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package for ROpenSci\"))", "Description": "Provides functions for fitting various penalized\nparametric and semi-parametric mixture cure models with\ndifferent penalty functions, testing for a significant cure\nfraction, and testing for sufficient follow-up as described in\nFu et al (2022) and Archer et al\n(2024). 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Downloads lake boundaries\nfrom 'OpenStreetMap', calculates directional fetch using a\nray-casting approach, and optionally integrates National\nHydrography Dataset ('NHD') data\n for hydrological\ncontext including outlet and inlet locations. Can estimate lake\ndepth from surface area using empirical relationships, and\nintegrate historical weather data for cumulative wave energy\ncalculations. Includes an optional interactive 'shiny'\napplication for visualization.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "URL": "https://github.com/jeremylfarrell/lakefetch", "BugReports": "https://github.com/jeremylfarrell/lakefetch/issues", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibxml2-dev libssl-dev libproj-dev libsqlite3-dev\nlibudunits2-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-07-13 01:21:32 UTC", "RemoteUrl": "https://github.com/ropensci/lakefetch", "RemoteRef": "main", "RemoteSha": "afff7e845fcbc6febf41112268e5ab76e553ab66", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-21 04:58:31 UTC", "User": "root" }, "Author": "Jeremy Lynch Farrell [aut, cre]", "Maintainer": "Jeremy Lynch Farrell ", "_user": "ropensci", "_type": "src", "_file": "lakefetch_0.1.3.tar.gz", "_fileid": "https://r2.ropensci.org/556e61f933aaa8ea0315103fbcda8af5a99f874e144a9d6efaf63e276ab4f350", "_filesize": 256639, "_sha256": "556e61f933aaa8ea0315103fbcda8af5a99f874e144a9d6efaf63e276ab4f350", "_expires": "2026-10-29T05:57:18.000Z", "_created": "2026-07-21T04:58:31.000Z", "_published": "2026-07-21T05:57:20.493Z", "_jobs": [ { "job": 88546724296, "time": 225, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8484360323" }, { "job": 88546724323, "time": 224, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8484360414" }, { "job": 88546724303, "time": 149, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8484339247" }, { "job": 88546724297, "time": 145, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8484337953" }, { "job": 88546264019, "time": 3697, "config": "pkgdown", "r": "", "check": "ERROR", "artifact": "" }, { "job": 88546263998, "time": 211, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8484299219" }, { "job": 88546724306, "time": 159, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8484341737" }, { "job": 88546724311, "time": 178, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8484347987" }, { "job": 88546724317, "time": 135, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8484334876" }, { "job": 88546724340, "time": 123, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8484331952" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/29802526209", "_status": "success", "_upstream": "https://github.com/ropensci/lakefetch", "_commit": { "id": "afff7e845fcbc6febf41112268e5ab76e553ab66", "author": "Farrell ", "committer": "Farrell ", "message": "Fix stale sample_sites.csv (Blue Mountain Lake, not Lake George)\n\nBackport the corrected sample_sites.csv from the ropensci-software-review\nbranch. The version on main placed both sites near Lake George (43.419,\n-73.698 / 43.416, -73.693) rather than on Blue Mountain Lake, which broke\ndownstream examples: fetch_calculate() returned NAs, the pkgdown site\ndemonstrated the wrong location, and the fetch_app_upload Shiny app\ndisplayed points on the wrong lake (see lakefetch#3).\n\nThis is a targeted cherry-pick of just the input data file. The full\nrOpenSci review response (v0.1.4-v0.1.10 on ropensci-software-review)\nwill be merged to main after the review is formally approved.\n\nCo-Authored-By: Claude Opus 4.7 \n", "time": 1783905692 }, "_maintainer": { "name": "Jeremy Lynch Farrell", "email": "farrej2@rpi.edu" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "sf", "version": ">= 1.0-0", "role": "Imports" }, { "package": "osmdata", "version": ">= 0.2.0", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.0.0", "role": "Imports" }, { "package": "nhdplusTools", "role": "Suggests" }, { "package": "jsonlite", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" }, { "package": "leaflet", "role": "Suggests" }, { "package": "base64enc", "role": "Suggests" }, { "package": "parallel", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": 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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. 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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": "2026-07-01 08:17:17 UTC", "User": "root" }, "Author": "R. 