Check if the 'param' has the list elements of a valid 'param' object.", "topics": [ "check_param_names" ] }, { "page": "check_param_types", "title": "Check if the 'param' has the list elements of the right type for a valid 'param' object.", "topics": [ "check_param_types" ] }, { "page": "check_phylogeny", "title": "Check if the phylogeny is a valid phylogeny object.", "topics": [ "check_phylogeny" ] }, { "page": "check_rename_fun", "title": "Check if the rename function is a valid filename rename function", "topics": [ "check_rename_fun" ] }, { "page": "check_rln_clock_model", "title": "Check if the clock model is a valid clock model.", "topics": [ "check_rln_clock_model" ] }, { "page": "check_screenlog", "title": "Check if a 'screenlog' is valid.", "topics": [ "check_screenlog" ] }, { "page": "check_screenlog_names", "title": "Check if the 'screenlog' has the list elements of a valid 'screenlog' object.", "topics": [ "check_screenlog_names" ] }, { "page": "check_screenlog_values", "title": "Check if the screenlog has the list elements with valid values for being a valid screenlog object.", "topics": [ "check_screenlog_values" ] }, { "page": "check_site_model", "title": "Check if the site model is a valid site model", "topics": [ "check_site_model" ] }, { "page": "check_site_model_names", "title": "Check if the 'site_model' has the list elements of a valid 'site_model' object.", "topics": [ "check_site_model_names" ] }, { "page": "check_site_model_types", "title": "Check if the 'site_model' has the list elements of the right type for a valid 'site_model' object.", "topics": [ "check_site_model_types" ] }, { "page": "check_site_models", "title": "Check if the object is a list of one or more site models.", "topics": [ "check_site_models" ] }, { "page": "check_store_every", "title": "Check if 'store_every' holds a valid value", "topics": [ "check_store_every" ] }, { "page": "check_strict_clock_model", "title": "Check if the clock model is a valid clock model.", "topics": [ "check_strict_clock_model" ] }, { "page": "check_string", "title": "Determine if `x` is one string", "topics": [ "check_string" ] }, { "page": "check_tipdates_file", "title": "Check if the tip dates file is valid", "topics": [ "check_tipdates_file" ] }, { "page": "check_tn93_site_model", "title": "Check if the 'tn93_site_model' is a valid TN93 nucleotide substitution model.", "topics": [ "check_tn93_site_model" ] }, { "page": "check_tn93_site_model_names", "title": "Check if the 'tn93_site_model' has the list elements of a valid 'tn93_site_model' object.", "topics": [ "check_tn93_site_model_names" ] }, { "page": "check_tracelog", "title": "Check if a 'tracelog' is valid.", "topics": [ "check_tracelog" ] }, { "page": "check_tracelog_names", "title": "Check if the 'tracelog' has the list elements of a valid 'tracelog' object.", "topics": [ "check_tracelog_names" ] }, { "page": "check_tracelog_values", "title": "Check if the tracelog has the list elements with valid values for being a valid tracelog object.", "topics": [ "check_tracelog_values" ] }, { "page": "check_tree_prior", "title": "Check if the tree prior is a valid tree prior", "topics": [ "check_tree_prior" ] }, { "page": "check_tree_priors", "title": "Check if the object is a list of one or more tree priors.", "topics": [ "check_tree_priors" ] }, { "page": "check_treelog", "title": "Check if a 'treelog' is valid.", "topics": [ "check_treelog" ] }, { "page": "check_treelog_names", "title": "Check if the 'treelog' has the list elements of a valid 'treelog' object.", "topics": [ "check_treelog_names" ] }, { "page": "check_treelog_values", "title": "Check if the treelog has the list elements with valid values for being a valid treelog object.", "topics": [ "check_treelog_values" ] }, { "page": "check_true", "title": "Determine if `x` is one TRUE", "topics": [ "check_true" ] }, { "page": "clock_model_to_xml_operators", "title": "Internal function", "topics": [ "clock_model_to_xml_operators" ] }, { "page": "clock_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "clock_model_to_xml_prior_distr" ] }, { "page": "clock_model_to_xml_state", "title": "Internal function", "topics": [ "clock_model_to_xml_state" ] }, { "page": "clock_model_to_xml_tracelog", "title": "Internal function", "topics": [ "clock_model_to_xml_tracelog" ] }, { "page": "clock_model_to_xml_treelogger", "title": "Convert a clock model to the XML of the 'TreeLogger'", "topics": [ "clock_model_to_xml_treelogger" ] }, { "page": "clock_rate_param_to_xml", "title": "Internal function", "topics": [ "clock_rate_param_to_xml" ] }, { "page": "compare_lines", "title": "Internal function", "topics": [ "compare_lines" ] }, { "page": "count_trailing_spaces", "title": "Count the number of spaces before the first character", "topics": [ "count_trailing_spaces" ] }, { "page": "create_alpha_param", "title": "Create a parameter called alpha", "topics": [ "create_alpha_param", "create_param_alpha" ] }, { "page": "create_b_pop_sizes_param", "title": "Create a parameter called `b_pop_sizes`.", "topics": [ "create_b_pop_sizes_param", "create_param_b_pop_sizes" ] }, { "page": "create_bd_tree_prior", "title": "Create a Birth-Death tree prior", "topics": [ "create_bd_tree_prior", "create_tree_prior_bd" ] }, { "page": "create_beast2_beast_xml", "title": "Create the '' XML", "topics": [ "create_beast2_beast_xml" ] }, { "page": "create_beast2_input", "title": "Create a BEAST2 XML input text", "topics": [ "create_beast2_input" ] }, { "page": "create_beast2_input_beast", "title": "Creates the XML text for the 'beast' tag of a BEAST2 parameter file.", "topics": [ "create_beast2_input_beast" ] }, { "page": "create_beast2_input_data", "title": "Creates the 'data' section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_data" ] }, { "page": "create_beast2_input_data_sequences", "title": "Creates the data section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_data_sequences" ] }, { "page": "create_beast2_input_distr", "title": "Creates the distribution section of a BEAST2 XML parameter file.", "topics": [ "create_beast2_input_distr" ] }, { "page": "create_beast2_input_distr_lh", "title": "Creates the XML text for the 'distribution' tag with the 'likelihood' ID, of a BEAST2 parameter file.", "topics": [ "create_beast2_input_distr_lh" ] }, { "page": "create_beast2_input_distr_prior", "title": "Creates the prior section in the distribution section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_distr_prior" ] }, { "page": "create_beast2_input_file", "title": "Create a BEAST2 input file", "topics": [ "create_beast2_input_file" ] }, { "page": "create_beast2_input_file_from_model", "title": "Create a BEAST2 input file from an inference model", "topics": [ "create_beast2_input_file_from_model" ] }, { "page": "create_beast2_input_from_model", "title": "Create a BEAST2 XML input text from an inference model", "topics": [ "create_beast2_input_from_model" ] }, { "page": "create_beast2_input_init", "title": "Creates the 'init' section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_init" ] }, { "page": "create_beast2_input_map", "title": "Creates the map section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_map" ] }, { "page": "create_beast2_input_operators", "title": "Creates the operators section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_operators" ] }, { "page": "create_beast2_input_run", "title": "Creates the ''run'' section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_run" ] }, { "page": "create_beast2_input_state", "title": "Creates the ''state'' section of a BEAST2 XML parameter file", "topics": [ "create_beast2_input_state" ] }, { "page": "create_beauti_options", "title": "Function to create a set of `BEAUti` options.", "topics": [ "create_beauti_options" ] }, { "page": "create_beauti_options_v2_4", "title": "Function to create the BEAUti options for version 2.4.", "topics": [ "create_beauti_options_v2_4" ] }, { "page": "create_beauti_options_v2_6", "title": "Function to create the BEAUti options for version 2.6.", "topics": [ "create_beauti_options_v2_6" ] }, { "page": "create_beautier_tempfolder", "title": "Create the default `beautier` temporary folder", "topics": [ "create_beautier_tempfolder" ] }, { "page": "create_beta_distr", "title": "Create a beta distribution", "topics": [ "create_beta_distr", "create_distr_beta" ] }, { "page": "create_beta_param", "title": "Create a parameter called beta", "topics": [ "create_beta_param", "create_param_beta" ] }, { "page": "create_branch_rate_model_xml", "title": "Internal function to create the 'branchRateModel' section of the XML as text.", "topics": [ "create_branch_rate_model_xml" ] }, { "page": "create_cbs_tree_prior", "title": "Create a Coalescent Bayesian Skyline tree prior", "topics": [ "create_cbs_tree_prior", "create_tree_prior_cbs" ] }, { "page": "create_ccp_tree_prior", "title": "Create a Coalescent Constant Population tree prior", "topics": [ "create_ccp_tree_prior", "create_tree_prior_ccp" ] }, { "page": "create_cep_tree_prior", "title": "Create a Coalescent Exponential Population tree prior", "topics": [ "create_cep_tree_prior", "create_tree_prior_cep" ] }, { "page": "create_clock_model", "title": "General function to create a clock model", "topics": [ "create_clock_model" ] }, { "page": "create_clock_model_from_name", "title": "Create a clock model from name", "topics": [ "create_clock_model_from_name" ] }, { "page": "create_clock_models", "title": "Creates all supported clock models, which is a list of the types returned by 'create_rln_clock_model', and 'create_strict_clock_model'", "topics": [ "create_clock_models" ] }, { "page": "create_clock_models_from_names", "title": "Create clock models from their names", "topics": [ "create_clock_models_from_names" ] }, { "page": "create_clock_rate_param", "title": "Create a parameter called 'clock_rate', as needed by 'create_strict_clock_model'", "topics": [ "create_clock_rate_param", "create_param_clock_rate" ] }, { "page": "create_clock_rate_state_node_parameter_xml", "title": "Internal function", "topics": [ "create_clock_rate_state_node_parameter_xml" ] }, { "page": "create_data_xml", "title": "Create the '' XML", "topics": [ "create_data_xml" ] }, { "page": "create_distr", "title": "General function to create a distribution.", "topics": [ "create_distr" ] }, { "page": "create_exp_distr", "title": "Create an exponential distribution", "topics": [ "create_distr_exp", "create_exp_distr" ] }, { "page": "create_freq_param", "title": "Create a parameter called freq", "topics": [ "create_freq_param", "create_param_freq" ] }, { "page": "create_gamma_distr", "title": "Create a gamma distribution", "topics": [ "create_distr_gamma", "create_gamma_distr" ] }, { "page": "create_gamma_site_model", "title": "Create a gamma site model, part of a site model", "topics": [ "create_gamma_site_model" ] }, { "page": "create_gtr_site_model", "title": "Create a GTR site model", "topics": [ "create_gtr_site_model", "create_site_model_gtr" ] }, { "page": "create_gtr_subst_model_xml", "title": "Converts a GTR site model to XML, used in the 'substModel' section", "topics": [ "create_gtr_subst_model_xml" ] }, { "page": "create_hky_site_model", "title": "Create an HKY site model", "topics": [ "create_hky_site_model", "create_site_model_hky" ] }, { "page": "create_hky_subst_model_xml", "title": "Converts a site model to XML, used in the 'substModel' section", "topics": [ "create_hky_subst_model_xml" ] }, { "page": "create_inference_model", "title": "Create a Bayesian phylogenetic inference model.", "topics": [ "create_inference_model" ] }, { "page": "create_inv_gamma_distr", "title": "Create an inverse-gamma distribution", "topics": [ "create_distr_inv_gamma", "create_inv_gamma_distr" ] }, { "page": "create_jc69_site_model", "title": "Create a JC69 site model", "topics": [ "create_jc69_site_model", "create_site_model_jc69" ] }, { "page": "create_jc69_subst_model_xml", "title": "Converts a JC69 site model to XML, used in the 'substModel' section", "topics": [ "create_jc69_subst_model_xml" ] }, { "page": "create_kappa_1_param", "title": "Create a parameter called kappa 1", "topics": [ "create_kappa_1_param", "create_param_kappa_1" ] }, { "page": "create_kappa_2_param", "title": "Create a parameter called kappa 2", "topics": [ "create_kappa_2_param", "create_param_kappa_2" ] }, { "page": "create_kappa_param", "title": "Create a parameter called kappa", "topics": [ "create_kappa_param", "create_param_kappa" ] }, { "page": "create_lambda_param", "title": "Create a parameter called lambda", "topics": [ "create_lambda_param", "create_param_lambda" ] }, { "page": "create_laplace_distr", "title": "Create a Laplace distribution", "topics": [ "create_distr_laplace", "create_laplace_distr" ] }, { "page": "create_log_normal_distr", "title": "Create a log-normal distribution", "topics": [ "create_distr_log_normal", "create_log_normal_distr" ] }, { "page": "create_loggers_xml", "title": "Creates the three logger sections of a BEAST2 XML parameter file", "topics": [ "create_loggers_xml" ] }, { "page": "create_m_param", "title": "Create a parameter called m", "topics": [ "create_m_param", "create_param_m" ] }, { "page": "create_mcmc", "title": "Create an MCMC configuration.", "topics": [ "create_mcmc" ] }, { "page": "create_mean_param", "title": "Create a parameter called mean", "topics": [ "create_mean_param", "create_param_mean" ] }, { "page": "create_mrca_prior", "title": "Create a Most Recent Common Ancestor prior", "topics": [ "create_mrca_prior" ] }, { "page": "create_mu_param", "title": "Create a parameter called mu", "topics": [ "create_mu_param", "create_param_mu" ] }, { "page": "create_normal_distr", "title": "Create an normal distribution", "topics": [ "create_distr_normal", "create_normal_distr" ] }, { "page": "create_ns_inference_model", "title": "Create an inference model to measure the evidence of.", "topics": [ "create_ns_inference_model" ] }, { "page": "create_ns_mcmc", "title": "Create an MCMC object to estimate the marginal likelihood using Nested Sampling.", "topics": [ "create_mcmc_nested_sampling", "create_ns_mcmc" ] }, { "page": "create_one_div_x_distr", "title": "Create a 1/x distribution", "topics": [ "create_distr_one_div_x", "create_one_div_x_distr" ] }, { "page": "create_param", "title": "General function to create a parameter.", "topics": [ "create_param" ] }, { "page": "create_poisson_distr", "title": "Create a Poisson distribution", "topics": [ "create_distr_poisson", "create_poisson_distr" ] }, { "page": "create_rate_ac_param", "title": "Create a parameter called 'rate AC'", "topics": [ "create_param_rate_ac", "create_rate_ac_param" ] }, { "page": "create_rate_ag_param", "title": "Create a parameter called 'rate AG'", "topics": [ "create_param_rate_ag", "create_rate_ag_param" ] }, { "page": "create_rate_at_param", "title": "Create a parameter called 'rate AT'", "topics": [ "create_param_rate_at", "create_rate_at_param" ] }, { "page": "create_rate_categories_state_node_xml", "title": "Internal function", "topics": [ "create_rate_categories_state_node_xml" ] }, { "page": "create_rate_cg_param", "title": "Create a parameter called 'rate CG'", "topics": [ "create_param_rate_cg", "create_rate_cg_param" ] }, { "page": "create_rate_ct_param", "title": "Create a parameter called 'rate CT'", "topics": [ "create_param_rate_ct", "create_rate_ct_param" ] }, { "page": "create_rate_gt_param", "title": "Create a parameter called 'rate GT'", "topics": [ "create_param_rate_gt", "create_rate_gt_param" ] }, { "page": "create_rln_clock_branch_rate_model_xml", "title": "Internal function", "topics": [ "create_rln_clock_branch_rate_model_xml" ] }, { "page": "create_rln_clock_model", "title": "Create a relaxed log-normal clock model", "topics": [ "create_clock_model_rln", "create_rln_clock_model" ] }, { "page": "create_s_param", "title": "Create a parameter called s", "topics": [ "create_param_s", "create_s_param" ] }, { "page": "create_scale_param", "title": "Create a parameter called scale", "topics": [ "create_param_scale", "create_scale_param" ] }, { "page": "create_screenlog", "title": "Create a 'screenlog' object", "topics": [ "create_screenlog" ] }, { "page": "create_screenlog_xml", "title": "Creates the 'screenlog' section of the 'logger' section of a BEAST2 XML parameter file", "topics": [ "create_screenlog_xml" ] }, { "page": "create_sigma_param", "title": "Create a parameter called sigma", "topics": [ "create_param_sigma", "create_sigma_param" ] }, { "page": "create_site_model", "title": "General function to create a site model.", "topics": [ "create_site_model" ] }, { "page": "create_site_model_from_name", "title": "Create a site model from name", "topics": [ "create_site_model_from_name" ] }, { "page": "create_site_model_parameters_xml", "title": "Internal function to creates the XML text for the 'parameter's within the 'siteModel' section of a BEAST2 parameter file.", "topics": [ "create_site_model_parameters_xml" ] }, { "page": "create_site_model_xml", "title": "Internal function to creates the XML text for the 'siteModel' tag of a BEAST2 parameter file.", "topics": [ "create_site_model_xml" ] }, { "page": "create_site_models", "title": "Creates all supported site models which is a list of the types returned by 'create_gtr_site_model', 