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\"ctb\"),\ncomment = c(ORCID = \"0000-0003-4055-0835\")),\nperson(\"Taras\", \"Kaduk\", , \"taras.kaduk@gmail.com\", role = \"ctb\",\ncomment = \"Suggestion for handling bulk station downloads more\\n efficiently\"),\nperson(\"Gwenael\", \"Giboire\", , \"gwenael.giboire@oda-groupe.com\", role = \"ctb\",\ncomment = \"Several bug reports in early versions and testing feedback\"),\nperson(\"Łukasz\", \"Pawlik\", , \"lukpawlik@gmail.com\", role = \"ctb\",\ncomment = \"Reported bug in windspeed conversion calculation\"),\nperson(\"Ross\", \"Darnell\", , \"Ross.Darnell@data61.csiro.au\", role = \"ctb\",\ncomment = c(\"Reported bug in 'Windows OS' versions causing 'GSOD' data untarring to\\n fail\", ORCID = \"0000-0002-7973-6322\")),\nperson(\"Tyler\", \"Widdison\", , \"Tyler.Widdison@usav.org\", role = \"ctb\",\ncomment = \"Reported bug where\\n `nearest_stations()` did not return stations in order of nearest to\\n farthest\"),\nperson(\"Wenbo\", \"Lv\", , \"lyu.geosocial@gmail.com\", role = \"ctb\",\ncomment = \"Provided suggestions for improving documentation\"),\nperson(\"Curtin University\", role = c(\"fnd\", \"cph\"),\ncomment = c(url = \"http://www.curtin.edu.au/\", ROR = \"02n415q13\"))\n)", "Description": "Provides automated downloading, parsing, cleaning, unit\nconversion and formatting of Global Surface Summary of the Day\n('GSOD') weather data from the from the USA National Centers\nfor Environmental Information ('NCEI'). The data were retired\non 2025-08-29 and are no longer updated. Units are converted\nfrom from United States Customary System ('USCS') units to\nInternational System of Units ('SI'). Stations may be\nindividually checked for number of missing days defined by the\nuser, where stations with too many missing observations are\nomitted. Only stations with valid reported latitude and\nlongitude values are permitted in the final data. Additional\nuseful elements, saturation vapour pressure ('es'), actual\nvapour pressure ('ea') and relative humidity ('RH') are\ncalculated from the original data using the improved\nAugust-Roche-Magnus approximation (Alduchov & Eskridge 1996)\nand included in the final data set. The resulting metadata\ninclude station identification information, country, state,\nlatitude, longitude, elevation, weather observations and\nassociated flags. For information on the 'GSOD' data from\n'NCEI', please see the 'GSOD' 'readme.txt' file available from,\n.", "License": "MIT + file LICENSE", "URL": "https://docs.ropensci.org/GSODR/,\nhttps://codeberg.org/ropensci/GSODR", "BugReports": "https://codeberg.org/ropensci/GSODR/issues", "VignetteBuilder": "knitr", "ByteCompile": "TRUE", "Config/Needs/build": "maelle/devtag2", "Config/roxygen2/version": "8.0.0", "Config/roxyglobals/filename": "globals.R", "Config/roxyglobals/unique": "FALSE", "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\", \"roxyglobals::global_roclet\", \"roxylint::roxylint\",\n\"devtag2::super_rd\"))", "Config/pak/sysreqs": "libssl-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-05-17 05:56:10 UTC", "RemoteUrl": "https://github.com/ropensci/GSODR", "RemoteRef": "main", "RemoteSha": "40d9d454757c6bf28a26a612904dd09b54be2a0a", "Packaged": { "Date": "2026-07-01 08:27:04 UTC", "User": "root" }, "Author": "Adam H. Sparks [aut, cre] (ORCID:\n),\nTomislav Hengl [aut] (ORCID: ),\nAndrew Nelson [aut] (ORCID: ),\nHugh Parsonage [cph, ctb] (ORCID:\n),\nTaras Kaduk [ctb] (Suggestion for handling bulk station downloads more\nefficiently),\nGwenael Giboire [ctb] (Several bug reports in early versions and\ntesting feedback),\nŁukasz Pawlik [ctb] (Reported bug in windspeed conversion calculation),\nRoss Darnell [ctb] (Reported bug in 'Windows OS' versions causing\n'GSOD' data untarring to fail, ORCID:\n),\nTyler Widdison [ctb] (Reported bug where `nearest_stations()` did not\nreturn stations in order of nearest to farthest),\nWenbo Lv [ctb] (Provided suggestions for improving documentation),\nCurtin University [fnd, cph] (url: http://www.curtin.edu.au/, ROR:\n)", "Maintainer": "Adam H. 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"Title": "Recodes Sex/Gender Descriptions into a Standard Set", "Version": "0.1.1", "Authors@R": "c(\nperson(\"Yaoxiang\", \"Li\", role = c(\"aut\", \"cre\"),\nemail = \"liyaoxiang@outlook.com\",\ncomment = c(ORCID = \"0000-0001-9200-1016\")),\nperson(\"Jennifer\", \"Beaudry\", role = \"aut\",\nemail = \"jbeaudry@swin.edu.au\",\ncomment = c(ORCID = \"0000-0003-1596-6708\")),\nperson(\"Emily\", \"Kothe\", role = \"aut\",\nemail = \"emily.kothe@deakin.edu.au\",\ncomment = c(ORCID = \"0000-0003-1210-0554\")),\nperson(\"Felix\", \"Singleton Thorn\", role = \"aut\",\nemail = \"fsingletonthorn@gmail.com\",\ncomment = c(ORCID = \"0000-0002-0237-6146\")),\nperson(\"Rhydwyn\", \"McGuire\", role = \"aut\",\nemail = \"rhydwyn@rhydwyn.net\"),\nperson(\"Nicholas\", \"Tierney\",\nrole = \"aut\",\nemail = \"nicholas.tierney@gmail.com\",\ncomment = c(ORCID = \"0000-0003-1460-8722\")),\nperson(\"Mathew\", \"Ling\",\nrole = \"aut\",\nemail = \"mathewtyling@gmail.com\",\ncomment = c(ORCID = 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"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", 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(2019) ). It\ncan be used to convert GPS relocations to gambit-of-the-group\nformat to build proximity-based social networks, and perform\ndata-stream randomization methods suitable for GPS data. 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role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-6378-6229\", affiliation = \"Research Institute for Nature and Forest (INBO)\")),\nperson(\"Peter\", \"Desmet\", , \"peter.desmet@inbo.be\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-8442-8025\", affiliation = \"Research Institute for Nature and Forest (INBO)\")),\nperson(\"Els\", \"Lommelen\", , \"els.lommelen@inbo.be\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-3481-5684\", affiliation = \"Research Institute for Nature and Forest (INBO)\")),\nperson(\"Research Institute for Nature and Forest (INBO)\", , , \"info@inbo.be\", role = c(\"cph\", \"fnd\"),\ncomment = c(ROR = \"00j54wy13\"))\n)", "Description": "The git2rdata package is an R package for writing and\nreading dataframes as plain text files. A metadata file stores\nimportant information. 