'create_hky_site_model', 'create_jc69_site_model' and 'create_tn93_site_model'", "topics": [ "create_site_models" ] }, { "page": "create_site_models_from_names", "title": "Create site models from their names", "topics": [ "create_site_models_from_names" ] }, { "page": "create_strict_clock_branch_rate_model_xml", "title": "Internal function.", "topics": [ "create_strict_clock_branch_rate_model_xml" ] }, { "page": "create_strict_clock_model", "title": "Create a strict clock model", "topics": [ "create_clock_model_strict", "create_strict_clock_model" ] }, { "page": "create_strict_clock_rate_scaler_operator_xml", "title": "Internal function", "topics": [ "create_strict_clock_rate_scaler_operator_xml" ] }, { "page": "create_subst_model_xml", "title": "Internal function to create the 'substModel' section", "topics": [ "create_subst_model_xml" ] }, { "page": "create_temp_screenlog_filename", "title": "Create a filename for a temporary `screenlog` file", "topics": [ "create_temp_screenlog_filename" ] }, { "page": "create_temp_tracelog_filename", "title": "Create a filename for a temporary `tracelog` file", "topics": [ "create_temp_tracelog_filename" ] }, { "page": "create_temp_treelog_filename", "title": "Create a filename for a temporary `treelog` file", "topics": [ "create_temp_treelog_filename" ] }, { "page": "create_test_inference_model", "title": "Create a testing inference model.", "topics": [ "create_test_inference_model" ] }, { "page": "create_test_mcmc", "title": "Create an MCMC configuration for testing.", "topics": [ "create_test_mcmc" ] }, { "page": "create_test_ns_inference_model", "title": "Create an inference model to be tested by Nested Sampling", "topics": [ "create_test_ns_inference_model" ] }, { "page": "create_test_ns_mcmc", "title": "Create an NS MCMC object for testing", "topics": [ "create_test_ns_mcmc" ] }, { "page": "create_test_screenlog", "title": "Create a 'screenlog' object, to be used in testing", "topics": [ "create_test_screenlog" ] }, { "page": "create_test_tracelog", "title": "Create a 'tracelog' object, as used for testing", "topics": [ "create_test_tracelog" ] }, { "page": "create_test_treelog", "title": "Create a 'treelog' object to be used in testing", "topics": [ "create_test_treelog" ] }, { "page": "create_tn93_site_model", "title": "Create a TN93 site model", "topics": [ "create_site_model_tn93", "create_tn93_site_model" ] }, { "page": "create_tn93_subst_model_xml", "title": "Converts a TN93 site model to XML, used in the 'substModel' section", "topics": [ "create_tn93_subst_model_xml" ] }, { "page": "create_tracelog", "title": "Create a 'tracelog' object", "topics": [ "create_tracelog" ] }, { "page": "create_tracelog_xml", "title": "Internal function", "topics": [ "create_tracelog_xml" ] }, { "page": "create_trait_set_string", "title": "Create a trait set string.", "topics": [ "create_trait_set_string" ] }, { "page": "create_tree_likelihood_distr_xml", "title": "Creates the XML text for the 'distribution' tag with the 'treeLikelihood' ID, of a BEAST2 parameter file.", "topics": [ "create_tree_likelihood_distr_xml" ] }, { "page": "create_tree_prior", "title": "Internal function to create a tree prior", "topics": [ "create_tree_prior" ] }, { "page": "create_tree_priors", "title": "Creates all supported tree priors, which is a list of the types returned by 'create_bd_tree_prior', 'create_cbs_tree_prior', 'create_ccp_tree_prior', 'create_cep_tree_prior' and 'create_yule_tree_prior'", "topics": [ "create_tree_priors" ] }, { "page": "create_treelog", "title": "Create a 'treelog' object", "topics": [ "create_treelog" ] }, { "page": "create_treelog_xml", "title": "Creates the XML text for the `logger` tag with ID `treelog`. This section has these elements: ``` # nolint indeed long # nolint indeed long ```", "topics": [ "create_treelog_xml" ] }, { "page": "create_ucld_mean_state_node_param_xml", "title": "Internal function", "topics": [ "create_ucld_mean_state_node_param_xml" ] }, { "page": "create_ucld_stdev_state_node_param_xml", "title": "Internal function", "topics": [ "create_ucld_stdev_state_node_param_xml" ] }, { "page": "create_uniform_distr", "title": "Create a uniform distribution", "topics": [ "create_distr_uniform", "create_uniform_distr" ] }, { "page": "create_xml_declaration", "title": "Create the XML declaration of the BEAST2 XML input file", "topics": [ "create_xml_declaration" ] }, { "page": "create_yule_tree_prior", "title": "Create a Yule tree prior", "topics": [ "create_tree_prior_yule", "create_yule_tree_prior" ] }, { "page": "default_parameters_doc", "title": "Documentation of parameters (for example, 'create_param'. This function does nothing. It is intended to inherit documentation from.", "topics": [ "default_parameters_doc" ] }, { "page": "default_params_doc", "title": "Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.", "topics": [ "default_params_doc" ] }, { "page": "distr_to_xml", "title": "Internal function", "topics": [ "distr_to_xml" ] }, { "page": "distr_to_xml_beta", "title": "Internal function", "topics": [ "distr_to_xml_beta" ] }, { "page": "distr_to_xml_exp", "title": "Internal function", "topics": [ "distr_to_xml_exp" ] }, { "page": "distr_to_xml_inv_gamma", "title": "Internal function", "topics": [ "distr_to_xml_inv_gamma" ] }, { "page": "distr_to_xml_laplace", "title": "Internal function", "topics": [ "distr_to_xml_laplace" ] }, { "page": "distr_to_xml_log_normal", "title": "Internal function", "topics": [ "distr_to_xml_log_normal" ] }, { "page": "distr_to_xml_normal", "title": "Internal function", "topics": [ "distr_to_xml_normal" ] }, { "page": "distr_to_xml_one_div_x", "title": "Internal function", "topics": [ "distr_to_xml_one_div_x" ] }, { "page": "distr_to_xml_poisson", "title": "Internal function", "topics": [ "distr_to_xml_poisson" ] }, { "page": "distr_to_xml_uniform", "title": "Internal function", "topics": [ "distr_to_xml_uniform" ] }, { "page": "extract_xml_loggers_from_lines", "title": "Extract everything between first loggers and last loggers line", "topics": [ "extract_xml_loggers_from_lines" ] }, { "page": "extract_xml_operators_from_lines", "title": "Extract everything between first operators and last operators line", "topics": [ "extract_xml_operators_from_lines" ] }, { "page": "extract_xml_section_from_lines", "title": "Get the lines of an XML section, including the section tags", "topics": [ "extract_xml_section_from_lines" ] }, { "page": "fasta_file_to_sequences", "title": "Convert a FASTA file to a table of sequences", "topics": [ "fasta_file_to_sequences" ] }, { "page": "find_clock_model", "title": "Finds a clock model with a certain ID", "topics": [ "find_clock_model" ] }, { "page": "find_first_regex_line", "title": "Find the first line that satisfies a regex", "topics": [ "find_first_regex_line" ] }, { "page": "find_first_xml_opening_tag_line", "title": "Find the line number of the first section's opening tag", "topics": [ "find_first_xml_opening_tag_line" ] }, { "page": "find_last_regex_line", "title": "Find the index of the last line that matches a regex", "topics": [ "find_last_regex_line" ] }, { "page": "find_last_xml_closing_tag_line", "title": "Find the highest line number of a section's closing tag", "topics": [ "find_last_xml_closing_tag_line" ] }, { "page": "freq_equilibrium_to_xml", "title": "Creates the 'freq_equilibrium' as XML", "topics": [ "freq_equilibrium_to_xml" ] }, { "page": "freq_param_to_xml", "title": "Internal function", "topics": [ "freq_param_to_xml" ] }, { "page": "gamma_distr_to_xml", "title": "Internal function", "topics": [ "gamma_distr_to_xml" ] }, { "page": "gamma_site_model_to_xml_prior_distr", "title": "Internal function.", "topics": [ "gamma_site_model_to_xml_prior_distr" ] }, { "page": "gamma_site_model_to_xml_state", "title": "Converts a gamma site model to XML, used in the 'state' section", "topics": [ "gamma_site_model_to_xml_state" ] }, { "page": "gamma_site_models_to_xml_prior_distr", "title": "Deprecated function", "topics": [ "gamma_site_models_to_xml_prior_distr" ] }, { "page": "get_alignment_id", "title": "Conclude the ID from a FASTA filename.", "topics": [ "get_alignment_id" ] }, { "page": "get_alignment_ids", "title": "Get the alignment IDs from one or more files.", "topics": [ "get_alignment_ids" ] }, { "page": "get_alignment_ids_from_fasta_filenames", "title": "Get the alignment ID from one or more FASTA filenames.", "topics": [ "get_alignment_ids_from_fasta_filenames" ] }, { "page": "get_beautier_folder", "title": "Get the path to the beautier temporary files folder", "topics": [ "get_beautier_folder" ] }, { "page": "get_beautier_path", "title": "Get the full path of a file in the 'inst/extdata' folder", "topics": [ "get_beautier_path" ] }, { "page": "get_beautier_paths", "title": "Get the full paths of files in the 'inst/extdata' folder", "topics": [ "get_beautier_paths" ] }, { "page": "get_beautier_tempfilename", "title": "Get a temporary filename", "topics": [ "get_beautier_tempfilename" ] }, { "page": "get_clock_model_name", "title": "Get the BEAUti name for a clock model", "topics": [ "get_clock_model_name" ] }, { "page": "get_clock_model_names", "title": "Get the clock model names", "topics": [ "get_clock_model_names" ] }, { "page": "get_clock_models_ids", "title": "Collect the IDs of the list of clock models", "topics": [ "get_clock_models_ids" ] }, { "page": "get_crown_age", "title": "Obtain the crown age of a phylogeny.", "topics": [ "get_crown_age" ] }, { "page": "get_default_beast_namespace", "title": "Get the default `namespace` element value of the `beast` XML tag.", "topics": [ "get_default_beast_namespace" ] }, { "page": "get_default_beast_namespace_v2_4", "title": "Get the default `namespace` element value of the `beast` XML tag for BEAST 2.4", "topics": [ "get_default_beast_namespace_v2_4" ] }, { "page": "get_default_beast_namespace_v2_6", "title": "Get the default `namespace` element value of the `beast` XML tag for BEAST 2.6", "topics": [ "get_default_beast_namespace_v2_6" ] }, { "page": "get_distr_n_params", "title": "Get the number of parameters a distribution uses", "topics": [ "get_distr_n_params" ] }, { "page": "get_distr_names", "title": "Get the distribution names", "topics": [ "get_distr_names" ] }, { "page": "get_fasta_filename", "title": "Get the path of a FASTA file used in testing", "topics": [ "get_fasta_filename" ] }, { "page": "get_file_base_sans_ext", "title": "Get the base of the filename base without extension", "topics": [ "get_file_base_sans_ext" ] }, { "page": "get_freq_equilibrium_names", "title": "Returns valid values for the 'freq_equilibrium' argument", "topics": [ "get_freq_equilibrium_names" ] }, { "page": "get_gamma_site_model_n_distrs", "title": "Get the number of distributions in a gamma site model", "topics": [ "get_gamma_site_model_n_distrs" ] }, { "page": "get_gamma_site_model_n_params", "title": "Get the number of distributions a site model has", "topics": [ "get_gamma_site_model_n_params" ] }, { "page": "get_has_non_strict_clock_model", "title": "Determines if there is at least one non-strict clock model in the list of one or more clock models", "topics": [ "get_has_non_strict_clock_model" ] }, { "page": "get_inference_model_filenames", "title": "Get the filenames stored in an inference model.", "topics": [ "get_inference_model_filenames" ] }, { "page": "get_log_modes", "title": "Get the possible log modes", "topics": [ "get_log_modes" ] }, { "page": "get_log_sorts", "title": "Get the possible log sorts", "topics": [ "get_log_sorts" ] }, { "page": "get_mcmc_filenames", "title": "Get the filenames stored in an MCMC.", "topics": [ "get_mcmc_filenames" ] }, { "page": "get_n_taxa", "title": "Extract the number of taxa from a file", "topics": [ "get_n_taxa" ] }, { "page": "get_operator_id_pre", "title": "Get the prefix of operator IDs", "topics": [ "get_operator_id_pre" ] }, { "page": "get_param_names", "title": "Get the parameter names", "topics": [ "get_param_names" ] }, { "page": "get_remove_dir_fun", "title": "Get a function that, from a filename, returns the part without the directory.", "topics": [ "get_remove_dir_fun" ] }, { "page": "get_remove_hex_fun", "title": "Get a function that removes the hex string from filenames.", "topics": [ "get_remove_hex_fun" ] }, { "page": "get_replace_dir_fun", "title": "Get a function to replace the directory of a filename", "topics": [ "get_replace_dir_fun" ] }, { "page": "get_site_model_n_distrs", "title": "Get the number of distributions a site model has", "topics": [ "get_site_model_n_distrs" ] }, { "page": "get_site_model_n_params", "title": "Get the number of distributions a site model has", "topics": [ "get_site_model_n_params" ] }, { "page": "get_site_model_names", "title": "Get the site models' names", "topics": [ "get_site_model_names" ] }, { "page": "get_site_models_n_distrs", "title": "Get the number of distributions a site model has", "topics": [ "get_site_models_n_distrs" ] }, { "page": "get_site_models_n_params", "title": "Get the number of distributions one or more site models have", "topics": [ "get_site_models_n_params" ] }, { "page": "get_taxa_names", "title": "Extract the names of taxa from a file", "topics": [ "get_taxa_names" ] }, { "page": "get_tree_prior_n_distrs", "title": "Get the number of distributions a tree prior has", "topics": [ "get_tree_prior_n_distrs" ] }, { "page": "get_tree_prior_n_params", "title": "Get the number of parameters a tree prior has", "topics": [ "get_tree_prior_n_params" ] }, { "page": "get_tree_prior_names", "title": "Get the tree prior names", "topics": [ "get_tree_prior_names" ] }, { "page": "get_tree_priors_n_distrs", "title": "Get the number of distributions a tree prior has", "topics": [ "get_tree_priors_n_distrs" ] }, { "page": "get_tree_priors_n_params", "title": "Get the number of parameters a list of tree priors has", "topics": [ "get_tree_priors_n_params" ] }, { "page": "get_xml_closing_tag", "title": "Get the XML closing tag", "topics": [ "get_xml_closing_tag" ] }, { "page": "get_xml_opening_tag", "title": "Get the XML opening tag", "topics": [ "get_xml_opening_tag" ] }, { "page": "gtr_site_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "gtr_site_model_to_xml_prior_distr" ] }, { "page": "gtr_site_model_to_xml_state", "title": "Converts a site model to XML, used in the 'state' section", "topics": [ "gtr_site_model_to_xml_state" ] }, { "page": "has_mrca_prior", "title": "Determines if the inference model has an MRCA prior.", "topics": [ "has_mrca_prior" ] }, { "page": "has_mrca_prior_with_distr", "title": "See if the inference model has one MRCA prior with a distribution", "topics": [ "has_mrca_prior_with_distr" ] }, { "page": "has_rln_clock_model", "title": "Determine if the 'inference_model' uses a relaxed log-normal clock model.", "topics": [ "has_rln_clock_model" ] }, { "page": "has_strict_clock_model", "title": "Determine if the 'inference_model' uses a strict clock model.", "topics": [ "has_strict_clock_model" ] }, { "page": "has_tip_dating", "title": "Determine if the 'inference_model' uses tip dating.", "topics": [ "has_tip_dating" ] }, { "page": "has_xml_closing_tag", "title": "Is an XML closing tag with the value of 'section' present among the lines of the text?", "topics": [ "has_xml_closing_tag" ] }, { "page": "has_xml_opening_tag", "title": "Is an XML opening tag with value 'section' present among the lines of the text?", "topics": [ "has_xml_opening_tag" ] }, { "page": "has_xml_short_closing_tag", "title": "Is an XML closing tag with short closing text in one of the lines of the text?", "topics": [ "has_xml_short_closing_tag" ] }, { "page": "hky_site_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "hky_site_model_to_xml_prior_distr" ] }, { "page": "hky_site_model_to_xml_state", "title": "Converts a site model to XML, used in the 'state' section", "topics": [ "hky_site_model_to_xml_state" ] }, { "page": "indent", "title": "Indent text for a certain number of spaces. If the text is only whitespace, leave it as such", "topics": [ "indent" ] }, { "page": "init_bd_tree_prior", "title": "Initializes a Birth-Death tree prior", "topics": [ "init_bd_tree_prior" ] }, { "page": "init_beta_distr", "title": "Initializes a beta distribution", "topics": [ "init_beta_distr" ] }, { "page": "init_ccp_tree_prior", "title": "Initializes a Coalescent Constant Population tree prior", "topics": [ "init_ccp_tree_prior" ] }, { "page": "init_cep_tree_prior", "title": "Initializes a Coalescent Exponential Population tree prior", "topics": [ "init_cep_tree_prior" ] }, { "page": "init_clock_models", "title": "Initializes all clock models", "topics": [ "init_clock_models" ] }, { "page": "init_distr", "title": "Initializes a distribution", "topics": [ "init_distr" ] }, { "page": "init_exp_distr", "title": "Initializes an exponential distribution", "topics": [ "init_exp_distr" ] }, { "page": "init_gamma_distr", "title": "Initializes a gamma distribution", "topics": [ "init_gamma_distr" ] }, { "page": "init_gamma_site_model", "title": "Initializes a gamma site model", "topics": [ "init_gamma_site_model" ] }, { "page": "init_gtr_site_model", "title": "Initializes a GTR site model", "topics": [ "init_gtr_site_model" ] }, { "page": "init_hky_site_model", "title": "Initializes an HKY site model", "topics": [ "init_hky_site_model" ] }, { "page": "init_inference_model", "title": "Initialize