1) Storing metadata allows to maintain\nthe classes of variables. By default, git2rdata optimizes the\ndata for file storage. The optimization is most effective on\ndata containing factors. The optimization makes the data less\nhuman readable. The user can turn this off when they prefer a\nhuman readable format over smaller files. Details on the\nimplementation are available in vignette(\"plain_text\", package\n= \"git2rdata\"). 2) Storing metadata also allows smaller row\nbased diffs between two consecutive commits. This is a useful\nfeature when storing data as plain text files under version\ncontrol. Details on this part of the implementation are\navailable in vignette(\"version_control\", package =\n\"git2rdata\"). 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/6160d557081fde3af3056b0a53f892bbdc046156dec6be03637d5fb68ef1fd0d", "_filesize": 1301205, "_sha256": "6160d557081fde3af3056b0a53f892bbdc046156dec6be03637d5fb68ef1fd0d", "_expires": "2026-10-09T08:19:40.000Z", "_created": "2026-07-01T08:14:38.000Z", "_published": "2026-07-01T08:19:41.375Z", "_jobs": [ { "job": 84486121730, "time": 184, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8004060200" }, { "job": 84486121732, "time": 148, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8004048143" }, { "job": 84486121778, "time": 98, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8004030296" }, { "job": 84486121729, "time": 78, "config": 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\"ctb\",\ncomment = c(ORCID = \"0000-0002-1896-4516\", \"Contributed code and ideas for original bomrang package that was used in the creation of weatherOz.\")),\nperson(\"Maëlle\", \"Salmon\", email = \"maelle.salmon@yahoo.se\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-2815-0399\", \"Contributed to debugging a nasty little bug with CI where timezones caused tests to fail due to vcr not recognising the URL when run outside of Australia-Perth TZ! 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. BOM data are\n(c) Australian Government Bureau of Meteorology and released\nunder a Creative Commons (CC) Attribution 3.0 licence or Public\nAccess Licence (PAL) as appropriate, see\n for further details.", "License": "GPL (>= 3)", "URL": "https://github.com/ropensci/weatherOz/,\nhttps://docs.ropensci.org/weatherOz/", "BugReports": "https://github.com/ropensci/weatherOz/issues", "VignetteBuilder": "knitr", "Config/roxyglobals/filename": "globals.R", "Config/roxyglobals/unique": "FALSE", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "true", "Roxygen": "list(markdown = TRUE, roclets = c(\"collate\", \"namespace\",\n\"rd\", \"roxyglobals::global_roclet\"))", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibmagick++-dev gsfonts libxml2-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-04-08 01:07:53 UTC", "RemoteUrl": "https://github.com/ropensci/weatherOz", "RemoteRef": "main", "RemoteSha": "0d0df1d67f149d21980970fe781d7085c99d20ac", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-01 08:19:47 UTC", "User": "root" }, "Author": "Rodrigo Pires [aut, cre] (ORCID:\n),\nAnna Hepworth [aut] (ORCID: ),\nRebecca O'Leary [aut],\nJonathan Carroll [aut] (ORCID: ),\nJames Goldie [aut] (ORCID: ),\nDean Marchiori [aut] (ORCID: ),\nPaul Melloy [aut] (ORCID: ),\nMark Padgham [aut] (ORCID: ),\nHugh Parsonage [aut] (ORCID: ),\nKeith Pembleton [ctb] (ORCID: ,\nContributed code and ideas for original bomrang package that was\nused in the creation of weatherOz.),\nMaëlle Salmon [ctb] (ORCID: ,\nContributed to debugging a nasty little bug with CI where timezones\ncaused tests to fail due to vcr not recognising the URL when run\noutside of Australia-Perth TZ! 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. Sparks [aut] (ORCID: ),\nLaurens Geffert [rev],\nSam Rogers [rev],\nWestern Australia Agriculture Authority (WAAA) [cph],\nCurtin University [cph]", "Maintainer": "Rodrigo Pires ", "_user": "ropensci", "_type": "src", "_file": "weatherOz_3.0.0.tar.gz", "_fileid": "https://r2.ropensci.org/5ff31aafadb0aab5666ad3823a4f1486a490bae706f9c9400396ae2161fe6096", "_filesize": 3968017, "_sha256": "5ff31aafadb0aab5666ad3823a4f1486a490bae706f9c9400396ae2161fe6096", "_expires": "2026-10-09T08:43:02.000Z", "_created": "2026-07-01T08:19:47.000Z", "_published": "2026-07-01T08:43:03.264Z", "_jobs": [ { "job": 84487074103, "time": 277, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8004247700" }, { "job": 84487074150, "time": 279, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8004248263" }, { "job": 84487074092, "time": 183, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8004607209" }, { "job": 84487074065, "time": 208, 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"page": "find_nearby_stations", "title": "Find the Nearest Weather Stations to a Given Geographic Point or Known Station", "concept": [ "DPIRD", "SILO", "metadata" ], "topics": [ "find_nearby_stations" ] }, { "page": "find_stations_in", "title": "Find Stations Within a Geospatially Defined Geographic Area of Interest", "concept": [ "DPIRD", "SILO", "metadata" ], "topics": [ "find_stations_in" ] }, { "page": "get_available_imagery", "title": "Get a List of Available BOM Satellite Imagery", "concept": [ "BOM", "metadata" ], "topics": [ "get_available_imagery" ] }, { "page": "get_available_radar", "title": "Get a List of Available BOM Radar Imagery", "concept": [ "BOM", "metadata" ], "topics": [ "get_available_radar" ] }, { "page": "get_coastal_forecast", "title": "Get a BOM Coastal Waters Forecast", "concept": [ "BOM", "data fetching" ], "topics": [ "get_coastal_forecast" ] }, { "page": "get_data_drill", "title": "Get DataDrill Weather Data From SILO", "concept": [ "SILO", "data fetching" ], "topics": [ "get_data_drill" ] }, { "page": "get_data_drill_apsim", "title": "Get DataDrill Weather Data in the APSIM Format From SILO", "concept": [ "APSIM", "SILO", "data fetching" ], "topics": [ "get_data_drill_apsim" ] }, { "page": "get_dpird_apsim", "title": "Get DPIRD Summary Weather Data in the APSIM Format From the Weather 2.0 API", "concept": [ "APSIM", "DPIRD", "data fetching" ], "topics": [ "get_dpird_apsim" ] }, { "page": "get_dpird_availability", "title": "Get the Availability for DPIRD Weather Stations", "concept": [ "DPIRD", "metadata" ], "topics": [ "get_dpird_availability" ] }, { "page": "get_dpird_extremes", "title": "Get DPIRD Extreme Weather Event Summaries", "concept": [ "DPIRD", "data fetching" ], "topics": [ "get_dpird_extremes" ] }, { "page": "get_dpird_minute", "title": "Get DPIRD Weather Data by the Minute", "concept": [ "DPIRD", "data fetching" ], "topics": [ "get_dpird_minute" ] }, { "page": "get_dpird_summaries", "title": "Get DPIRD Weather Data in Summarised Formats", "concept": [ "DPIRD", "data fetching" ], "topics": [ "get_dpird_summaries" ] }, { "page": "get_key", "title": "Get or Set Up API Keys", "topics": [ "get_key" ] }, { "page": "get_metno_daily_forecast", "title": "Get Daily Weather Forecast Data from MET Weather API", "concept": [ "METNO", "data fetching" ], "topics": [ "get_metno_daily_forecast" ] }, { "page": "get_metno_forecast", "title": "Get Weather Forecast Data from MET Weather API", "concept": [ "METNO", "data fetching" ], "topics": [ "get_metno_forecast" ] }, { "page": "get_patched_point", "title": "Get PatchedPoint Weather Data From SILO", "concept": [ "SILO", "data fetching" ], "topics": [ "get_patched_point" ] }, { "page": "get_patched_point_apsim", "title": "Get PatchedPoint Weather Data in the APSIM Format From SILO", "concept": [ "APSIM", "SILO", "data fetching" ], "topics": [ "get_patched_point_apsim" ] }, { "page": "get_precis_forecast", "title": "Get a BOM Daily Précis Forecast", "concept": [ "BOM", "data fetching" ], "topics": [ "get_precis_forecast" ] }, { "page": "get_radar_imagery", "title": "Get BOM Radar Imagery", "concept": [ "BOM", "data fetching" ], "topics": [ "get_radar_imagery" ] }, { "page": "get_satellite_imagery", "title": "Get BOM Satellite Imagery", "concept": [ "BOM", "data fetching" ], "topics": [ "get_satellite_imagery" ] }, { "page": "get_stations_metadata", "title": "Get Weather Station Metadata for Both DPIRD and SILO Weather Stations", "concept": [ "DPIRD", "SILO", "metadata" ], "topics": [ "get_stations_metadata" ] }, { "page": "parse_coastal_forecast", "title": "Parse BOM Coastal Waters Forecast XML Files", "concept": [ "BOM", "parse" ], "topics": [ "parse_coastal_forecast" ] }, { "page": "parse_precis_forecast", "title": "Parse BOM Précis Forecast XML Files", "concept": [ "BOM", "parse" ], "topics": [ "parse_precis_forecast" ] }, { "page": "silo_daily_values", "title": "A List of SILO Daily Weather Values", "concept": [ "SILO", "data" ], "topics": [ "silo_daily_values" ] }, { "page": "south_west_agriculture_region", "title": "Western Australia Southwest Agriculture Region Geospatial Polygon", "topics": [ "south_west_agricultural_region", "south_west_agriculture_region" ] } ], "_pkglogo": "https://github.com/ropensci/weatherOz/raw/main/man/figures/logo.png", "_readme": "https://github.com/ropensci/weatherOz/raw/main/README.md", "_rundeps": [ "abind", "apsimx", "bit", "bit64", "blob", "cachem", "class", "classInt", "cli", "clock", "cpp11", "crayon", "crul", "curl", "data.table", "DBI", "e1071", "evaluate", "fastmap", "foreign", "generics", "glue", "highr", "httpcode", "jsonlite", "KernSmooth", "knitr", "lifecycle", "lubridate", "magick", "magrittr", "MASS", "memoise", "mime", "pkgconfig", "proxy", "R6", "Rcpp", "rlang", "RSQLite", "s2", "sf", "stars", "terra", "timechange", "triebeard", "tzdb", "units", "urltools", "vctrs", "wk", "xfun", "xml2", "yaml" ], "_vignettes": [ { "source": "weatherOz.Rmd", "filename": "weatherOz.html", "title": "weatherOz", "author": "Rodrigo Pires, Anna Hepworth, Rebecca O'Leary, Jonathan Carroll, Dean Marchiori, Paul Melloy, Mark Padgham, Hugh Parsonage, Keith Pembleton and 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)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "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": "2026-04-03 12:01:51 UTC", "RemoteUrl": "https://github.com/ropensci/chopin", "RemoteRef": "main", "RemoteSha": "352b79f9a7d132f053db106ec064e5145fae4d8d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-01 08:19:12 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_0.9.9-5.tar.gz", "_fileid": "https://r2.ropensci.org/8fa8d7682fbeedc25f47d4cc59df9c1869c976b77b73b414263306a4ac33ffee", "_filesize": 5079847, "_sha256": "8fa8d7682fbeedc25f47d4cc59df9c1869c976b77b73b414263306a4ac33ffee", "_expires": "2026-10-09T08:44:02.000Z", "_created": "2026-07-01T08:19:12.000Z", "_published": "2026-07-01T08:44:02.735Z", "_jobs": [ { "job": 84487092064, "time": 310, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8004263762" }, { "job": 84487092047, "time": 287, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8004254114" }, { "job": 84487092048, "time": 298, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8004583574" }, { "job": 84487092036, "time": 240, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": 