an inference model", "topics": [ "init_inference_model" ] }, { "page": "init_inv_gamma_distr", "title": "Initializes an inverse gamma distribution", "topics": [ "init_inv_gamma_distr" ] }, { "page": "init_jc69_site_model", "title": "Initializes a JC69 site model", "topics": [ "init_jc69_site_model" ] }, { "page": "init_laplace_distr", "title": "Initializes an Laplace distribution", "topics": [ "init_laplace_distr" ] }, { "page": "init_log_normal_distr", "title": "Initializes an log-normal distribution", "topics": [ "init_log_normal_distr" ] }, { "page": "init_mrca_prior", "title": "Initialize the MRCA prior.", "topics": [ "init_mrca_prior" ] }, { "page": "init_mrca_priors", "title": "Initializes all MRCA priors", "topics": [ "init_mrca_priors" ] }, { "page": "init_normal_distr", "title": "Initializes an normal distribution", "topics": [ "init_normal_distr" ] }, { "page": "init_one_div_x_distr", "title": "Initializes an one-divided-by-x distribution", "topics": [ "init_one_div_x_distr" ] }, { "page": "init_param", "title": "Initializes a parameter", "topics": [ "init_param" ] }, { "page": "init_poisson_distr", "title": "Initializes an Poisson distribution", "topics": [ "init_poisson_distr" ] }, { "page": "init_rln_clock_model", "title": "Initializes a Relaxed Log-Normal clock model", "topics": [ "init_rln_clock_model" ] }, { "page": "init_site_models", "title": "Initializes all site models", "topics": [ "init_site_models" ] }, { "page": "init_strict_clock_model", "title": "Initializes a strict clock model", "topics": [ "init_strict_clock_model" ] }, { "page": "init_tn93_site_model", "title": "Initializes a TN93 site model", "topics": [ "init_tn93_site_model" ] }, { "page": "init_tree_priors", "title": "Initializes all tree priors", "topics": [ "init_tree_priors" ] }, { "page": "init_uniform_distr", "title": "Initializes a uniform distribution", "topics": [ "init_uniform_distr" ] }, { "page": "init_yule_tree_prior", "title": "Initializes a Yule tree prior", "topics": [ "init_yule_tree_prior" ] }, { "page": "interspace", "title": "Puts spaces in between the lines", "topics": [ "interspace" ] }, { "page": "is_alpha_param", "title": "Determine if the object is a valid alpha parameter", "topics": [ "is_alpha_param" ] }, { "page": "is_b_pop_sizes_param", "title": "Determine if the object is a valid b_pop_sizes parameter", "topics": [ "is_b_pop_sizes_param" ] }, { "page": "is_bd_tree_prior", "title": "Determine if the object is a valid Birth Death tree prior", "topics": [ "is_bd_tree_prior" ] }, { "page": "is_beast2_input_file_with_tipdates", "title": "Determine if the file is a BEAST2 input file that has tip dating", "topics": [ "is_beast2_input_file_with_tipdates" ] }, { "page": "is_beauti_options", "title": "Determine if the object is a valid 'beauti_options'", "topics": [ "is_beauti_options" ] }, { "page": "is_beta_distr", "title": "Determine if the object is a valid beta distribution, as created by 'create_beta_distr'", "topics": [ "is_beta_distr" ] }, { "page": "is_beta_param", "title": "Determine if the object is a valid beta parameter", "topics": [ "is_beta_param" ] }, { "page": "is_cbs_tree_prior", "title": "Determine if the object is a valid constant coalescent Bayesian skyline prior", "topics": [ "is_cbs_tree_prior" ] }, { "page": "is_ccp_tree_prior", "title": "Determine if the object is a valid constant coalescence population tree prior", "topics": [ "is_ccp_tree_prior" ] }, { "page": "is_cep_tree_prior", "title": "Determine if the object is a valid coalescent exponential population tree prior", "topics": [ "is_cep_tree_prior" ] }, { "page": "is_clock_model", "title": "Determine if the object is a valid clock_model", "topics": [ "is_clock_model" ] }, { "page": "is_clock_model_name", "title": "Determines if the name is a valid clock model name", "topics": [ "is_clock_model_name" ] }, { "page": "is_clock_rate_param", "title": "Determine if the object is a valid clock_rate parameter", "topics": [ "is_clock_rate_param" ] }, { "page": "is_default_mcmc", "title": "Determine if the MCMC is a default MCMC", "topics": [ "is_default_mcmc" ] }, { "page": "is_distr", "title": "Determine if the object is a valid distribution", "topics": [ "is_distr" ] }, { "page": "is_distr_name", "title": "Determines if the name is a valid distribution name", "topics": [ "is_distr_name" ] }, { "page": "is_exp_distr", "title": "Determine if the object is a valid exponential distribution as created by 'create_exp_distr'", "topics": [ "is_exp_distr" ] }, { "page": "is_freq_equilibrium_name", "title": "Checks if 'name' is a valid 'freq_equilibrium' argument value", "topics": [ "is_freq_equilibrium_name" ] }, { "page": "is_freq_param", "title": "Determine if the object is a valid freq parameter", "topics": [ "is_freq_param" ] }, { "page": "is_gamma_distr", "title": "Determine if the object is a valid gamma distribution, as created by 'create_gamma_distr'", "topics": [ "is_gamma_distr" ] }, { "page": "is_gamma_site_model", "title": "Is object x a gamma site model?", "topics": [ "is_gamma_site_model" ] }, { "page": "is_gtr_site_model", "title": "Determine if the object is a valid GTR site model, as created by 'create_gtr_site_model'", "topics": [ "is_gtr_site_model" ] }, { "page": "is_hky_site_model", "title": "Determine if the object is a valid HKY site model, as created by 'create_hky_site_model'", "topics": [ "is_hky_site_model" ] }, { "page": "is_id", "title": "Determine if the object is a valid ID", "topics": [ "is_id" ] }, { "page": "is_in_patterns", "title": "Is there at least one regular expression having a match with the line?", "topics": [ "is_in_patterns" ] }, { "page": "is_inference_model", "title": "Determine if the input is an inference model", "topics": [ "is_inference_model" ] }, { "page": "is_init_bd_tree_prior", "title": "Determine if x is an initialized Birth-Death tree_prior object", "topics": [ "is_init_bd_tree_prior" ] }, { "page": "is_init_beta_distr", "title": "Determine if x is an initialized beta distribution object as created by 'create_beta_distr'", "topics": [ "is_init_beta_distr" ] }, { "page": "is_init_cbs_tree_prior", "title": "Determine if x is an initialized Coalescent Bayesian Skyline tree_prior object", "topics": [ "is_init_cbs_tree_prior" ] }, { "page": "is_init_ccp_tree_prior", "title": "Determine if x is an initialized Coalescent Constant Population tree_prior object", "topics": [ "is_init_ccp_tree_prior" ] }, { "page": "is_init_cep_tree_prior", "title": "Determine if x is an initialized Coalescent Exponential Population tree_prior object", "topics": [ "is_init_cep_tree_prior" ] }, { "page": "is_init_clock_model", "title": "Determine if x is an initialized clock_model object, as created by 'create_clock_model'", "topics": [ "is_init_clock_model" ] }, { "page": "is_init_distr", "title": "Determine if x is an initialized distribution object as created by 'create_distr'", "topics": [ "is_init_distr" ] }, { "page": "is_init_exp_distr", "title": "Determine if x is an initialized exponential distribution object as created by 'create_exp_distr'", "topics": [ "is_init_exp_distr" ] }, { "page": "is_init_gamma_distr", "title": "Determine if x is an initialized gamma distribution object", "topics": [ "is_init_gamma_distr" ] }, { "page": "is_init_gamma_site_model", "title": "Determine if x is an initialized gamma site model, as created by 'create_gamma_site_model'", "topics": [ "is_init_gamma_site_model" ] }, { "page": "is_init_gtr_site_model", "title": "Determine if x is an initialized GTR site model as created by 'create_gtr_site_model'", "topics": [ "is_init_gtr_site_model" ] }, { "page": "is_init_hky_site_model", "title": "Determine if x is an initialized HKY site model as created by 'create_hky_site_model'", "topics": [ "is_init_hky_site_model" ] }, { "page": "is_init_inv_gamma_distr", "title": "Determine if x is an initialized inverse-gamma distribution as created by 'create_inv_gamma_distr'", "topics": [ "is_init_inv_gamma_distr" ] }, { "page": "is_init_jc69_site_model", "title": "Determine if x is an initialized JC69 site model as created by 'create_jc69_site_model'", "topics": [ "is_init_jc69_site_model" ] }, { "page": "is_init_laplace_distr", "title": "Determine if x is an initialized Laplace distribution as created by 'create_laplace_distr'", "topics": [ "is_init_laplace_distr" ] }, { "page": "is_init_log_normal_distr", "title": "Determine if x is an initialized log_normal distribution object as created by 'create_log_normal_distr'", "topics": [ "is_init_log_normal_distr" ] }, { "page": "is_init_mrca_prior", "title": "Determine if x is an initialized MRCA prior", "topics": [ "is_init_mrca_prior" ] }, { "page": "is_init_normal_distr", "title": "Determine if x is an initialized normal distribution object as created by 'create_normal_distr'", "topics": [ "is_init_normal_distr" ] }, { "page": "is_init_one_div_x_distr", "title": "Determine if x is an initialized one_div_x distribution object as created by 'create_one_div_x_distr'", "topics": [ "is_init_one_div_x_distr" ] }, { "page": "is_init_param", "title": "Determine if x is an initialized parameter, as created by create_param", "topics": [ "is_init_param" ] }, { "page": "is_init_poisson_distr", "title": "Determine if x is an initialized Poisson distribution object as created by 'create_poisson_distr'", "topics": [ "is_init_poisson_distr" ] }, { "page": "is_init_rln_clock_model", "title": "Determine if x is an initialized relaxed log-normal clock_model object", "topics": [ "is_init_rln_clock_model" ] }, { "page": "is_init_site_model", "title": "Determine if x is an initialized site model, as created by 'create_site_model'", "topics": [ "is_init_site_model" ] }, { "page": "is_init_strict_clock_model", "title": "Determine if x is an initialized strict clock_model object", "topics": [ "is_init_strict_clock_model" ] }, { "page": "is_init_tn93_site_model", "title": "Determine if x is an initialized tn93 site model as created by 'create_tn93_site_model'", "topics": [ "is_init_tn93_site_model" ] }, { "page": "is_init_tree_prior", "title": "Determine if x is an initialized tree_prior objects", "topics": [ "is_init_tree_prior" ] }, { "page": "is_init_uniform_distr", "title": "Determine if x is an initialized uniform distribution object as created by 'create_uniform_distr'", "topics": [ "is_init_uniform_distr" ] }, { "page": "is_init_yule_tree_prior", "title": "Determine if x is an initialized Yule tree_prior object", "topics": [ "is_init_yule_tree_prior" ] }, { "page": "is_inv_gamma_distr", "title": "Determine if the object is a valid inverse-gamma distribution as created by 'create_inv_gamma_distr'", "topics": [ "is_inv_gamma_distr" ] }, { "page": "is_jc69_site_model", "title": "Determine if the object is a valid JC69 site model", "topics": [ "is_jc69_site_model" ] }, { "page": "is_kappa_1_param", "title": "Determine if the object is a valid kappa 1 parameter", "topics": [ "is_kappa_1_param" ] }, { "page": "is_kappa_2_param", "title": "Determine if the object is a valid kappa 2 parameter", "topics": [ "is_kappa_2_param" ] }, { "page": "is_kappa_param", "title": "Determine if the object is a valid kappa parameter", "topics": [ "is_kappa_param" ] }, { "page": "is_lambda_param", "title": "Determine if the object is a valid lambda parameter", "topics": [ "is_lambda_param" ] }, { "page": "is_laplace_distr", "title": "Determine if the object is a valid Laplace distribution, as created by 'create_laplace_distr'", "topics": [ "is_laplace_distr" ] }, { "page": "is_log_normal_distr", "title": "Determine if the object is a valid log-normal distribution, as created by 'create_log_normal_distr'", "topics": [ "is_log_normal_distr" ] }, { "page": "is_m_param", "title": "Determine if the object is a valid m parameter", "topics": [ "is_m_param" ] }, { "page": "is_mcmc", "title": "Determine if the object is a valid MCMC", "topics": [ "is_mcmc" ] }, { "page": "is_mcmc_nested_sampling", "title": "Determine if the object is a valid Nested-Sampling MCMC, as used in [1]", "topics": [ "is_mcmc_nested_sampling", "is_nested_sampling_mcmc" ] }, { "page": "is_mean_param", "title": "Determine if the object is a valid mean parameter", "topics": [ "is_mean_param" ] }, { "page": "is_mrca_align_id_in_fasta", "title": "Determine if an MRCA prior's alignment IDs is present in the FASTA file", "topics": [ "is_mrca_align_id_in_fasta" ] }, { "page": "is_mrca_align_ids_in_fastas", "title": "Determine if an MRCA prior's alignment IDs are present in the FASTA files", "topics": [ "is_mrca_align_ids_in_fastas" ] }, { "page": "is_mrca_prior", "title": "Determine of the object is an empty ('NA') or valid MRCA prior.", "topics": [ "is_mrca_prior" ] }, { "page": "is_mrca_prior_with_distr", "title": "See if x is one MRCA prior with a distribution", "topics": [ "is_mrca_prior_with_distr" ] }, { "page": "is_mu_param", "title": "Determine if the object is a valid mu parameter", "topics": [ "is_mu_param" ] }, { "page": "is_normal_distr", "title": "Determine if the object is a valid normal distribution as created by 'create_normal_distr'", "topics": [ "is_normal_distr" ] }, { "page": "is_on_appveyor", "title": "Determines if the environment is AppVeyor", "topics": [ "is_on_appveyor" ] }, { "page": "is_on_ci", "title": "Determines if the environment is a continuous integration service", "topics": [ "is_on_ci" ] }, { "page": "is_on_github_actions", "title": "Determines if the environment is GitHub Actions", "topics": [ "is_on_github_actions" ] }, { "page": "is_on_travis", "title": "Determines if the environment is Travis CI", "topics": [ "is_on_travis" ] }, { "page": "is_one_bool", "title": "Check if the argument is one boolean", "topics": [ "is_one_bool" ] }, { "page": "is_one_div_x_distr", "title": "Determine if the object is a valid 1/x distribution, as created by 'create_one_div_x_distr'", "topics": [ "is_one_div_x_distr" ] }, { "page": "is_one_double", "title": "Determines if the argument is a double", "topics": [ "is_one_double" ] }, { "page": "is_one_empty_string", "title": "Determine if an object is one empty string", "topics": [ "is_one_empty_string" ] }, { "page": "is_one_int", "title": "Determines if the argument is a whole number", "topics": [ "is_one_int" ] }, { "page": "is_one_na", "title": "Determines if x is one NA", "topics": [ "is_one_na" ] }, { "page": "is_one_string", "title": "Determines if the argument is one string", "topics": [ "is_one_string" ] }, { "page": "is_one_string_that_is_a_number", "title": "General function to create a distribution.", "topics": [ "is_one_string_that_is_a_number" ] }, { "page": "is_param", "title": "Determine if the object is a valid parameter", "topics": [ "is_param" ] }, { "page": "is_param_name", "title": "Determines if the name is a valid parameter name", "topics": [ "is_param_name" ] }, { "page": "is_phylo", "title": "Checks if the input is a phylogeny", "topics": [ "is_phylo" ] }, { "page": "is_poisson_distr", "title": "Determine if the object is a valid Poisson distribution as created by 'create_poisson_distr'", "topics": [ "is_poisson_distr" ] }, { "page": "is_rate_ac_param", "title": "Determine if the object is a valid 'rate AC' parameter", "topics": [ "is_rate_ac_param" ] }, { "page": "is_rate_ag_param", "title": "Determine if the object is a valid 'rate AG' parameter", "topics": [ "is_rate_ag_param" ] }, { "page": "is_rate_at_param", "title": "Determine if the object is a valid 'rate AT' parameter", "topics": [ "is_rate_at_param" ] }, { "page": "is_rate_cg_param", "title": "Determine if the object is a valid 'rate CG' parameter", "topics": [ "is_rate_cg_param" ] }, { "page": "is_rate_ct_param", "title": "Determine if the object is a valid 'rate CT' parameter", "topics": [ "is_rate_ct_param" ] }, { "page": "is_rate_gt_param", "title": "Determine if the object is a valid 'rate GT' parameter", "topics": [ "is_rate_gt_param" ] }, { "page": "is_rln_clock_model", "title": "Determine if the object is a valid relaxed log normal clock model", "topics": [ "is_rln_clock_model" ] }, { "page": "is_s_param", "title": "Determine if the object is a valid s parameter", "topics": [ "is_s_param" ] }, { "page": "is_scale_param", "title": "Determine if the object is a valid scale parameter", "topics": [ "is_scale_param" ] }, { "page": "is_sigma_param", "title": "Determine if the object is a valid sigma parameter", "topics": [ "is_sigma_param" ] }, { "page": "is_site_model", "title": "Determine if the object is a valid site_model", "topics": [ "is_site_model" ] }, { "page": "is_site_model_name", "title": "Determines if the name is a valid site_model name", "topics": [ "is_site_model_name" ] }, { "page": "is_strict_clock_model", "title": "Determine if the object is a valid strict clock model, as returned by 'create_strict_clock_model'", "topics": [ "is_strict_clock_model" ] }, { "page": "is_tn93_site_model", "title": "Determine if the object is a valid TN93 site model,", "topics": [ "is_tn93_site_model" ] }, { "page": "is_tree_prior", "title": "Determine if an object is a valid tree prior", "topics": [ "is_tree_prior" ] }, { "page": "is_tree_prior_name", "title": "Determines if the name is a valid tree prior name", "topics": [ "is_tree_prior_name" ] }, { "page": "is_uniform_distr", "title": "Determine if the object is a valid uniform distribution as