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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) .", "Author": "Marc Burri [aut, cre, cph] (ORCID:\n), Philipp Wegmueller\n[aut, cph]", "Maintainer": "Marc Burri ", "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": "2026-04-01 08:08:26 UTC", "RemoteUrl": "https://github.com/ropensci/reviser", "RemoteRef": "main", "RemoteSha": "3b9f065cb095183e6b9e32fd9aba71e3eae7e6e5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-01 08:28:09 UTC", "User": "root" }, "_user": 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Enables access to the UK's official road safety\nstatistics, 'STATS19'. Enables users to specify a download\ndirectory for the data, which can be set permanently by adding\n`STATS19_DOWNLOAD_DIRECTORY=/path/to/a/dir` to your `.Renviron`\nfile, which can be opened with `usethis::edit_r_environ()`. The\ndata is provided as a series of `.csv` files. This package\ndownloads, reads-in and formats the data, making it suitable\nfor analysis. See the stats19 vignette for details. Data\navailable from 1979 to 2024. See the official data series at\n.\nThe package is described in a paper in the Journal of Open\nSource Software (Lovelace et al. 2019)\n. See Gilardi et al. (2022)\n, Vidal-Tortosa et al. (2021)\n, Tait et al. (2023)\n, and León et al. 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https://github.com/richelbilderbeek/onboarding/issues/209\"),\nperson(\"David\", \"Winter\", role = \"rev\", comment = \"David reviewed the package for rOpenSci, see https://github.com/richelbilderbeek/onboarding/issues/209\"),\nperson(\"Jason\", \"Griffiths\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1667-8233\")),\nperson(\"Olivier\", \"Roy\", role = \"ctb\"),\nperson(\"Tanmay\", \"Dimri\", role = \"ctb\"),\nperson(\"Giovanni\", \"Laudanno\", email = \"glaudanno@gmail.com\", role = \"ctb\"))", "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 commonly accompanied by\n'BEAUti 2', 'Tracer' and 'DensiTree'. 'babette' provides for an\nalternative workflow of using all these tools separately. 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"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", 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tree, etc.", "topics": [ "diff.git_repository", "diff.git_tree" ] }, { "page": "discover_repository", "title": "Find path to repository for any file", "topics": [ "discover_repository" ] }, { "page": "fetch", "title": "Fetch new data and update tips", "topics": [ "fetch" ] }, { "page": "fetch_heads", "title": "Get updated heads during the last fetch.", "topics": [ "fetch_heads" ] }, { "page": "git_config_files", "title": "Locate the path to configuration files", "topics": [ "git_config_files" ] }, { "page": "git_time", "title": "Time", "topics": [ "as.character.git_time", "as.POSIXct.git_time", "format.git_time", "git_time", "print.git_time" ] }, { "page": "git2r", "title": "git2r: R bindings to the libgit2 library", "topics": [ "git2r-package", "git2r" ] }, { "page": "hash", "title": "Determine the sha from a blob string", "topics": [ "hash" ] }, { "page": "hashfile", "title": "Determine the sha from a blob in a file", "topics": [ "hashfile" ] }, { "page": "head.git_repository", "title": "Get HEAD for a repository", "topics": [ "head.git_repository" ] }, { "page": "in_repository", "title": "Determine if a directory is in a git repository", "topics": [ "in_repository" ] }, { "page": "index_remove_bypath", "title": "Remove an index entry corresponding to a file on disk", "topics": [ "index_remove_bypath" ] }, { "page": "init", "title": "Init a repository", "topics": [ "init" ] }, { "page": "is_bare", "title": "Check if repository is bare", "topics": [ "is_bare" ] }, { "page": "is_binary", "title": "Is blob binary", "topics": [ "is_binary" ] }, { "page": "is_blob", "title": "Check if object is S3 class git_blob", "topics": [ "is_blob" ] }, { "page": "is_branch", "title": "Check if object is 'git_branch'", "topics": [ "is_branch" ] }, { "page": "is_commit", "title": "Check if object is a git_commit object", "topics": [ "is_commit" ] }, { "page": "is_detached", "title": "Check if HEAD of repository is detached", "topics": [ "is_detached" ] }, { "page": "is_empty", "title": "Check if repository is empty", "topics": [ "is_empty" ] }, { "page": "is_head", "title": "Check if branch is head", "topics": [ "is_head" ] }, { "page": "is_local", "title": "Check if branch is local", "topics": [ "is_local" ] }, { "page": "is_merge", "title": "Is merge", "topics": [ "is_merge" ] }, { "page": "is_shallow", "title": "Determine if the repository is a shallow clone", "topics": [ "is_shallow" ] }, { "page": "is_tag", "title": "Check if object is a git_tag object", "topics": [ "is_tag" ] }, { "page": "is_tree", "title": "Check if object is S3 class git_tree", "topics": [ "is_tree" ] }, { "page": "last_commit", "title": "Last commit", "topics": [ "last_commit" ] }, { "page": "length.git_blob", "title": "Size in bytes of the contents of a blob", "topics": [ "length.git_blob" ] }, { "page": "length.git_diff", "title": "Number of files in git_diff object", "topics": [ "length.git_diff" ] }, { "page": "length.git_tree", "title": "Number of entries in tree", "topics": [ 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"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": [ "PhoneNumberProvider_fa_IR" ] }, { "page": "PhoneNumberProvider_fi_FI", "title": "PhoneNumberProvider for Finland", "concept": [ "FI", "fi" ], "topics": [ "PhoneNumberProvider_fi_FI" ] }, { "page": "PhoneNumberProvider_fr_CH", "title": "PhoneNumberProvider