created by 'create_uniform_distr'", "topics": [ "is_uniform_distr" ] }, { "page": "is_xml", "title": "Checks if the text is a valid XML node, that is, it has a opening and matching closing tag", "topics": [ "is_xml" ] }, { "page": "is_yule_tree_prior", "title": "Determine if the object is a valid Yule tree prior,", "topics": [ "is_yule_tree_prior" ] }, { "page": "jc69_site_model_to_xml_state", "title": "Converts a site model to XML, used in the 'state' section", "topics": [ "jc69_site_model_to_xml_state" ] }, { "page": "kappa_param_to_xml", "title": "Internal function", "topics": [ "kappa_param_to_xml" ] }, { "page": "m_param_to_xml", "title": "Internal function", "topics": [ "m_param_to_xml" ] }, { "page": "mcmc_to_xml_run", "title": "Converts an MCMC object to the run section's XML", "topics": [ "mcmc_to_xml_run" ] }, { "page": "mcmc_to_xml_run_default", "title": "Converts an MCMC object to the run section's XML for a default MCMC", "topics": [ "mcmc_to_xml_run_default" ] }, { "page": "mcmc_to_xml_run_nested_sampling", "title": "Converts an MCMC object to the run section's XML for a Nested-Sampling MCMC", "topics": [ "mcmc_to_xml_run_nested_sampling" ] }, { "page": "mrca_prior_to_xml_prior_distr", "title": "Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.", "topics": [ "mrca_prior_to_xml_prior_distr" ] }, { "page": "mrca_prior_to_xml_state", "title": "Internal function to create the XML of an MRCA prior, as used in the 'state' section", "topics": [ "mrca_prior_to_xml_state" ] }, { "page": "mrca_prior_to_xml_taxonset", "title": "Creates the 'taxonset' section in the prior section of the distribution section of a BEAST2 XML parameter file.", "topics": [ "mrca_prior_to_xml_taxonset" ] }, { "page": "mrca_prior_to_xml_tracelog", "title": "Internal function", "topics": [ "mrca_prior_to_xml_tracelog" ] }, { "page": "mrca_priors_to_xml_prior_distr", "title": "Creates the the 'distribution''s prior section (which is part of a posterior distribution section) of a BEAST2 XML parameter file.", "topics": [ "mrca_priors_to_xml_prior_distr" ] }, { "page": "needs_trait_set_str", "title": "Is it needed to add the tip dates as a string to the BEAST2 XML input file?", "topics": [ "needs_trait_set_str" ] }, { "page": "no_taxa_to_xml_tree", "title": "Internal function", "topics": [ "no_taxa_to_xml_tree" ] }, { "page": "obj_type_friendly", "title": "Return English-friendly type", "topics": [ "obj_type_friendly" ] }, { "page": "parameter_to_xml", "title": "Internal function", "topics": [ "parameter_to_xml" ] }, { "page": "parameter_to_xml_kappa_1", "title": "Internal function", "topics": [ "parameter_to_xml_kappa_1" ] }, { "page": "parameter_to_xml_kappa_2", "title": "Internal function", "topics": [ "parameter_to_xml_kappa_2" ] }, { "page": "parameter_to_xml_lambda", "title": "Internal function", "topics": [ "parameter_to_xml_lambda" ] }, { "page": "parameter_to_xml_mean", "title": "Internal function", "topics": [ "parameter_to_xml_mean" ] }, { "page": "parameter_to_xml_mu", "title": "Internal function", "topics": [ "parameter_to_xml_mu" ] }, { "page": "parameter_to_xml_rate_ac", "title": "Internal function", "topics": [ "parameter_to_xml_rate_ac" ] }, { "page": "parameter_to_xml_rate_ag", "title": "Internal function", "topics": [ "parameter_to_xml_rate_ag" ] }, { "page": "parameter_to_xml_rate_at", "title": "Internal function", "topics": [ "parameter_to_xml_rate_at" ] }, { "page": "parameter_to_xml_rate_cg", "title": "Internal function", "topics": [ "parameter_to_xml_rate_cg" ] }, { "page": "parameter_to_xml_rate_ct", "title": "Internal function", "topics": [ "parameter_to_xml_rate_ct" ] }, { "page": "parameter_to_xml_rate_gt", "title": "Internal function", "topics": [ "parameter_to_xml_rate_gt" ] }, { "page": "parameter_to_xml_scale", "title": "Internal function", "topics": [ "parameter_to_xml_scale" ] }, { "page": "parameter_to_xml_sigma", "title": "Internal function", "topics": [ "parameter_to_xml_sigma" ] }, { "page": "read_tipdates_file", "title": "Read a tip dates file", "topics": [ "read_tipdates_file" ] }, { "page": "remove_beautier_folder", "title": "Check there are no files in the default beautier folder", "topics": [ "remove_beautier_folder" ] }, { "page": "remove_empty_lines", "title": "Remove all lines that are only whitespace", "topics": [ "remove_empty_lines" ] }, { "page": "remove_multiline", "title": "Remove consecutive lines", "topics": [ "remove_multiline" ] }, { "page": "rename_inference_model_filenames", "title": "Rename the filenames in an inference model", "topics": [ "rename_inference_model_filenames" ] }, { "page": "rename_mcmc_filenames", "title": "Rename the filenames within an MCMC", "topics": [ "rename_mcmc_filenames" ] }, { "page": "rln_clock_model_to_xml_mean_rate_prior", "title": "Internal function", "topics": [ "rln_clock_model_to_xml_mean_rate_prior" ] }, { "page": "rln_clock_model_to_xml_operators", "title": "Internal function", "topics": [ "rln_clock_model_to_xml_operators" ] }, { "page": "rln_clock_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "rln_clock_model_to_xml_prior_distr" ] }, { "page": "rln_clock_model_to_xml_state", "title": "Internal function", "topics": [ "rln_clock_model_to_xml_state" ] }, { "page": "rln_clock_model_to_xml_tracelog", "title": "Internal function", "topics": [ "rln_clock_model_to_xml_tracelog" ] }, { "page": "rnd_phylo_to_xml_init", "title": "Creates the XML of a random phylogeny, as used in the 'init' section", "topics": [ "rnd_phylo_to_xml_init" ] }, { "page": "s_parameter_to_xml", "title": "Internal function", "topics": [ "s_parameter_to_xml" ] }, { "page": "site_model_to_xml_operators", "title": "Converts a site model to XML, used in the 'operators' section", "topics": [ "site_model_to_xml_operators" ] }, { "page": "site_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "site_model_to_xml_prior_distr" ] }, { "page": "site_model_to_xml_state", "title": "Internal function to convert a site model to XML, used in the `state` section", "topics": [ "site_model_to_xml_state" ] }, { "page": "site_model_to_xml_tracelog", "title": "Creates the site model's XML for the tracelog section", "topics": [ "site_model_to_xml_tracelog" ] }, { "page": "site_models_to_xml_operators", "title": "Write the XML 'operators' section from the site models.", "topics": [ "site_models_to_xml_operators" ] }, { "page": "site_models_to_xml_prior_distr", "title": "Represent the site models as XML", "topics": [ "site_models_to_xml_prior_distr" ] }, { "page": "site_models_to_xml_tracelog", "title": "Creates the site models' XML for the tracelog section", "topics": [ "site_models_to_xml_tracelog" ] }, { "page": "stop_input_type", "title": "Stops on the input type.", "topics": [ "stop_input_type" ] }, { "page": "strict_clock_model_to_xml_operators", "title": "Internal function", "topics": [ "strict_clock_model_to_xml_operators" ] }, { "page": "strict_clock_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "strict_clock_model_to_xml_prior_distr" ] }, { "page": "strict_clock_model_to_xml_state", "title": "Internal function", "topics": [ "strict_clock_model_to_xml_state" ] }, { "page": "strict_clock_model_to_xml_tracelog", "title": "Internal function", "topics": [ "strict_clock_model_to_xml_tracelog" ] }, { "page": "taxa_to_xml_tree", "title": "Internal function", "topics": [ "taxa_to_xml_tree" ] }, { "page": "tipdate_taxa_to_xml_trait", "title": "Internal function", "topics": [ "tipdate_taxa_to_xml_trait" ] }, { "page": "tipdate_taxa_to_xml_tree", "title": "Internal function", "topics": [ "tipdate_taxa_to_xml_tree" ] }, { "page": "tn93_site_model_to_xml_prior_distr", "title": "Internal function", "topics": [ "tn93_site_model_to_xml_prior_distr" ] }, { "page": "tn93_site_model_to_xml_state", "title": "Converts a site model to XML, used in the 'state' section", "topics": [ "tn93_site_model_to_xml_state" ] }, { "page": "tree_model_to_tracelog_xml", "title": "Internal function", "topics": [ "tree_model_to_tracelog_xml" ] }, { "page": "tree_prior_to_xml_operators", "title": "Internal function", "topics": [ "tree_prior_to_xml_operators" ] }, { "page": "tree_prior_to_xml_prior_distr", "title": "Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.", "topics": [ "tree_prior_to_xml_prior_distr" ] }, { "page": "tree_prior_to_xml_state", "title": "Creates the XML of a tree prior, as used in the 'state' section", "topics": [ "tree_prior_to_xml_state" ] }, { "page": "tree_prior_to_xml_tracelog", "title": "Creates the tree prior's XML for the tracelog section", "topics": [ "tree_prior_to_xml_tracelog" ] }, { "page": "tree_priors_to_xml_prior_distr", "title": "Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.", "topics": [ "tree_priors_to_xml_prior_distr" ] }, { "page": "tree_priors_to_xml_tracelog", "title": "Creates the tree priors' XML for the tracelog section", "topics": [ "tree_priors_to_xml_tracelog" ] }, { "page": "unindent", "title": "Unindents text", "topics": [ "unindent" ] }, { "page": "yule_tree_prior_to_xml_operators", "title": "Internal function", "topics": [ "yule_tree_prior_to_xml_operators" ] }, { "page": "yule_tree_prior_to_xml_prior_distr", "title": "Creates the 'prior' section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Yule tree prior", "topics": [ "yule_tree_prior_to_xml_prior_distr" ] } ], "_readme": "https://github.com/ropensci/beautier/raw/main/README.md", "_rundeps": [ "ade4", "ape", "cli", "digest", "glue", "lattice", "lifecycle", "magrittr", "MASS", "nlme", "pixmap", "purrr", "rappdirs", "Rcpp", "RcppArmadillo", "rlang", "segmented", "seqinr", "sp", "stringi", "stringr", "vctrs" ], "_vignettes": [ { "source": "demo.Rmd", "filename": "demo.html", "title": "beautier demo", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Demonstration", "Cleanup" ], "created": "2016-03-11 14:29:40", "modified": "2022-06-01 09:36:07", "commits": 30 }, { "source": "examples.Rmd", "filename": "examples.html", "title": "Examples", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Getting started", "Example #1: all default", "Example #2: JC69 site model", "Example #3: Relaxed clock log normal", "Example #4: Birth-Death tree prior", "Example #5: Yule tree prior with a normally distributed birth rate", "Example #6: HKY site model with a non-zero proportion of invariants", "Example #7: Strict clock with a known clock rate", "Example #8: Use MRCA prior", "Example #9: Use MRCA prior to specify a close-to-fixed crown age", "Cleanup" ], "created": "2017-11-22 11:10:46", "modified": "2022-06-01 09:36:07", "commits": 34 }, { "source": "inference_models.Rmd", "filename": "inference_models.html", "title": "Inference Models", "author": "Richèl J.C. 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Bilderbeek ", "Description": "'BEAST2' () is a widely used\nBayesian phylogenetic tool, that uses DNA/RNA/protein data and\nmany model priors to create a posterior of jointly estimated\nphylogenies and parameters. 'BEAST2' is a command-line tool.\nThis package provides a way to call 'BEAST2' from an 'R'\nfunction call.", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "URL": "https://docs.ropensci.org/beastier/ (website)\nhttps://github.com/ropensci/beastier/", "BugReports": "https://github.com/ropensci/beastier/issues", "Language": "en-US", "VignetteBuilder": "knitr", "SystemRequirements": "BEAST2 (https://www.beast2.org/)", "Config/pak/sysreqs": "libglpk-dev make default-jdk libicu-dev libxml2-dev\nlibx11-dev zlib1g-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-12-08 18:23:47 UTC", "RemoteUrl": "https://github.com/ropensci/beastier", "RemoteRef": "HEAD", "RemoteSha": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-29 08:31:17 UTC", "User": "root" }, "Author": "Richèl J.C. 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"date": "2019-05-31" }, { "version": "2.0.15", "date": "2019-06-01" }, { "version": "2.1.1", "date": "2019-12-02" }, { "version": "2.1.3", "date": "2020-08-07" }, { "version": "2.2", "date": "2020-10-16" }, { "version": "2.2.1", "date": "2020-10-30" }, { "version": "2.4", "date": "2021-05-23" }, { "version": "2.4.2", "date": "2021-06-05" }, { "version": "2.4.6", "date": "2021-08-19" }, { "version": "2.4.7", "date": "2021-09-07" }, { "version": "2.4.8", "date": "2021-09-19" }, { "version": "2.4.9", "date": "2022-06-03" }, { "version": "2.4.10", "date": "2022-06-15" }, { "version": "2.4.11", "date": "2022-08-11" }, { "version": "2.4.12", "date": "2023-10-08" }, { "version": "2.5", "date": "2023-11-07" }, { "version": "2.5.1", "date": "2024-06-04" }, { "version": "2.5.2", "date": "2024-10-06" } ], "_exports": [ "add_quotes_if_has_spaces", "are_beast2_input_lines", "are_beast2_input_lines_deep", "are_beast2_input_lines_fast", "are_identical_alignments", "beast2_options_to_table", "beastier_report", "check_beast2", "check_beast2_options", "check_beast2_options_data_types", "check_beast2_options_do_not_overwrite_existing_files", "check_beast2_options_filenames_differ", "check_beast2_options_names", "check_beast2_optionses", "check_beast2_path", "check_can_create_dir_for_state_output_file", "check_can_create_file", "check_can_create_screenlog_file", "check_can_create_state_output_file", "check_can_create_tracelog_file", "check_can_create_treelog_file", "check_empty_beastier_folder", "check_empty_beaustier_folders", "check_input_filename", "check_input_filename_validity", "check_n_threads", "check_os", "check_rng_seed", "continue_beast2", "create_beast2_continue_cmd_from_options", "create_beast2_input_file_folder", "create_beast2_options", "create_beast2_run_cmd", "create_beast2_run_cmd_from_options", "create_beast2_screenlog_folder", "create_beast2_state_output_file_folder", "create_beast2_tracelog_folder", "create_beast2_treelog_folder", "create_beast2_validate_cmd", "create_beast2_validate_cmd_bin", "create_beast2_validate_cmd_jar", "create_beast2_version_cmd", "create_beast2_version_cmd_bin", "create_beast2_version_cmd_jar", "create_beastier_tempfolder", "create_mcbette_beast2_options", "create_random_alignment", "create_random_fasta", "create_random_phylogeny", "create_temp_input_filename", "create_temp_state_filename", "do_minimal_run", "extract_screenlog_filename_from_beast2_input_file", "extract_tracelog_filename_from_beast2_input_file", "extract_treelog_filename_from_beast2_input_file", "get_alignment_ids_from_xml_filename", "get_beast2_example_filename", "get_beast2_example_filenames", "get_beast2_main_class_name", "get_beast2_options_filenames", "get_beast2_version", "get_beastier_folder", "get_beastier_path", "get_beastier_paths", "get_beastier_tempfilename", "get_default_beast2_bin_path", "get_default_beast2_download_url", "get_default_beast2_download_url_linux", "get_default_beast2_download_url_win", "get_default_beast2_folder", "get_default_beast2_jar_path", "get_default_beast2_path", "get_default_beast2_version", "get_default_java_path", "get_duplicate_param_ids", "get_java_version", "get_trees_filenames", "gives_beast2_warning", "has_unique_ids", "install_beast2", "is_alignment", "is_beast2_input_file", "is_beast2_installed", "is_bin_path", "is_jar_path", "is_on_appveyor", "is_on_ci", "is_on_travis", "is_win_bin_path", "print_beast2_options", "remove_beastier_folder", "remove_beaustier_folders", "remove_file_if_present", "rename_beast2_options_filenames", "run_beast2", "run_beast2_from_options", "save_lines", "save_nexus_as_fasta", "uninstall_beast2" ], "_help": [ { "page": "add_quotes_if_has_spaces", "title": "Add quotes around the string if it contains spaces.", "topics": [ "add_quotes_if_has_spaces" ] }, { "page": "are_beast2_input_lines", "title": "Would these lines of text, when written to a file, result in a valid BEAST2 input file?", "topics": [ "are_beast2_input_lines" ] }, { "page": "are_beast2_input_lines_deep", "title": "Would these lines of text, when written to a file, result in a valid BEAST2 input file?", "topics": [ "are_beast2_input_lines_deep" ] }, { "page": "are_beast2_input_lines_fast", "title": "Would these lines of text, when written to a file, result in a valid BEAST2 input file?", "topics": [ "are_beast2_input_lines_fast" ] }, { "page": "are_identical_alignments", "title": "Determines if the two alignments are equal", "topics": [ "are_identical_alignments" ] }, { "page": "beast2_options_to_table", "title": "Convert a 'beast2_options' to a table", "topics": [ "beast2_options_to_table" ] }, { "page": "beastier_report", "title": "Creates a beastier report", "topics": [ "beastier_report" ] }, { "page": "check_beast2", "title": "Check if 'BEAST2' is installed properly.", "topics": [ "check_beast2" ] }, { "page": "check_beast2_options", "title": "Check if the 'beast2_options' is a valid BEAST2 options object.", "topics": [ "check_beast2_options" ] }, { "page": "check_beast2_options_data_types", "title": "Check if the 'beast2_options', which is a list, has all elements of the right data types", "topics": [ "check_beast2_options_data_types" ] }, { "page": "check_beast2_options_do_not_overwrite_existing_files", "title": "Internal function", "topics": [ "check_beast2_options_do_not_overwrite_existing_files" ] }, { "page": "check_beast2_options_filenames_differ", "title": "Check if the filenames in 'beast2_options' differ", "topics": [ "check_beast2_options_filenames_differ" ] }, { "page": "check_beast2_options_names", "title": "Check if the 