for Switserland", "concept": [ "CH", "fr" ], "topics": [ "PhoneNumberProvider_fr_CH" ] }, { "page": "PhoneNumberProvider_fr_FR", "title": "PhoneNumberProvider for France", "concept": [ "FR", "fr" ], "topics": [ "PhoneNumberProvider_fr_FR" ] }, { "page": "PhoneNumberProvider_he_IL", "title": "PhoneNumberProvider for Israel", "concept": [ "IL", "he" ], "topics": [ "PhoneNumberProvider_he_IL" ] }, { "page": "PhoneNumberProvider_hi_IN", "title": "PhoneNumberProvider for India", "concept": [ "IN", "hi" ], "topics": [ "PhoneNumberProvider_hi_IN" ] }, { "page": "PhoneNumberProvider_hr_HR", "title": "PhoneNumberProvider for Croatia", "concept": [ "HR", "hr" ], "topics": [ "PhoneNumberProvider_hr_HR" ] }, { "page": "PhoneNumberProvider_hu_HU", "title": "PhoneNumberProvider for Hungary", "concept": [ "HU", "hu" ], "topics": [ "PhoneNumberProvider_hu_HU" ] }, { "page": "PhoneNumberProvider_id_ID", "title": "PhoneNumberProvider for Indonesia", "concept": [ "ID", "id" ], "topics": [ "PhoneNumberProvider_id_ID" ] }, { "page": "PhoneNumberProvider_it_IT", "title": "PhoneNumberProvider for Italy", "concept": [ "IT", "it" ], "topics": [ "PhoneNumberProvider_it_IT" ] }, { "page": "PhoneNumberProvider_ja_JP", "title": "PhoneNumberProvider for Japan", "concept": [ "JP", "ja" ], "topics": [ "PhoneNumberProvider_ja_JP" ] }, { "page": "PhoneNumberProvider_ko_KR", "title": "PhoneNumberProvider for Korean Republic", "concept": [ "KR", "ko" ], "topics": [ "PhoneNumberProvider_ko_KR" ] }, { "page": "PhoneNumberProvider_lt_LT", "title": "PhoneNumberProvider for Lithuania", "concept": [ "LT", "lt" ], "topics": [ "PhoneNumberProvider_lt_LT" ] }, { "page": "PhoneNumberProvider_lv_LV", "title": "PhoneNumberProvider for Latvia", "concept": [ "LV", "lv" ], "topics": [ "PhoneNumberProvider_lv_LV" ] }, { "page": "PhoneNumberProvider_ne_NP", "title": "PhoneNumberProvider for Nepal", "concept": [ "NP", "ne" ], "topics": [ "PhoneNumberProvider_ne_NP" ] }, { "page": "PhoneNumberProvider_nl_BE", "title": "PhoneNumberProvider for Belgium", "concept": [ "BE", "nl" ], "topics": [ "PhoneNumberProvider_nl_BE" ] }, { "page": "PhoneNumberProvider_nl_NL", "title": "PhoneNumberProvider for the Netherlands", "concept": [ "NL", "nl" ], "topics": [ "PhoneNumberProvider_nl_NL" ] }, { "page": "PhoneNumberProvider_nn_NO", "title": "PhoneNumberProvider for Norway (nn_NO)", "concept": [ "NO", "nn" ], "topics": [ "PhoneNumberProvider_nn_NO" ] }, { "page": "PhoneNumberProvider_no_NO", "title": "PhoneNumberProvider for Norway (no_NO)", "concept": [ "NO", "no" ], "topics": [ "PhoneNumberProvider_no_NO" ] }, { "page": "PhoneNumberProvider_pl_PL", "title": "PhoneNumberProvider for Poland", "concept": [ "PL", "pl" ], "topics": [ "PhoneNumberProvider_pl_PL" ] }, { "page": "PhoneNumberProvider_pt_BR", "title": "PhoneNumberProvider for Brazil", "concept": [ "BR", "pt" ], "topics": [ "PhoneNumberProvider_pt_BR" ] }, { "page": "PhoneNumberProvider_pt_PT", "title": "PhoneNumberProvider for Portugal", "concept": [ "PT", "pt" ], "topics": [ "PhoneNumberProvider_pt_PT" ] }, { "page": "PhoneNumberProvider_ru_RU", "title": "PhoneNumberProvider for Russia", "concept": [ "RU", "ru" ], "topics": [ "PhoneNumberProvider_ru_RU" ] }, { "page": "PhoneNumberProvider_sk_SK", "title": "PhoneNumberProvider for Slovakia", "concept": [ "SK", "sk" ], "topics": [ "PhoneNumberProvider_sk_SK" ] }, { "page": "PhoneNumberProvider_sv_SE", "title": "PhoneNumberProvider for Sweden", "concept": [ "SE", "sv" ], "topics": [ "PhoneNumberProvider_sv_SE" ] }, { "page": "PhoneNumberProvider_th_TH", "title": "PhoneNumberProvider for Thailand", "concept": [ "TH", "th" ], "topics": [ "PhoneNumberProvider_th_TH" ] }, { "page": 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"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": 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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 commonly accompanied by\n'BEAUti 2' (), which, among others,\nallows one to install 'BEAST2' package. 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"dashboard_activity_list", "title": "Authorized user's dashboard activity stream", "topics": [ "dashboard_activity_list" ] }, { "page": "dashboard_count", "title": "Number of new activities of an authorized user", "topics": [ "dashboard_count" ] }, { "page": "dataset_purge", "title": "Permanently purge a dataset", "topics": [ "dataset_purge" ] }, { "page": "diagnostics", "title": "Diagnostics helpers", "topics": [ "diagnostics", "help_show", "status_show" ] }, { "page": "ds_create", "title": "Add a new table to a datastore", "topics": [ "ds_create" ] }, { "page": "ds_create_dataset", "title": "Datastore - create a new resource on an existing dataset", "topics": [ "ds_create_dataset" ] }, { "page": "ds_search", "title": "Datastore - search or get a dataset from CKAN datastore", "topics": [ "ds_search" ] }, { "page": "ds_search_sql", "title": "Datastore - search or get a dataset from CKAN datastore", "topics": [ "ds_search_sql" ] }, { "page": "follow_objects", "title": "Follow and 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"dataset_follower_list", "follower_lists", "group_follower_list", "user_follower_list" ] }, { "page": "group_create", "title": "Create a group", "topics": [ "group_create" ] }, { "page": "group_delete", "title": "Delete a group", "topics": [ "group_delete" ] }, { "page": "group_list", "title": "List groups.", "topics": [ "group_list" ] }, { "page": "group_list_authz", "title": "List groups the current user can edit", "topics": [ "group_list_authz" ] }, { "page": "group_member_create", "title": "Make a user a member of a group", "topics": [ "group_member_create" ] }, { "page": "group_member_delete", "title": "Remove a user from a group", "topics": [ "group_member_delete" ] }, { "page": "group_patch", "title": "Update a group's metadata", "topics": [ "group_patch" ] }, { "page": "group_show", "title": "Show a package", "topics": [ "group_show" ] }, { "page": "group_update", "title": "Update a group", "topics": [ "group_update" ] }, { "page": "job_queue", "title": "Background job 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"organization_list", "title": "List organization", "topics": [ "organization_list" ] }, { "page": "organization_list_for_user", "title": "List organizations a user can act on", "topics": [ "organization_list_for_user" ] }, { "page": "organization_member_create", "title": "Make a user a member of an organization", "topics": [ "organization_member_create" ] }, { "page": "organization_member_delete", "title": "Remove a user from an organization", "topics": [ "organization_member_delete" ] }, { "page": "organization_purge", "title": "Purge an organization", "topics": [ "organization_purge" ] }, { "page": "organization_show", "title": "Show an organization", "topics": [ "organization_show" ] }, { "page": "package_activity_list", "title": "Return a list of the package's activity", "topics": [ "package_activity_list" ] }, { "page": "package_collaborator_create", "title": "Create or update a dataset collaborator", "topics": [ "package_collaborator_create" ] }, { "page": 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"List relationships for a dataset", "topics": [ "package_relationships_list" ] }, { "page": "package_resource_reorder", "title": "Reorder resources for a dataset", "topics": [ "package_resource_reorder" ] }, { "page": "package_revise", "title": "Revise a dataset using match/filter/update semantics", "topics": [ "package_revise" ] }, { "page": "package_revision_list", "title": "Return a dataset (package's) revisions as a list of dictionaries.", "topics": [ "package_revision_list" ] }, { "page": "package_search", "title": "Search for packages.", "topics": [ "package_search" ] }, { "page": "package_show", "title": "Show a package.", "topics": [ "package_show" ] }, { "page": "package_update", "title": "Update a package", "topics": [ "package_update" ] }, { "page": "ping", "title": "Ping a CKAN server to test that it's up or down.", "topics": [ "ping" ] }, { "page": "related_create", "title": "Create a related item", "topics": [ "related_create" ] }, { "page": "related_delete", "title": 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comment=c(ORCID = \"0000-0003-1444-9135\")),\nperson(\"David\", \"Beckett\", role = c(\"cph\")),\nperson(\"University of Bristol\", role = c(\"cph\")),\nperson(\"Regents of the University of California\", role = c(\"cph\"))\n)", "Date": "2025-12-09", "VignetteBuilder": "knitr", "Description": "Provides methods to parse, query and serialize information\nstored in the Resource Description Framework (RDF). RDF is\ndescribed at . This package\nsupports RDF by implementing an R interface to the Redland RDF\nC library, described at\n. In brief, RDF\nprovides a structured graph consisting of Statements composed\nof Subject, Predicate, and Object Nodes.", "SystemRequirements": "Mac OSX: redland (>= 1.0.14) ; Linux: librdf0 (>=\n1.0.14), librdf0-dev (>= 1.0.14)", "Collate": "'redland.R' 'World.R' 'Node.R' 'Statement.R' 'Storage.R'\n'Model.R' 'Parser.R' 'Query.R' 'QueryResults.R' 'Serializer.R'\n'mergeNamespace_roclet.R' 'redland-package.R' 'util.R'", "License": "Apache License 2.0", "Copyright": "See file (inst/)COPYRIGHTS.", "BugReports": "https://github.com/ropensci/redland-bindings/issues", "RoxygenNote": "7.3.1", "URL": "https://github.com/ropensci/redland-bindings/tree/master/R/redland\nhttps://github.com/ropensci/redland-bindings/tree/master/R", "Encoding": "UTF-8", "Language": "en-US", "Roxygen": "list(roclets = c(\"collate\", \"rd\", \"namespace\",\n\"mergeNamespace_roclet\"), markdown=TRUE)", "Config/pak/sysreqs": "cmake make libuv1-dev libxml2-dev librdf0-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-12-09 21:59:18 UTC", "RemoteUrl": "https://github.com/ropensci/redland-bindings", "RemoteRef": "master", "RemoteSha": "62af8690663c136be09227f946ef6aa90c47cbb4", "RemoteSubdir": "R/redland", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-01 08:17:16 UTC", "User": "root" }, "Author": "Matthew B. Jones [aut, cre] (ORCID:\n),\nPeter Slaughter [aut] (ORCID: ),\nJeroen Ooms [aut] (ORCID: ),\nCarl Boettiger [aut] (ORCID: ),\nScott Chamberlain [ctb] (ORCID:\n),\nDavid Beckett [cph],\nUniversity of Bristol [cph],\nRegents of the University of California [cph]", "Maintainer": "Matthew B. 