'beast2_options', which is a list, has all the elements needed.", "topics": [ "check_beast2_options_names" ] }, { "page": "check_beast2_optionses", "title": "Check if the 'beast2_options' is a valid BEAST2 options object.", "topics": [ "check_beast2_optionses" ] }, { "page": "check_beast2_path", "title": "Checks the BEAST2 '.jar' path. Will stop if there is a problem with the BEAST2 '.jar' path.", "topics": [ "check_beast2_path" ] }, { "page": "check_can_create_dir_for_state_output_file", "title": "Internal function", "topics": [ "check_can_create_dir_for_state_output_file" ] }, { "page": "check_can_create_file", "title": "Internal function", "topics": [ "check_can_create_file" ] }, { "page": "check_can_create_screenlog_file", "title": "Internal function", "topics": [ "check_can_create_screenlog_file" ] }, { "page": "check_can_create_state_output_file", "title": "Internal function", "topics": [ "check_can_create_state_output_file" ] }, { "page": "check_can_create_tracelog_file", "title": "Internal function to check if the MCMC's tracelog file can be created.", "topics": [ "check_can_create_tracelog_file" ] }, { "page": "check_can_create_treelog_file", "title": "Internal function", "topics": [ "check_can_create_treelog_file" ] }, { "page": "check_empty_beastier_folder", "title": "Check there are no files in the default beastier folder", "topics": [ "check_empty_beastier_folder" ] }, { "page": "check_empty_beaustier_folders", "title": "Check there are no files in the default `beautier` and `beastier` folders", "topics": [ "check_empty_beaustier_folders" ] }, { "page": "check_input_filename", "title": "Checks the input filename. Will stop if there is a problem with the input filename.", "topics": [ "check_input_filename" ] }, { "page": "check_input_filename_validity", "title": "Checks the input filename. Will stop if there is a problem with the input filename.", "topics": [ "check_input_filename_validity" ] }, { "page": "check_n_threads", "title": "Check if the input is a valid number of threads.", "topics": [ "check_n_threads" ] }, { "page": "check_os", "title": "Checks if the operating system is supported", "topics": [ "check_os" ] }, { "page": "check_rng_seed", "title": "Check if the input is a valid RNG seed.", "topics": [ "check_rng_seed" ] }, { "page": "continue_beast2", "title": "Continue a BEAST2 run", "topics": [ "continue_beast2" ] }, { "page": "create_beast2_continue_cmd_from_options", "title": "Creates the terminal command to run BEAST2 from a 'beast2_options'", "topics": [ "create_beast2_continue_cmd_from_options" ] }, { "page": "create_beast2_input_file_folder", "title": "Create the folder where the BEAST2 input file will be created", "topics": [ "create_beast2_input_file_folder" ] }, { "page": "create_beast2_options", "title": "Function to create a set of BEAST2 options.", "topics": [ "create_beast2_options" ] }, { "page": "create_beast2_run_cmd", "title": "Creates the terminal command to run BEAST2", "topics": [ "create_beast2_run_cmd" ] }, { "page": "create_beast2_run_cmd_from_options", "title": "Creates the terminal command to run BEAST2 from a 'beast2_options'", "topics": [ "create_beast2_run_cmd_from_options" ] }, { "page": "create_beast2_screenlog_folder", "title": "Internal function", "topics": [ "create_beast2_screenlog_folder" ] }, { "page": "create_beast2_state_output_file_folder", "title": "Create the folder where the BEAST2 state output file will be created", "topics": [ "create_beast2_state_output_file_folder" ] }, { "page": "create_beast2_tracelog_folder", "title": "Internal function", "topics": [ "create_beast2_tracelog_folder" ] }, { "page": "create_beast2_treelog_folder", "title": "Internal function", "topics": [ "create_beast2_treelog_folder" ] }, { "page": "create_beast2_validate_cmd", "title": "Creates the terminal command to validate a BEAST2 input file", "topics": [ "create_beast2_validate_cmd" ] }, { "page": "create_beast2_validate_cmd_bin", "title": "Creates the terminal command to validate a BEAST2 input file using a call to the 'launcher.jar' file", "topics": [ "create_beast2_validate_cmd_bin" ] }, { "page": "create_beast2_validate_cmd_jar", "title": "Creates the terminal command to validate a BEAST2 input file using a call to the 'launcher.jar' file", "topics": [ "create_beast2_validate_cmd_jar" ] }, { "page": "create_beast2_version_cmd", "title": "Creates the terminal command to version a BEAST2 input file", "topics": [ "create_beast2_version_cmd" ] }, { "page": "create_beast2_version_cmd_bin", "title": "Creates the terminal command to version a BEAST2 input file using a call to the 'launcher.jar' file", "topics": [ "create_beast2_version_cmd_bin" ] }, { "page": "create_beast2_version_cmd_jar", "title": "Creates the terminal command to version a BEAST2 input file using a call to the 'launcher.jar' file", "topics": [ "create_beast2_version_cmd_jar" ] }, { "page": "create_beastier_tempfolder", "title": "Create the temporary folder as used by beastier", "topics": [ "create_beastier_tempfolder" ] }, { "page": "create_mcbette_beast2_options", "title": "Create a `beast2_options` structure for the `mcbette` R package", "topics": [ "create_mcbette_beast2_options" ] }, { "page": "create_random_alignment", "title": "Create a random alignment", "topics": [ "create_random_alignment" ] }, { "page": "create_random_fasta", "title": "Create a random FASTA file", "topics": [ "create_random_fasta" ] }, { "page": "create_random_phylogeny", "title": "Create a random phylogeny", "topics": [ "create_random_phylogeny" ] }, { "page": "create_temp_input_filename", "title": "Create a temporary filename for the BEAST2 XML filename", "topics": [ "create_temp_input_filename" ] }, { "page": "create_temp_state_filename", "title": "Create a temporary file for the BEAST2 XML output file that stores its state.", "topics": [ "create_temp_state_filename" ] }, { "page": "default_params_doc", "title": "This function does nothing. It is intended to inherit is parameters' documentation.", "topics": [ "default_params_doc" ] }, { "page": "do_minimal_run", "title": "Do a minimal BEAST2 run", "topics": [ "do_minimal_run" ] }, { "page": "extract_screenlog_filename_from_beast2_input_file", "title": "Internal function to extract the screenlog filename for a BEAST2 input file", "topics": [ "extract_screenlog_filename_from_beast2_input_file" ] }, { "page": "extract_tracelog_filename_from_beast2_input_file", "title": "Internal function to extract the tracelog filename for a BEAST2 input file", "topics": [ "extract_tracelog_filename_from_beast2_input_file" ] }, { "page": "extract_treelog_filename_from_beast2_input_file", "title": "Internal function to extract the treelog filename for a BEAST2 input file", "topics": [ "extract_treelog_filename_from_beast2_input_file" ] }, { "page": "get_alignment_ids_from_xml_filename", "title": "Get the alignment ID from a file with one alignment", "topics": [ "get_alignment_ids_from_xml_filename" ] }, { "page": "get_beast2_example_filename", "title": "Get the full path of a BEAST2 example file", "topics": [ "get_beast2_example_filename" ] }, { "page": "get_beast2_example_filenames", "title": "Get a list with the full paths of all BEAST2 example filenames", "topics": [ "get_beast2_example_filenames" ] }, { "page": "get_beast2_main_class_name", "title": "Get the BEAST2 main class name.", "topics": [ "get_beast2_main_class_name" ] }, { "page": "get_beast2_options_filenames", "title": "Extract the filenames from a `beast2_options`", "topics": [ "get_beast2_options_filenames" ] }, { "page": "get_beast2_version", "title": "Get the BEAST2 version", "topics": [ "get_beast2_version" ] }, { "page": "get_beastier_folder", "title": "Get the path to the beastier temporary files folder", "topics": [ "get_beastier_folder" ] }, { "page": "get_beastier_path", "title": "Get the full path of a file in the 'inst/extdata' folder", "topics": [ "get_beastier_path" ] }, { "page": "get_beastier_paths", "title": "Get the full paths of files in the 'inst/extdata' folder", "topics": [ "get_beastier_paths" ] }, { "page": "get_beastier_tempfilename", "title": "Get a temporary filename", "topics": [ "get_beastier_tempfilename" ] }, { "page": "get_default_beast2_bin_path", "title": "Get the default BEAST2 binary file ('beast', that is) path", "topics": [ "get_default_beast2_bin_path" ] }, { "page": "get_default_beast2_download_url", "title": "Get the default BEAST2 download URL, which depends on the operating system", "topics": [ "get_default_beast2_download_url" ] }, { "page": "get_default_beast2_download_url_linux", "title": "Get the BEAST2 download URL for Linux", "topics": [ "get_default_beast2_download_url_linux" ] }, { "page": "get_default_beast2_download_url_win", "title": "Get the BEAST2 download URL for Windows", "topics": [ "get_default_beast2_download_url_win" ] }, { "page": "get_default_beast2_folder", "title": "Get the path to the folder where this package installs BEAST2 by default", "topics": [ "get_default_beast2_folder" ] }, { "page": "get_default_beast2_jar_path", "title": "Get the default BEAST2 jar file's path", "topics": [ "get_default_beast2_jar_path" ] }, { "page": "get_default_beast2_path", "title": "Get the default BEAST2 path", "topics": [ "get_default_beast2_path" ] }, { "page": "get_default_beast2_version", "title": "Get the default BEAST2 version that is used by beastier", "topics": [ "get_default_beast2_version" ] }, { "page": "get_default_java_path", "title": "Obtains the default path to the Java executable", "topics": [ "get_default_java_path" ] }, { "page": "get_duplicate_param_ids", "title": "Find duplicate 'RealParameter' IDs", "topics": [ "get_duplicate_param_ids" ] }, { "page": "get_java_version", "title": "Get the Java version", "topics": [ "get_java_version" ] }, { "page": "get_trees_filenames", "title": "Get the .trees filenames that BEAST2 will produce", "topics": [ "get_trees_filenames" ] }, { "page": "gives_beast2_warning", "title": "Determines if BEAST2 issues a warning when using the BEAST2 XML input file", "topics": [ "gives_beast2_warning" ] }, { "page": "has_unique_ids", "title": "Determine if the XML text has unique parameter IDs", "topics": [ "has_unique_ids" ] }, { "page": "install_beast2", "title": "Deprecated function to install BEAST2", "topics": [ "install_beast2" ] }, { "page": "is_alignment", "title": "Determines if the input is an alignment of type DNAbin", "topics": [ "is_alignment" ] }, { "page": "is_beast2_input_file", "title": "Is a file a valid BEAST2 input file?", "topics": [ "is_beast2_input_file" ] }, { "page": "is_beast2_installed", "title": "Checks if BEAST2 is installed", "topics": [ "is_beast2_installed" ] }, { "page": "is_bin_path", "title": "Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present", "topics": [ "is_bin_path" ] }, { "page": "is_jar_path", "title": "Is the path a path to the BEAST2 jar file? Does not check if the file at that path is present", "topics": [ "is_jar_path" ] }, { "page": "is_on_appveyor", "title": "Deprecated function, use is_on_appveyor", "topics": [ "is_on_appveyor" ] }, { "page": "is_on_ci", "title": "Deprecated function, use is_on_ci", "topics": [ "is_on_ci" ] }, { "page": "is_on_travis", "title": "Deprecated function, use is_on_travis", "topics": [ "is_on_travis" ] }, { "page": "is_win_bin_path", "title": "Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present", "topics": [ "is_win_bin_path" ] }, { "page": "print_beast2_options", "title": "Pretty-print a `beast2_options`", "topics": [ "print_beast2_options" ] }, { "page": "remove_beastier_folder", "title": "Check there are no files in the default beautier folder", "topics": [ "remove_beastier_folder" ] }, { "page": "remove_beaustier_folders", "title": "Remove the `beautier` and `beastier` temporary folders", "topics": [ "remove_beaustier_folders" ] }, { "page": "remove_file_if_present", "title": "Remove a file if it is present, will do nothing if it is not.", "topics": [ "remove_file_if_present" ] }, { "page": "rename_beast2_options_filenames", "title": "Rename the filenames in the BEAST2 options", "topics": [ "rename_beast2_options_filenames" ] }, { "page": "run_beast2", "title": "Run BEAST2", "topics": [ "run_beast2" ] }, { "page": "run_beast2_from_options", "title": "Run BEAST2", "topics": [ "run_beast2_from_options" ] }, { "page": "save_lines", "title": "Save text (a container of strings) to a file", "topics": [ "save_lines" ] }, { "page": "save_nexus_as_fasta", "title": "Save a NEXUS file as a FASTA file", "topics": [ "save_nexus_as_fasta" ] }, { "page": "uninstall_beast2", "title": "Deprecated function to uninstall BEAST2", "topics": [ "uninstall_beast2" ] }, { "page": "upgrade_beast2", "title": "Deprecated function to upgrade BEAST2.", "topics": [ "upgrade_beast2" ] } ], "_readme": "https://github.com/ropensci/beastier/raw/HEAD/README.md", "_rundeps": [ "ade4", "ape", "beautier", "bit", "bit64", "cli", "clipr", "cpp11", "crayon", "digest", "fastmatch", "generics", "glue", "hms", "igraph", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "nlme", "phangorn", "pillar", "pixmap", "pkgconfig", "prettyunits", "progress", "purrr", "quadprog", "R6", "rappdirs", "Rcpp", "RcppArmadillo", "readr", "rJava", "rlang", "segmented", "seqinr", "sessioninfo", "sp", "stringi", "stringr", "tibble", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr", "xml2" ], "_sysdeps": [ { "shlib": "libjvm", "package": "openjdk-25-jre-headless", "headers": "openjdk-25-jre-headless", "source": "openjdk", "version": "25.0.4.1+1-1~26.04.4", "name": "openjdk", "homepage": "https://openjdk.java.net/", "description": "OpenJDK Java runtime, using Hotspot JIT (headless)" } ], "_vignettes": [ { "source": "demo.Rmd", "filename": "demo.html", "title": "beastier demo", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Introduction" ], "created": "2019-04-25 12:10:51", "modified": "2022-06-01 19:17:20", "commits": 8 } ], "_score": 7.368547197567656, "_indexed": true, "_nocasepkg": "beastier", "_universes": [ "ropensci", "richelbilderbeek" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.5.3", "date": "2026-10-29T08:33:39.000Z", "distro": "resolute", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "https://r2.ropensci.org/a1ec409b348bb55e4431f131f85a8dad645a14a6d56e758a4180f2cf98017eda", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40842128876" }, { "r": "4.6.1", "os": "linux", "version": "2.5.3", "date": "2026-10-29T08:33:43.000Z", "distro": "resolute", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "https://r2.ropensci.org/3b99cfa5a656395e40b9c6e978e126f3496875ec026ecdb1f8a82fcfe4b23ded", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40842128876" }, { "r": "4.5.3", "os": "mac", "version": "2.5.3", "date": "2026-10-29T08:34:18.000Z", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "https://r2.ropensci.org/59e09ea514bfc2421d7950e95b6dfc45cf71a9beeeb35977428ff07c36f247ca", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40842128876" }, { "r": "4.6.1", "os": "mac", "version": "2.5.3", "date": "2026-10-29T08:35:10.000Z", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "https://r2.ropensci.org/8904f550dc90a7e11b988719f1a3b42fe17f22f4d0d4a15cee198468003d544a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40842128876" }, { "r": "4.6.0", "os": "wasm", "version": "2.5.3", "date": "2026-10-29T08:33:31.000Z", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "https://r2.ropensci.org/867b14c80ae6e8dca3f6b2af274400a34509974874c3d24cd4af374d3b83d650", "status": "success", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40842128876" }, { "r": "4.7.0", "os": "win", "version": "2.5.3", "date": "2026-10-29T08:32:36.000Z", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "https://r2.ropensci.org/150d8ef903aa933ec9dc043425dbdbba3bdc82fc91c6fb342bca9d3ca563055c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40842128876" }, { "r": "4.5.3", "os": "win", "version": "2.5.3", "date": "2026-10-29T08:32:37.000Z", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "https://r2.ropensci.org/63f7dc91cbb19f11b67c917b70ceac3394e8fab4f3a4bbae50746b61afa3db57", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40842128876" }, { "r": "4.6.1", "os": "win", "version": "2.5.3", "date": "2026-10-29T08:32:26.000Z", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "https://r2.ropensci.org/baa236f5edd8083b1fb30b1ef80a7ee5d885287b90ab0f0f425683ca277e8090", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40842128876" } ] }, { "Type": "Package", "Package": "DataPackageR", "Title": "Construct Reproducible Analytic Data Sets as R Packages", "Version": "0.16.2", "Authors@R": "c(\nperson(\"Greg\", \"Finak\", , \"greg.finak@gmail.com\", role = c(\"aut\", \"cph\"),\ncomment = \"Original author and creator of DataPackageR\"),\nperson(\"Paul\", \"Obrecht\", role = \"ctb\"),\nperson(\"Ellis\", \"Hughes\", , \"ellishughes@live.com\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-0637-4436\")),\nperson(\"Jimmy\", \"Fulp\", , \"williamjfulp@gmail.com\", role = \"ctb\"),\nperson(\"Marie\", \"Vendettuoli\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-9321-1410\")),\nperson(\"Dave\", \"Slager\", , \"dslager@fredhutch.org\", role = c(\"ctb\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-2525-2039\")),\nperson(\"Jason\", \"Taylor\", , \"jmtaylor@fredhutch.org\", role = \"ctb\"),\nperson(\"Kara\", \"Woo\", role = \"rev\",\ncomment = \"Kara reviewed the package for rOpenSci, see \"),\nperson(\"William\", \"Landau\", role = \"rev\",\ncomment = \"William reviewed the package for rOpenSci, see \")\n)", "Description": "A framework to help construct R data packages in a\nreproducible manner. Potentially time consuming processing of\nraw data sets into analysis ready data sets is done in a\nreproducible manner and decoupled from the usual 'R CMD build'\nprocess so that data sets can be processed into R objects in\nthe data package and the data package can then be shared,\nbuilt, and installed by others without the need to repeat\ncomputationally costly data processing. The package maintains\ndata provenance by turning the data processing scripts into\npackage vignettes, as well as enforcing documentation and\nversion checking of included data objects. Data packages can be\nversion controlled on 'GitHub', and used to share data for\nmanuscripts, collaboration and reproducible research.", "License": "MIT + file LICENSE", "URL": "https://github.com/ropensci/DataPackageR,\nhttps://docs.ropensci.org/DataPackageR/", "BugReports": "https://github.com/ropensci/DataPackageR/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Language": "en-US", "RoxygenNote": "7.3.3", "SystemRequirements": "pandoc - https://pandoc.org", "Config/pak/sysreqs": "cmake git make libgit2-dev libuv1-dev libxml2-dev\nlibssl-dev libx11-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-12-08 06:27:46 UTC", "RemoteUrl": "https://github.com/ropensci/DataPackageR", "RemoteRef": "HEAD", "RemoteSha": "91c3001bcfab7dc84e99e858e847094b4bf1b733", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-29 07:54:21 UTC", "User": "root" }, "Author": "Greg Finak [aut, cph] (Original author and creator of DataPackageR),\nPaul Obrecht 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This package\nprovides a tile generator function for creating map tile sets\nfor use with packages such as 'leaflet'. In addition to\ngenerating map tiles based on a common raster layer source, it\nalso handles the non-geographic edge case, producing map tiles\nfrom arbitrary images. These map tiles, which have a\nnon-geographic, simple coordinate reference system (CRS), can\nalso be used with 'leaflet' when applying the simple CRS\noption. Map tiles can be created from an input file with any of\nthe following extensions: tif, grd and nc for spatial maps and\npng, jpg and bmp for basic images. This package requires\n'Python' and the 'gdal' library for 'Python'. 'Windows' users\nare recommended to install 'OSGeo4W'\n() as an easy way to obtain\nthe required 'gdal' support for 'Python'.", "License": "MIT + file LICENSE", "URL": "https://docs.ropensci.org/tiler/,\nhttps://github.com/ropensci/tiler", "BugReports": "https://github.com/ropensci/tiler/issues", "VignetteBuilder": "knitr", "ByteCompile": "true", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "SystemRequirements": "Python (>= 2.7), python-gdal library (For Windows,\ngdal installed via OSGeo4W \nrecommended) clipboard", "Config/pak/sysreqs": "libgdal-dev gdal-bin libgeos-dev libpng-dev\nlibproj-dev python3 libsqlite3-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-12-02 18:46:09 UTC", "RemoteUrl": "https://github.com/ropensci/tiler", "RemoteRef": "HEAD", "RemoteSha": "c4f970fc39f2cd8baa858fd6022dc1f068461a76", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-29 08:12:18 UTC", "User": "root" }, "Author": "Matthew 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This package aims to provide users with a\nstandardized way to automate genome, proteome, 'RNA', coding\nsequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI\nRefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases.\nFurthermore, an interface to the 'BioMart' database (Smedley et\nal. (2009) ) allows users to\nretrieve functional annotation for genomic loci. In addition,\nusers can download entire databases such as 'NCBI RefSeq'\n(Pruitt et al. (2007) ), 'NCBI nr',\n'NCBI nt', 'NCBI Genbank' (Benson et al. (2013)\n), etc. with only one command.", "VignetteBuilder": "knitr", "License": "GPL-2", "URL": "https://docs.ropensci.org/biomartr/,\nhttps://github.com/ropensci/biomartr", "BugReports": "https://github.com/ropensci/biomartr/issues", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-12-02 15:45:39 UTC", "RemoteUrl": "https://github.com/ropensci/biomartr", "RemoteRef": "HEAD", "RemoteSha": "5affece1736b5d3198c788456320a262c63ceb8e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-29 08:05:59 UTC", "User": "root" }, "Author": "Hajk-Georg Drost [aut, cre] (ORCID:\n),\nHaakon Tjeldnes [aut, ctb]", "Maintainer": "Hajk-Georg Drost ", "_user": "ropensci", "_type": "src", "_file": "biomartr_1.0.11.tar.gz", "_fileid": 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etc", "concept": [ "cachedir" ], "topics": [ "cachedir" ] }, { "page": "cachedir_set", "title": "Set directory to store back end files like kingdom summaries etc", "concept": [ "cachedir" ], "topics": [ "cachedir_set" ] }, { "page": "check_annotation_biomartr", "title": "Check whether an annotation file contains outlier lines", "topics": [ "check_annotation_biomartr" ] }, { "page": "clean.retrieval", "title": "Format 'meta.retrieval' output", "topics": [ "clean.retrieval" ] }, { "page": "download.database", "title": "Download a NCBI Database to Your Local Hard Drive", "topics": [ "download.database" ] }, { "page": "download.database.all", "title": "Download all elements of an NCBI databse", "topics": [ "download.database.all" ] }, { "page": "ensembl_divisions", "title": "List all available ENSEMBL divisions", "topics": [ "ensembl_divisions" ] }, { "page": "get.ensembl.info", "title": "Helper function to retrieve species information from the ENSEMBL API", "topics": [ "get.ensembl.info" 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"title": "Retrieve All Available Filters for a Specific Dataset", "topics": [ "getFilters" ] }, { "page": "getGenome", "title": "Genome Retrieval", "concept": [ "genome", "getBio" ], "topics": [ "getGenome" ] }, { "page": "getGENOMEREPORT", "title": "Retrieve NCBI GENOME_REPORTS file", "topics": [ "getGENOMEREPORT" ] }, { "page": "getGenomeSet", "title": "Genome Retrieval of multiple species", "concept": [ "genome", "getBioSet" ], "topics": [ "getGenomeSet" ] }, { "page": "getGFF", "title": "Genome Annotation Retrieval (GFF3)", "concept": [ "getBio", "gff" ], "topics": [ "getGFF" ] }, { "page": "getGFFSet", "title": "GFF retrieval of multiple species", "concept": [ "getBioSet", "gff" ], "topics": [ "getGFFSet" ] }, { "page": "getGO", "title": "Gene Ontology Query", "topics": [ "getGO" ] }, { "page": "getGroups", "title": "Retrieve available groups for a kingdom of life (only available for NCBI RefSeq and NCBI Genbank)", "topics": [ "getGroups" ] }, { "page": "getGTF", "title": "Genome 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for rOpenSci, see https://github.com/ropensci/software-review/issues/627#issuecomment-2037644081\")\n)", "Maintainer": "Ronald Visser ", "Description": "Creating dendrochronological networks based on the\nsimilarity between tree-ring series or chronologies. The\npackage includes various functions to compare tree-ring curves\nbuilding upon the 'dplR' package. The networks can be used to\nvisualise and understand the relations between tree-ring\ncurves. These networks are also very useful to estimate the\nprovenance of wood as described in Visser (2021)\n or wood-use within a\nstructure/context/site as described in Visser and Vorst (2022)\n.", "License": "GPL (>= 3)", "biocViews": "Visualization, GraphAndNetwork, ThirdPartyClient, Network", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "URL": "https://github.com/ropensci/dendroNetwork,\nhttps://docs.ropensci.org/dendroNetwork/", "BugReports": "https://github.com/ropensci/dendroNetwork/issues", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 libzmq3-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-08-03 06:21:22 UTC", "RemoteUrl": "https://github.com/ropensci/dendroNetwork", "RemoteRef": "main", "RemoteSha": "51ac08aa8194703a42bdcde875b0950ae49a892a", "NeedsCompilation": "no", 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'data.frame'", "topics": [ "as_data_frame" ] }, { "page": "as_taxon", "title": "Convert to a taxon vector", "topics": [ "as_taxon" ] }, { "page": "classification", "title": "Taxon class", "concept": [ "classes" ], "topics": [ "classification" ] }, { "page": "db_ref", "title": "Valid taxonomy databases", "topics": [ "db_ref" ] }, { "page": "internodes", "title": "Get internodes", "concept": [ "internode functions", "taxonomy functions" ], "topics": [ "internodes" ] }, { "page": "is_classification", "title": "Check if is a classification", "topics": [ "is_classification" ] }, { "page": "is_internode", "title": "Check if taxa are internodes", "concept": [ "internode functions" ], "topics": [ "is_internode" ] }, { "page": "is_leaf", "title": "Check if taxa are leaves", "concept": [ "leaf functions" ], "topics": [ "is_leaf" ] }, { "page": "is_root", "title": "Test if taxa are roots", "concept": [ "root functions" ], "topics": [ "is_root" ] }, { "page": "is_stem", "title": "Check if taxa are stems", "concept": [ "stem functions" ], "topics": [ "is_stem" ] }, { "page": "is_taxon", "title": "Check if something is a taxon object", "topics": [ "is_taxon" ] }, { "page": "is_taxon_authority", "title": "Check if is a taxon_authority", "topics": [ "is_taxon_authority" ] }, { "page": "is_taxon_db", "title": "Check if something is a taxon_db", "topics": [ "is_taxon_db" ] }, { "page": "is_taxon_id", "title": "Check if something is a taxon_id object", "topics": [ "is_taxon_id" ] }, { "page": "is_taxon_rank", "title": "Check if something is a taxon_rank", "topics": [ "is_taxon_rank" ] }, { "page": "is_taxonomy", "title": "Check if something is a taxonomy", "topics": [ "is_taxonomy" ] }, { "page": "leaves", "title": "Get leaves", "concept": [ "leaf functions", "taxonomy functions" ], "topics": [ "leaves" ] }, { "page": "n_leaves", "title": "Number of leaves per taxon", "concept": [ "leaf functions" ], "topics": [ "n_leaves" ] }, { "page": "n_subtaxa", "title": "Number of subtaxa per taxon", "concept": [ "subtaxa functions" ], "topics": [ "n_subtaxa" ] }, { "page": "n_supertaxa", "title": "Number of supertaxa per taxon", "concept": [ "supertaxa functions" ], "topics": [ "n_supertaxa" ] }, { "page": "roots", "title": "Get root taxa", "concept": [ "root functions", "taxonomy functions" ], "topics": [ "roots" ] }, { "page": "stems", "title": "Get stems", "concept": [ "stem functions", "taxonomy functions" ], "topics": [ "stems" ] }, { "page": "subtaxa", "title": "Get subtaxa", "concept": [ "subtaxa functions", "taxonomy functions" ], "topics": [ "subtaxa" ] }, { "page": "supertaxa", "title": "Get supertaxa", "concept": [ "supertaxa functions", "taxonomy functions" ], "topics": [ "supertaxa" ] }, { "page": "tax_auth", "title": "Set and get taxon authorities", "topics": [ "tax_auth", "tax_auth.taxa_classification", "tax_auth.taxa_taxon", "tax_auth.taxa_taxonomy", "tax_auth<-", "tax_auth<-.taxa_classification", "tax_auth<-.taxa_taxon", "tax_auth<-.taxa_taxonomy" ] }, { "page": "tax_author", "title": "Set and get taxon authors", "topics": [ "tax_author", "tax_author.taxa_classification", "tax_author.taxa_taxon", "tax_author.taxa_taxonomy", "tax_author.taxa_taxon_authority", "tax_author<-", "tax_author<-.taxa_classification", "tax_author<-.taxa_taxon", "tax_author<-.taxa_taxonomy", "tax_author<-.taxa_taxon_authority" ] }, { "page": "tax_cite", "title": "Set and get taxon authority citations", "topics": [ "tax_cite", "tax_cite.taxa_classification", "tax_cite.taxa_taxon", "tax_cite.taxa_taxonomy", "tax_cite.taxa_taxon_authority", "tax_cite<-", "tax_cite<-.taxa_classification", "tax_cite<-.taxa_taxon", "tax_cite<-.taxa_taxonomy", "tax_cite<-.taxa_taxon_authority" ] }, { "page": "tax_date", "title": "Set and get taxon authority dates", "topics": [ "tax_date", "tax_date.taxa_classification", "tax_date.taxa_taxon", "tax_date.taxa_taxonomy", "tax_date.taxa_taxon_authority", "tax_date<-", "tax_date<-.taxa_classification", "tax_date<-.taxa_taxon", 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\"cre\"),\nemail = \"vbaliga87@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9367-8974\")),\nperson(given = \"Melissa S.\",\nfamily = \"Armstrong\",\nrole = \"aut\",\nemail = \"melissa.armstrong@gmail.com\",\ncomment = c(ORCID = \"0000-0002-3059-0094\")),\nperson(given = \"Eric R.\",\nfamily = \"Press\",\nrole = \"aut\",\nemail = \"epress12@gmail.com\",\ncomment = c(ORCID = \"0000-0002-1944-3755\")),\nperson(given = \"Anne-Sophie\",\nfamily = \"Bonnet-Lebrun\",\nrole = \"rev\"),\nperson(given = \"Marco\",\nfamily = \"Sciaini\",\nrole = \"rev\")\n)", "Description": "Tools to import, clean, and visualize movement data,\nparticularly from motion capture systems such as Optitrack's\n'Motive', the Straw Lab's 'Flydra', or from other sources. We\nprovide functions to remove artifacts, standardize tunnel\nposition and tunnel axes, select a region of interest, isolate\nspecific trajectories, fill gaps in trajectory data, and\ncalculate 3D and per-axis velocity. For experiments of visual\nguidance, we also provide functions that use subject position\nto estimate perception of visual stimuli.", "Maintainer": "Vikram B. 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common spatial and temporal errors\nin biological and paleontological collection data, for the use\nin conservation, ecology and paleontology. Includes automated\ntests to easily flag (and exclude) records assigned to country\nor province centroid, the open ocean, the headquarters of the\nGlobal Biodiversity Information Facility, urban areas or the\nlocation of biodiversity institutions (museums, zoos, botanical\ngardens, universities). Furthermore identifies per species\noutlier coordinates, zero coordinates, identical\nlatitude/longitude and invalid coordinates. Also implements an\nalgorithm to identify data sets with a significant proportion\nof rounded coordinates. Especially suited for large data sets.\nThe reference for the methodology is: Zizka et al. 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A typical use case considers\npatient with medically coded data, such as codes from the\nInternational Classification of Diseases ('ICD') or the\nAnatomic Therapeutic Chemical ('ATC') classification system.\nFunctions of the package relies on a triad of objects: (1) case\ndata with unit id:s and possible dates of interest; (2)\nexternal code data for corresponding units in (1) and with\noptional dates of interest and; (3) a classification scheme\n('classcodes' object) with regular expressions to identify and\ncategorize relevant codes from (2). It is easy to introduce new\nclassification schemes ('classcodes' objects) or to use default\nschemes included in the package. Use cases includes patient\ncategorization based on 'comorbidity indices' such as\n'Charlson', 'Elixhauser', 'RxRisk V', or the\n'comorbidity-polypharmacy' score (CPS), as well as adverse\nevents after hip and knee replacement surgery.", "License": "GPL-2", "LazyData": "TRUE", "RoxygenNote": "7.3.2", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "URL": "https://docs.ropensci.org/coder/", "BugReports": "https://github.com/ropensci/coder/issues", "Encoding": "UTF-8", "Language": "en-US", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-05-05 15:19:55 UTC", "RemoteUrl": "https://github.com/ropensci/coder", "RemoteRef": "HEAD", "RemoteSha": "730d445598249bcafffdbbd47e450408befe486f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-29 07:46:21 UTC", "User": "root" }, "Author": "Erik Bulow [aut, cre] (ORCID: ),\nEmely C Zabore [rev] (Emily reviewed the package (v. 0.12.1) for\nrOpenSci, see\n),\nDavid Robinson [rev] (David reviewed the 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"rows": 2376, "table": true, "tojson": true }, { "name": "ex_people", "title": "Example data for random people", "object": "ex_people", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "name", "surgery" ], "rows": 100, "table": true, "tojson": true }, { "name": "hip_ae", "title": "Classcodes for adverse events after knee and hip arthroplasty", "object": "hip_ae", "class": [ "classcodes", "tbl_df", "tbl", "data.frame" ], "fields": [ "group", "icd10", "kva", "condition", "icd10_fracture" ], "rows": 7, "table": true, "tojson": true }, { "name": "hip_ae_hailer", "title": "Classcodes for infection and dislocation after hip arthroplasty", "object": "hip_ae_hailer", "class": [ "classcodes", "tbl_df", "tbl", "data.frame" ], "fields": [ "group", "icd10", "kva" ], "rows": 2, "table": true, "tojson": true }, { "name": "knee_ae", "title": "Classcodes for adverse events after knee and hip arthroplasty", "object": "knee_ae", "class": [ "classcodes", "tbl_df", "tbl", "data.frame" ], "fields": [ "group", "icd10", "kva", "condition" ], "rows": 7, "table": true, "tojson": true }, { "name": "rxriskv", "title": "Classcodes for RxRisk V based on ATC codes", "object": "rxriskv", "class": [ "classcodes", "tbl_df", "tbl", "data.frame" ], "fields": [ "group", "atc_pratt", "atc_caughey", "atc_garland", "pratt", "sum_all" ], "rows": 46, "table": true, "tojson": true } ], "_help": [ { "page": "ae", "title": "Classcodes for adverse events after knee and hip arthroplasty", "concept": [ "default classcodes" ], "topics": [ "ae", "hip_ae", "knee_ae" ] }, { "page": "all_classcodes", "title": "Summary data for all default classcodes object in the package", "concept": [ "classcodes" ], "topics": [ "all_classcodes" ] }, { "page": "as.data.frame.classified", "title": "Convert output from classify() to matrix/data.frame/data.table", "concept": [ "classcodes" ], "topics": [ "as.data.frame.classified", "as.data.table.classified", "as.matrix.classified" ] }, { "page": "as.keyvalue.classcodes", 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\"0000-0002-7953-0260\")),\nperson(\"Virgilio\", \"Gómez-Rubio\", role = \"rev\",\ncomment = \"Virgilio reviewed the package (v. 0.2.0.9000) for rOpenSci, see \"),\nperson(\"Jakub\", \"Nowosad\", role = \"rev\",\ncomment = \"Jakub reviewed the package (v. 0.2.0.9000) for rOpenSci, see \"),\nperson(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"))\n)", "Description": "Assessing predictive models of spatial data can be\nchallenging, both because these models are typically built for\nextrapolating outside the original region represented by\ntraining data and due to potential spatially structured errors,\nwith \"hot spots\" of higher than expected error clustered\ngeographically due to spatial structure in the underlying data.\nMethods are provided for assessing models fit to spatial data,\nincluding approaches for measuring the spatial structure of\nmodel errors, assessing model predictions at multiple spatial\nscales, and evaluating where predictions can be made safely.\nMethods are particularly useful for models fit using the\n'tidymodels' framework. Methods include Moran's I ('Moran'\n(1950) ), Geary's C ('Geary' (1954)\n), Getis-Ord's G ('Ord' and 'Getis' (1995)\n), agreement\ncoefficients from 'Ji' and Gallo (2006) (), agreement metrics from 'Willmott'\n(1981) () and 'Willmott'\n'et' 'al'. (2012) (), an implementation\nof the area of applicability methodology from 'Meyer' and\n'Pebesma' (2021) (), and an\nimplementation of multi-scale assessment as described in\n'Riemann' 'et' 'al'. 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Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the Centers for Disease Control and Prevention.\"), role = c(\"fnd\")),\nperson(\"MIDAS-NIH COVID-19 urgent grant program\", role = c(\"fnd\")),\nperson(\"Paul G. Allen School for Global Health, Washington State University\", role = c(\"cph\")))", "Description": "A set of functions of increasing complexity allows users\nto (1) convert QuadKey-identified datasets, based on\n'Microsoft's Bing Maps Tile System', into Simple Features data\nframes, (2) transform Simple Features data frames into rasters,\nand (3) process multiple 'Meta' ('Facebook') QuadKey-identified\nhuman mobility files directly into raster files. For more\ndetails, see D’Andrea et al. (2024) .", "License": "MIT + file LICENSE", "URL": "https://docs.ropensci.org/quadkeyr/,\nhttps://github.com/ropensci/quadkeyr", "BugReports": "https://github.com/ropensci/quadkeyr/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "LazyData": "true", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libuv1-dev libssl-dev libproj-dev libsqlite3-dev\nlibudunits2-dev libx11-dev zlib1g-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-03-25 19:31:35 UTC", "RemoteUrl": "https://github.com/ropensci/quadkeyr", "RemoteRef": "HEAD", "RemoteSha": "07cc343b2d77d25b8e3e802fc3a5ca5e9bd72d0e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-29 07:50:54 UTC", "User": "root" }, "Author": "Florencia D'Andrea [aut, cre] (ORCID:\n),\nPilar Fernandez [aut] (ORCID: ),\nMaria Paula Caldas [rev] (ORCID:\n, Maria Paula Caldas\nreviewed the package (v. 0.0.0.9000) for rOpenSci, see\nhttps://github.com/ropensci/software-review/issues/619),\nVincent van Hees [rev] (ORCID: ,\nVincent van Hees reviewed the package (v. 0.0.0.9000) for rOpenSci,\nsee https://github.com/ropensci/software-review/issues/619),\nAndrew Pulsipher [ctb] (ORCID: ),\nCDC's Center for Forecasting and Outbreak Analytics [fnd] (This project\nwas made possible by cooperative agreement CDC-RFA-FT-23-0069\n(grant # NU38FT000009-01-00) from the CDC's Center for Forecasting\nand Outbreak Analytics. Its contents are solely the responsibility\nof the authors and do not necessarily represent the official views\nof the Centers for Disease Control and Prevention.),\nMIDAS-NIH COVID-19 urgent grant program [fnd],\nPaul G. 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"credibility_rating", "credibility_ratings", "currency", "date_data", "description", "experts", "full_record", "geographic_divisions", "geographic_values", "global_species_completeness", "hierarchy_down", "hierarchy_full", "hierarchy_up", "itis_facet", "itis_group", "itis_highlight", "itis_search", "jurisdiction_origin_values", "jurisdiction_values", "jurisdictional_origin", "kingdom_name", "kingdom_names", "last_change_date", "lsid2tsn", "other_sources", "parent_tsn", "publications", "rank_name", "rank_names", "record", "review_year", "scientific_name", "search_any_match_paged", "search_anymatch", "search_common", "search_scientific", "synonym_names", "taxon_authorship", "terms", "tsn_by_vernacular_language", "tsn2lsid", "unacceptability_reason", "usage", "vernacular_languages" ], "_datasets": [ { "name": "solr_fields", "title": "List of fields that can be used in solr functions", "object": "solr_fields", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "ritis-package", "title": "ritis", "topics": [ "ritis-package", "ritis" ] }, { "page": "accepted_names", "title": "Get accepted names from tsn", "topics": [ "accepted_names" ] }, { "page": "any_match_count", "title": "Get any match count.", "topics": [ "any_match_count" ] }, { "page": "comment_detail", "title": "Get comment detail from TSN", "topics": [ "comment_detail" ] }, { "page": "common_names", "title": "Get common names from tsn", "topics": [ "common_names" ] }, { "page": "core_metadata", "title": "Get core metadata from tsn", "topics": [ "core_metadata" ] }, { "page": "coverage", "title": "Get coverge from tsn", "topics": [ "coverage" ] }, { "page": "credibility", "title": "Get credibility rating from tsn", "topics": [ "credibility", "credibility_rating", "credibility_ratings" ] }, { "page": "currency", "title": "Get currency from tsn", "topics": [ "currency" ] }, { "page": "date_data", "title": "Get date data from tsn", "topics": [ "date_data" ] }, { "page": "description", "title": "Get description of the ITIS service", "topics": [ "description" ] }, { "page": "experts", "title": "Get expert information for the TSN.", "topics": [ "experts" ] }, { "page": "full_record", "title": "Get full record from TSN or lsid", "topics": [ "full_record" ] }, { "page": "geographic_divisions", "title": "Get geographic divisions from tsn", "topics": [ "geographic_divisions" ] }, { "page": "geographic_values", "title": "Get all possible geographic values", "topics": [ "geographic_values" ] }, { "page": "global_species_completeness", "title": "Get global species completeness from tsn", "topics": [ "global_species_completeness" ] }, { "page": "hierarchy", "title": "Get hierarchy down from tsn", "topics": [ "hierarchy", "hierarchy_down", "hierarchy_full", "hierarchy_up" ] }, { "page": "itis_facet", "title": "ITIS Solr facet", "topics": [ "itis_facet" ] }, { "page": "itis_group", "title": "ITIS Solr group search", "topics": [ "itis_group" ] }, { "page": "itis_highlight", "title": "ITIS Solr highlight", "topics": [ "itis_highlight" ] }, { "page": "itis_search", "title": "ITIS Solr search", "topics": [ "itis_search" ] }, { "page": "jurisdiction", "title": "Get jurisdictional origin from tsn", "topics": [ "jurisdiction", "jurisdictional_origin", "jurisdiction_origin_values", "jurisdiction_values" ] }, { "page": "kingdoms", "title": "Get kingdom names from tsn", "topics": [ "kingdoms", "kingdom_name", "kingdom_names" ] }, { "page": "last_change_date", "title": "Provides the date the ITIS database was last updated", "topics": [ "last_change_date" ] }, { "page": "lsid2tsn", "title": "Gets the TSN corresponding to the LSID, or an empty result if there is no match.", "topics": [ "lsid2tsn" ] }, { "page": "other_sources", "title": "Returns a list of the other sources used for the TSN.", "topics": [ "other_sources" ] }, { "page": "parent_tsn", "title": "Returns the parent TSN for the entered TSN.", "topics": [ "parent_tsn" ] }, { "page": "publications", "title": "Returns a list of the pulications used for the TSN.", "topics": [ "publications" ] }, { "page": "rank_name", "title": "Returns the kingdom and rank information for the TSN.", "topics": [ "rank_name" ] }, { "page": "rank_names", "title": "Provides a list of all the unique rank names contained in the database and their kingdom and rank ID values.", "topics": [ "rank_names" ] }, { "page": "record", "title": "Gets a record from an LSID", "topics": [ "record" ] }, { "page": "review_year", "title": "Returns the review year for the TSN.", "topics": [ "review_year" ] }, { "page": "scientific_name", "title": "Returns the scientific name for the TSN. Also returns the component parts (names and indicators) of the scientific name.", "topics": [ "scientific_name" ] }, { "page": "search_any_match_paged", "title": "Search for any matched page", "topics": [ "search_any_match_paged" ] }, { "page": "search_anymatch", "title": "Search for any match", "topics": [ "search_anymatch" ] }, { "page": "search_common", "title": "Search for tsn by common name", "topics": [ "search_common" ] }, { "page": "search_scientific", "title": "Search by scientific name", "topics": [ "search_scientific" ] }, { "page": "solr", "title": "ITIS Solr Methods", "topics": [ "solr" ] }, { "page": "solr_fields", "title": "List of fields that can be used in solr functions", "topics": [ "solr_fields" ] }, { "page": "synonym_names", "title": "Returns a list of the synonyms (if any) for the TSN.", "topics": [ "synonym_names" ] }, { "page": "taxon_authorship", "title": "Returns the author information for the TSN.", "topics": [ "taxon_authorship" ] }, { "page": "terms", 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The MCTQ is a quantitative and validated tool used\nto assess chronotypes based on individuals' sleep behavior. 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}, { "page": "build_times", "title": "See the time it took to build each target. *[Stable]*", "topics": [ "build_times" ] }, { "page": "cached", "title": "List targets in the cache. *[Stable]*", "topics": [ "cached" ] }, { "page": "cached_planned", "title": "List targets in both the plan and the cache. *[Stable]*", "topics": [ "cached_planned" ] }, { "page": "cached_unplanned", "title": "List targets in the cache but not the plan. *[Stable]*", "topics": [ "cached_unplanned" ] }, { "page": "cancel", "title": "Cancel a target mid-build *[Stable]*", "topics": [ "cancel" ] }, { "page": "cancel_if", "title": "Cancel a target mid-build under some condition *[Stable]*", "topics": [ "cancel_if" ] }, { "page": "clean", "title": "Invalidate and deregister targets. *[Stable]*", "topics": [ "clean" ] }, { "page": "clean_mtcars_example", "title": "Clean the mtcars example from 'drake_example(\"mtcars\")' *[Stable]*", "topics": [ "clean_mtcars_example" ] }, { "page": "code_to_function", "title": "Turn a script into a function. *[Stable]*", "topics": [ "code_to_function" ] }, { "page": "code_to_plan", "title": "Turn an R script file or 'knitr' / R Markdown report into a 'drake' plan. *[Questioning]*", "topics": [ "code_to_plan" ] }, { "page": "deps_code", "title": "List the dependencies of a function or command *[Stable]*", "topics": [ "deps_code" ] }, { "page": "deps_knitr", "title": "Find the drake dependencies of a dynamic knitr report target. *[Stable]*", "topics": [ "deps_knitr" ] }, { "page": "deps_profile", "title": "Find out why a target is out of date. *[Stable]*", "topics": [ "deps_profile" ] }, { "page": "deps_target", "title": "List the dependencies of a target *[Stable]*", "topics": [ "deps_target" ] }, { "page": "diagnose", "title": "Get diagnostic metadata on a target. *[Stable]*", "topics": [ "diagnose" ] }, { "page": "drake_build", "title": "Build/process a single target or import. *[Questioning]*", "topics": [ "drake_build" ] }, { "page": "drake_cache", "title": "Get the cache of a 'drake' project. *[Stable]*", "topics": [ "drake_cache" ] }, { "page": "drake_cache_log", "title": "Get the state of the cache. *[Stable]*", "topics": [ "drake_cache_log" ] }, { "page": "drake_cancelled", "title": "List cancelled targets. *[Stable]*", "topics": [ "drake_cancelled" ] }, { "page": "drake_config", "title": "Ending of _drake.R for r_make() and friends *[Stable]*", "topics": [ "drake_config" ] }, { "page": "drake_debug", "title": "Run a single target's command in debug mode.' *[Questioning]*", "topics": [ "drake_debug" ] }, { "page": "drake_done", "title": "List done targets. *[Stable]*", "topics": [ "drake_done" ] }, { "page": "drake_envir", "title": "Get the environment where drake builds targets *[Questioning]*", "topics": [ "drake_envir" ] }, { "page": "drake_example", "title": "Download the files of an example 'drake' project. *[Stable]*", "topics": [ "drake_example" ] }, { "page": "drake_examples", "title": "List the names of all the drake examples. *[Stable]*", "topics": [ "drake_examples" ] }, { "page": "drake_failed", "title": "List failed targets. *[Stable]*", "topics": [ "drake_failed" ] }, { "page": "drake_gc", "title": "Do garbage collection on the drake cache. *[Stable]*", "topics": [ "drake_gc" ] }, { "page": "drake_get_session_info", "title": "Session info of the last call to 'make()'. *[Stable]*", "topics": [ "drake_get_session_info" ] }, { "page": "drake_ggraph", "title": "Visualize the workflow with 'ggraph'/'ggplot2' *[Stable]*", "topics": [ "drake_ggraph" ] }, { "page": "drake_graph_info", "title": "Prepare the workflow graph for visualization *[Stable]*", "topics": [ "drake_graph_info" ] }, { "page": "drake_history", "title": "History and provenance *[Stable]*", "topics": [ "drake_history" ] }, { "page": "drake_hpc_template_file", "title": "Write a template file for deploying work to a cluster / job scheduler. *[Stable]*", "topics": [ "drake_hpc_template_file" ] }, { "page": "drake_hpc_template_files", "title": "List the available example template files for deploying work to a cluster / job scheduler. *[Stable]*", "topics": [ "drake_hpc_template_files" ] }, { "page": "drake_plan", "title": "Create a drake plan for the 'plan' argument of 'make()'. *[Stable]*", "topics": [ "drake_plan" ] }, { "page": "drake_plan_source", "title": "Show the code required to produce a given 'drake' plan *[Stable]*", "topics": [ "drake_plan_source" ] }, { "page": "drake_progress", "title": "Get the build progress of your targets *[Stable]*", "topics": [ "drake_progress" ] }, { "page": "drake_running", "title": "List running targets. *[Stable]*", "topics": [ "drake_running" ] }, { "page": "drake_script", "title": "Write an example _drake.R script to the current working directory.", "topics": [ "drake_script" ] }, { "page": "drake_slice", "title": "Take a strategic subset of a dataset. *[Stable]*", "topics": [ "drake_slice" ] }, { "page": "drake_tempfile", "title": "drake tempfile *[Stable]*", "topics": [ "drake_tempfile" ] }, { "page": "file_in", "title": "Declare input files and directories. *[Stable]*", "topics": [ "file_in" ] }, { "page": "file_out", "title": "Declare output files and directories. *[Stable]*", "topics": [ "file_out" ] }, { "page": "file_store", "title": "Show a file's encoded representation in the cache *[Stable]*", "topics": [ "file_store" ] }, { "page": "find_cache", "title": "Search up the file system for the nearest drake cache. *[Stable]*", "topics": [ "find_cache" ] }, { "page": "id_chr", "title": "Name of the current target *[Stable]*", "topics": [ "id_chr" ] }, { "page": "ignore", "title": "Ignore code *[Stable]*", "topics": [ "ignore" ] }, { "page": "knitr_in", "title": "Declare 'knitr'/'rmarkdown' source files as dependencies. *[Stable]*", "topics": [ "knitr_in" ] }, { "page": "legend_nodes", "title": "Create the nodes data frame used in the legend of the graph visualizations. *[Soft-deprecated]*", "topics": [ "legend_nodes" ] }, { "page": "load_mtcars_example", "title": "Load the mtcars example. *[Stable]*", "topics": [ "load_mtcars_example" ] }, { "page": "make", "title": "Run your project (build the outdated targets). *[Stable]*", "topics": [ "make" ] }, { "page": "missed", "title": "Report any import objects required by your drake_plan plan but missing from your workspace or file system. *[Stable]*", "topics": [ "missed" ] }, { "page": "new_cache", "title": "Make a new 'drake' cache. *[Stable]*", "topics": [ "new_cache" ] }, { "page": "no_deps", "title": "Suppress dependency detection. *[Stable]*", "topics": [ "no_deps" ] }, { "page": "outdated", "title": "List the targets that are out of date. *[Stable]*", "topics": [ "outdated" ] }, { "page": "plan_to_code", "title": "Turn a 'drake' plan into a plain R script file. *[Questioning]*", "topics": [ "plan_to_code" ] }, { "page": "plan_to_notebook", "title": "Turn a 'drake' plan into an R notebook. *[Questioning]*", "topics": [ "plan_to_notebook" ] }, { "page": "predict_runtime", "title": "Predict the elapsed runtime of the next call to 'make()' for non-staged parallel backends. *[Stable]*", "topics": [ "predict_runtime" ] }, { "page": "predict_workers", "title": "Predict the load balancing of the next call to 'make()' for non-staged parallel backends. *[Stable]*", "topics": [ "predict_workers" ] }, { "page": "r_make", "title": "Launch a drake function in a fresh new R process *[Stable]*", "topics": [ "r_deps_target", "r_drake_build", "r_drake_ggraph", "r_drake_graph_info", "r_make", "r_missed", "r_outdated", "r_predict_runtime", "r_predict_workers", "r_recoverable", "r_sankey_drake_graph", "r_text_drake_graph", "r_vis_drake_graph" ] }, { "page": "read_drake_seed", "title": "Read the pseudo-random number generator seed of the project. *[Stable]*", "topics": [ "read_drake_seed" ] }, { "page": "read_trace", "title": "Read a trace of a dynamic target. *[Stable]*", "topics": [ "read_trace" ] }, { "page": "readd", "title": "Read and return a drake target/import from the cache. *[Stable]*", "topics": [ "loadd", "readd" ] }, { "page": "recoverable", "title": "List the most upstream _recoverable_ outdated targets. *[Stable]*", "topics": [ "recoverable" ] }, { "page": "render_drake_ggraph", "title": "Visualize the workflow with 'ggplot2'/'ggraph' using 'drake_graph_info()' output. *[Stable]*", "topics": [ "render_drake_ggraph" ] }, { "page": "render_drake_graph", "title": "Render a visualization using the data frames generated by 'drake_graph_info()'. *[Stable]*", "topics": [ "render_drake_graph" ] }, { "page": "render_sankey_drake_graph", "title": "Render a Sankey diagram from 'drake_graph_info()'. *[Stable]*", "topics": [ "render_sankey_drake_graph" ] }, { "page": "render_text_drake_graph", "title": "Show a workflow graph as text in your terminal window using 'drake_graph_info()' output. *[Stable]*", "topics": [ "render_text_drake_graph" ] }, { "page": "rescue_cache", "title": "Try to repair a drake cache that is prone to throwing 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The 'epubr' package\nprovides functions supporting the reading and parsing of\ninternal e-book content from EPUB files. E-book metadata and\ntext content are parsed separately and joined together in a\ntidy, nested tibble data frame. E-book formatting is not\ncompletely standardized across all literature. It can be\nchallenging to curate parsed e-book content across an arbitrary\ncollection of e-books perfectly and in completely general form,\nto yield a singular, consistently formatted output. Many EPUB\nfiles do not even contain all the same pieces of information in\ntheir respective metadata. EPUB file parsing functionality in\nthis package is intended for relatively general application to\narbitrary EPUB e-books. However, poorly formatted e-books or\ne-books with highly uncommon formatting may not work with this\npackage. There may even be cases where an EPUB file has DRM or\nsome other property that makes it impossible to read with\n'epubr'. Text is read 'as is' for the most part. The only\nnominal changes are minor substitutions, for example curly\nquotes changed to straight quotes. Substantive changes are\nexpected to be performed subsequently by the user as part of\ntheir text analysis. Additional text cleaning can be performed\nat the user's discretion, such as with functions from packages\nlike 'tm' or 'qdap'.", "Authors@R": "person(\"Matthew\", \"Leonawicz\", email = \"rpkgs@pm.me\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-9452-2771\"))", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "ByteCompile": "true", "URL": "https://docs.ropensci.org/epubr/,\nhttps://github.com/ropensci/epubr", "BugReports": "https://github.com/ropensci/epubr/issues", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libicu-dev libxml2-dev libxslt-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2024-09-11 21:37:54 UTC", "RemoteUrl": "https://github.com/ropensci/epubr", "RemoteRef": "HEAD", "RemoteSha": "0d4097e9a3e87dd790c59230801356a0b8faf9da", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-29 08:08:57 UTC", "User": "root" }, "Author": "Matthew Leonawicz [aut, cre] (ORCID:\n)", "Maintainer": "Matthew 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This includes\ncreating a presentation that will contain all stimuli, renaming\nand concatenating multiple sound files recorded during a\nsession, automatic annotation in 'Praat' TextGrids (this is one\nof the sound annotation standards provided by 'Praat' software,\nsee Boersma & Weenink 2020\n), creating an html table\nwith annotations and spectrograms, and converting multiple\nformats ('Praat' TextGrid, 'ELAN', 'EXMARaLDA', 'Audacity',\nsubtitles '.srt', and 'FLEx' flextext). All of these tasks can\nbe solved by a mixture of different tools (any programming\nlanguage has programs for automatic renaming, and Praat\ncontains scripts for concatenating and renaming files, etc.).\n'phonfieldwork' provides a functionality that will make it\neasier to solve those tasks independently of any additional\ntools. You can also compare the functionality with other\npackages: 'rPraat' ,\n'textgRid' .", "License": "GPL (>= 2)", "SystemRequirements": "pandoc (>= 1.14) - http://pandoc.org", "URL": "https://CRAN.R-project.org/package=phonfieldwork,\nhttps://docs.ropensci.org/phonfieldwork/", "BugReports": "https://github.com/ropensci/phonfieldwork/issues", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Language": "en-US", "Config/pak/sysreqs": "cmake make libuv1-dev libxml2-dev libx11-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2024-07-29 17:18:30 UTC", "RemoteUrl": "https://github.com/ropensci/phonfieldwork", "RemoteRef": "HEAD", "RemoteSha": "9a5996a9e7112a7df905530b6abb65ac180cc43a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-29 08:15:30 UTC", "User": "root" }, "Author": "George Moroz [aut, cre] (ORCID:\n),\nJonathan Keane [rev] (ORCID: ),\nNiko Partanen [rev] (ORCID: ),\nValeria Buntiakova [ctb] (ORCID:\n)", "Maintainer": 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E. Pattis at Stanford\nUniversity in 1981. Karel is an useful tool to teach\nintroductory concepts about general programming, such as\nalgorithmic decomposition, conditional statements, loops, etc.,\nin an interactive and fun way, by writing programs to make\nKarel the robot achieve certain tasks in the world she lives\nin. Originally based on Pascal, Karel was implemented in many\nlanguages through these decades, including 'Java', 'C++',\n'Ruby' and 'Python'. 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The work loop\ntechnique is used to evaluate the mechanical work and power\noutput of muscle. Josephson (1985) \nmodernized the technique for application in comparative\nbiomechanics. Although our initial motivation was to provide\nfunctions to analyze work loop experiment data, as we developed\nthe package we incorporated the ability to analyze data from\nexperiments that are often complementary to work loops. There\nare currently three supported experiment types: work loops,\nsimple twitches, and tetanus trials. Data can be imported\ndirectly from .ddf files or via an object constructor function.\nThrough either method, data can then be cleaned or transformed\nvia methods typically used in studies of muscle physiology.\nData can then be analyzed to determine the timing and magnitude\nof force development and relaxation (for isometric trials) or\nthe magnitude of work, net power, and instantaneous power among\nother things (for work loops). 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"_exports": [ "calculate_deltacq_bysampleid", "calculate_deltadeltacq_bytargetid", "calculate_drdt_plate", "calculate_dydx", "calculate_efficiency", "calculate_efficiency_bytargetid", "calculate_normvalue", "create_blank_plate", "create_blank_plate_1536well", "create_blank_plate_96well", "create_colkey_4diln_2ctrl_in_24", "create_colkey_6_in_24", "create_colkey_6diln_2ctrl_in_24", "create_rowkey_4_in_16", "create_rowkey_8_in_16_plain", "debaseline", "display_plate", "display_plate_qpcr", "display_plate_value", "label_plate_rowcol", "make_row_names_echo1536", "make_row_names_lc1536", "read_lightcycler_1colour_cq", "read_lightcycler_1colour_raw" ], "_help": [ { "page": "calculate_deltacq_bysampleid", "title": "Calculate delta cq (Delta Cq) to normalize quantification cycle (log2-fold) data within sample_id.", "topics": [ "calculate_deltacq_bysampleid" ] }, { "page": "calculate_deltadeltacq_bytargetid", "title": "Calculate delta delta cq (Delta Delta Cq) to globally normalize quantification cycle (log2-fold) data across sample_id.", "topics": [ "calculate_deltadeltacq_bytargetid" ] }, { "page": "calculate_drdt_plate", "title": "Calculate dR/dT of melt curves for of every well in a plate.", "concept": [ "melt_curve_functions" ], "topics": [ "calculate_drdt_plate" ] }, { "page": "calculate_dydx", "title": "Calculate dy/dx vector from vectors y and x", "concept": [ "melt_curve_functions" ], "topics": [ "calculate_dydx" ] }, { "page": "calculate_efficiency", "title": "Calibrate primer sets / probes by calculating detection efficiency and R squared", "topics": [ "calculate_efficiency" ] }, { "page": "calculate_efficiency_bytargetid", "title": "Calibrate multiple probes by calculating detection efficiency and R squared", "topics": [ "calculate_efficiency_bytargetid" ] }, { "page": "calculate_normvalue", "title": "Calculate a normalized value for a subset of reference ids", "topics": [ "calculate_normvalue" ] }, { "page": "create_blank_plate", "title": "Create a blank plate template as a tibble (with helper functions for common plate sizes)", "concept": [ "plate creation functions" ], "topics": [ "create_blank_plate", "create_blank_plate_1536well", "create_blank_plate_96well" ] }, { "page": "create_colkey_4diln_2ctrl_in_24", "title": "Create a 4-dilution column key for primer calibration", "concept": [ "plate creation functions" ], "topics": [ "create_colkey_4diln_2ctrl_in_24" ] }, { "page": "create_colkey_6_in_24", "title": "Create a 6-value, 24-column key for plates", "concept": [ "plate creation functions" ], "topics": [ "create_colkey_6_in_24" ] }, { "page": "create_colkey_6diln_2ctrl_in_24", "title": "Create a 6-dilution column key for primer calibration", "concept": [ "plate creation functions" ], "topics": [ "create_colkey_6diln_2ctrl_in_24" ] }, { "page": "create_rowkey_4_in_16", "title": "Create a 4-value, 16-row key for plates", "concept": [ "plate creation functions" ], "topics": [ "create_rowkey_4_in_16" ] }, { "page": "create_rowkey_8_in_16_plain", "title": "Create a plain 8-value, 16-row key for plates", "concept": [ "plate creation functions" ], "topics": [ "create_rowkey_8_in_16_plain" ] }, { "page": "debaseline", "title": "Remove baseline from amplification curves (BETA)", "topics": [ "debaseline" ] }, { "page": "display_plate", "title": "Display an empty plate plan which can be populated with ggplot2 geom elements.", "concept": [ "plate creation functions" ], "topics": [ "display_plate" ] }, { "page": "display_plate_qpcr", "title": "Display qPCR plate plan with sample_id, target_id, prep_type per well", "concept": [ "plate creation functions" ], "topics": [ "display_plate_qpcr" ] }, { "page": "display_plate_value", "title": "Display the value of each well across the plate.", "concept": [ "plate creation functions" ], "topics": [ "display_plate_value" ] }, { "page": "label_plate_rowcol", "title": "Label a plate with sample and probe information", "concept": [ "plate creation functions" ], 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combination", "Plot delta Cq for each OD separately across genes", "Plot relative abundance for each OD separately across genes", "Plot relative abundance for each gene separately across ODs", "Doubly normalized data: delta delta Cq", "Calculate delta delta cq against a chosen reference sample", "Plot delta delta Cq (log2-fold change) for each target gene", "Plot fold change for each target gene", "Conclusion", "Notes on normalization, reference targets, and reference samples" ], "created": "2020-09-04 09:08:41", "modified": "2022-06-08 12:31:06", "commits": 11 }, { "source": "platesetup_vignette.Rmd", "filename": "platesetup_vignette.html", "title": "Introduction to designing an experiment and setting up a plate plan in tidyqpcr", "author": "Edward Wallace", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Setup knitr options and load packages", "Essential information: target_id, sample_id, prep_type", "Using rows and columns to make life easier", "A Minimal 48-well plate 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"Load and summarize data", "Plot unnormalized data", "-RT controls are low", "Normalize Cq to PGK1, within Sample only", "Plot normalized data, all reps", "Plot normalized data, summarized vs target_id", "All on same axes", "Faceted by drug treatment", "Faceted by heat shock condition", "Melt and Amplification Curves", "Melt Curves, biol_rep 1", "Melt Curves, biol_rep 2", "Amp Curves, biol_rep 1" ], "created": "2019-09-25 21:54:43", "modified": "2022-06-08 12:31:06", "commits": 19 }, { "source": "calibration_vignette.Rmd", "filename": "calibration_vignette.html", "title": "Primers and probes calibration vignette", "author": "Edward Wallace", "engine": "knitr::rmarkdown", "headings": [ "Summary: calibrating primer sets from a real experimental test", "Setup knitr options and load packages", "Set up experiment", "Describe which primer set we put in which well using a row key", "Combine the row key describing primer sets with column key describing on samples and dilutions.", "Spot-check 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"Package": "birdsize", "Title": "Estimate Avian Body Size Distributions", "Version": "0.0.0.9000", "Date": "2023-02-27", "Authors@R": "c(\nperson(\"Renata\", \"Diaz\", , \"renata.diaz@weecology.org\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0803-4734\")),\nperson(\"John\", \"Dunning\", role = \"dtc\")\n)", "Description": "Generate estimated body size distributions for populations\nor communities of birds, given either species ID or species'\nmean body size. Designed to work naturally with the North\nAmerican Breeding Bird Survey, or with any dataset of bird\nspecies, abundance, and/or mean size data.", "License": "MIT + file LICENSE", "URL": "https://github.com/diazrenata/birdsize", "BugReports": "https://github.com/diazrenata/birdsize/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2023-12-08 19:24:29 UTC", "RemoteUrl": "https://github.com/ropensci/birdsize", "RemoteRef": "HEAD", "RemoteSha": "78d7840018d750a5917547e71843da953a3a89cb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-29 08:02:14 UTC", "User": "root" }, "Author": "Renata Diaz [aut, cre] (ORCID: ),\nJohn Dunning [dtc]", "Maintainer": "Renata Diaz ", "_user": "ropensci", "_type": "src", "_file": "birdsize_0.0.0.9000.tar.gz", "_fileid": "https://r2.ropensci.org/4b9106c2e96e8820eafe582ca506b4752fa976d8a8deddd12e5dc193d09ff0a6", "_filesize": 720179, "_sha256": "4b9106c2e96e8820eafe582ca506b4752fa976d8a8deddd12e5dc193d09ff0a6", "_expires": "2027-02-06T08:05:19.000Z", "_created": "2026-10-29T08:02:14.000Z", "_published": "2026-10-29T08:05:21.611Z", "_upstream": "https://github.com/ropensci/birdsize", "_status": "success", "_maintainer": { "name": "Renata Diaz", "email": "renata.diaz@weecology.org", "login": "diazrenata", "mastodon": "@diaz_renm@ecoevo.social", "orcid": "0000-0003-0803-4734", "description": "Data engineer @ebird; previously @cct-datascience, @ecoevomatics, and @weecology. 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}, { "r": "4.6.1", "os": "win", "version": "1.0.8", "date": "2026-10-29T08:11:04.000Z", "commit": "b2d05a3a89120e15c0a0bea635ec1884adacb17d", "fileid": "https://r2.ropensci.org/33f45e118542ee95de4150db7d725045b1b5c4e663ee03a09d635e6016ac3b8a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40839782985" } ] }, { "Package": "chlorpromazineR", "Title": "Convert Antipsychotic Doses to Chlorpromazine Equivalents", "Version": "0.2.0", "Authors@R": "c(person(\"Eric\", \"Brown\",\nrole = c(\"aut\", \"cre\"),\nemail = \"eb@ericebrown.com\",\ncomment = c(ORCID = \"0000-0002-1575-2606\")),\nperson(\"Parita\", \"Shah\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-7302-0411\")),\nperson(\"Julia\", \"Kim\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-0379-1333\")),\nperson(\"Frederick\", \"Boehm\",\nrole = \"rev\",\ncomment = c(ORCID = \"0000-0002-1644-5931\")))", "Description": "As different antipsychotic medications have different\npotencies, the doses of different medications cannot be\ndirectly compared. Various strategies are used to convert doses\ninto a common reference so that comparison is meaningful.\nChlorpromazine (CPZ) has historically been used as a reference\nmedication into which other antipsychotic doses can be\nconverted, as \"chlorpromazine-equivalent doses\". Using\nconversion keys generated from widely-cited scientific papers,\ne.g. Gardner et. al 2010 \nand Leucht et al. 2016 ,\nantipsychotic doses are converted to CPZ (or any specified\nantipsychotic) equivalents. The use of the package is described\nin the included vignette. 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