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{ "ropensci_category": "data-extraction" }, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/redland.html", "manual.pdf" ], "_realowner": "ropensci", "_cranurl": false, "_releases": [ { "version": "1.0.17-6", "date": "2016-02-18" }, { "version": "1.0.17-7", "date": "2016-03-12" }, { "version": "1.0.17-8", "date": "2016-04-26" }, { "version": "1.0.17-9", "date": "2016-12-14" }, { "version": "1.0.17-10", "date": "2018-07-20" }, { "version": "1.0.17-11", "date": "2019-10-13" }, { "version": "1.0.17-12", "date": "2020-09-25" }, { "version": "1.0.17-13", "date": "2020-10-09" }, { "version": "1.0.17-14", "date": "2020-10-21" }, { "version": "1.0.17-15", "date": "2021-12-17" }, { "version": "1.0.17-16", "date": "2022-01-20" }, { "version": "1.0.17-16.1", "date": "2023-05-19" }, { "version": "1.0.17-17", "date": "2023-05-23" }, { "version": "1.0.17-18", "date": "2024-02-24" }, { "version": "1.0.17-19", "date": "2025-12-11" } ], "_exports": [ "addStatement", "executeQuery", "freeModel", "freeParser", "freeQuery", "freeQueryResults", "freeSerializer", "freeStatement", "freeStorage", "freeWorld", "getBlankNodeId", "getNodeType", "getNodeValue", "getQueryResultLimit", "getResults", "getTermType", "initialize", "is.null.externalptr", "librdf_copyright_string", "librdf_copyright_string_get", "librdf_digest_final", "librdf_digest_init", "librdf_digest_to_string", "librdf_digest_update", "librdf_digest_update_string", "librdf_free_digest", "librdf_free_hash", "librdf_free_iterator", "librdf_free_model", "librdf_free_node", "librdf_free_parser", "librdf_free_query", "librdf_free_query_results", "librdf_free_serializer", "librdf_free_statement", "librdf_free_storage", "librdf_free_stream", "librdf_free_uri", "librdf_free_world", "librdf_hash_to_string", "librdf_internal_test_error", "librdf_internal_test_warning", "librdf_iterator_end", "librdf_iterator_get_context", "librdf_iterator_get_object", "librdf_iterator_next", "librdf_log_message_code", "librdf_log_message_facility", "librdf_log_message_level", "librdf_log_message_locator", "librdf_log_message_message", "librdf_model_add", "librdf_model_add_statement", "librdf_model_add_statements", "librdf_model_add_string_literal_statement", "librdf_model_add_typed_literal_statement", "librdf_model_as_stream", "librdf_model_contains_context", "librdf_model_contains_statement", "librdf_model_context_add_statement", "librdf_model_context_add_statements", "librdf_model_context_as_stream", "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": [ 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\"Chehida\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7269-9082\")),\nperson(\"Katharine S.\", \"Walter\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0065-2204\")),\nperson(\"Gary\", \"Napier\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1077-0055\")),\nperson(\"Jason\", \"Griffiths\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1667-8233\")),\nperson(\"Thijs\", \"Janzen\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4162-1140\")),\nperson(\"Pedro\", \"Taucce\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3088-4543\")),\nperson(\"Olivier\", \"Roy\", role = \"ctb\"),\nperson(\"Jianhui\", \"Wang\", role = \"ctb\"),\nperson(\"Ngoc X.B.\", \"Nguyen\", role = \"ctb\", comment = c(ORCID = \"0000-0002-6802-5509\")),\nperson(\"Jana\", \"Riederer\", role = \"ctb\", comment = c(ORCID = \"0000-0001-6951-9984\")))", "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. '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": "2026-07-01 08:24:50 UTC", "User": "root" }, "Author": "Richèl J.C. Bilderbeek [aut, cre] (ORCID:\n),\nJoëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci,\nsee https://github.com/ropensci/onboarding/issues/209),\nDavid Winter [rev] (David reviewed the package for rOpenSci, see\nhttps://github.com/ropensci/onboarding/issues/209),\nPaul Van Els [ctb] (ORCID: ),\nRaphael Scherrer [ctb] (ORCID: ),\nYacine B. Chehida [ctb] (ORCID:\n),\nKatharine S. Walter [ctb] (ORCID:\n),\nGary Napier [ctb] (ORCID: ),\nJason Griffiths [ctb] (ORCID: ),\nThijs Janzen [ctb] (ORCID: ),\nPedro Taucce [ctb] (ORCID: ),\nOlivier Roy [ctb],\nJianhui Wang [ctb],\nNgoc X.B. Nguyen [ctb] (ORCID: ),\nJana Riederer [ctb] (ORCID: )", "Maintainer": "Richèl J.C. 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"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": [ 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"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/main/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": "25.0.3+9-2~26.04.2", "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. 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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 libuv1-dev libxml2-dev libssl-dev\nlibx11-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-12-08 06:27:46 UTC", "RemoteUrl": "https://github.com/ropensci/DataPackageR", "RemoteRef": "main", "RemoteSha": "91c3001bcfab7dc84e99e858e847094b4bf1b733", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-01 08:16:17 UTC", "User": "root" }, "Author": "Greg Finak [aut, cph] (Original author and creator of DataPackageR),\nPaul Obrecht [ctb],\nEllis Hughes 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This package\ncombines API calling methods from various web scraping packages\nwith specific strings to retrieve data from the EPA API. It\nalso contains easy to use loaded variables that help a user\nnavigate services offered by the API and aid the user in\ndetermining the appropriate way to make a an API call.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "BugReports": "https://github.com/ropensci/epair/issues", "URL": "https://github.com/ropensci/epair", "VignetteBuilder": "knitr", "SystemRequirements": "pandoc", "Config/pak/sysreqs": "libicu-dev libssl-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-12-01 19:01:14 UTC", "RemoteUrl": "https://github.com/ropensci/epair", "RemoteRef": "master", "RemoteSha": "e8f1f1d4ba115f8189e76ddea2f9206d2ab8cc11", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-01 08:27:14 UTC", "User": "root" }, "Author": "G.L. 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organization.", "topics": [ "get_qa_ca_in_pqao" ] }, { "page": "get_qa_ca_in_site", "title": "Get quality assurance collocated assessment data at a site.", "topics": [ "get_qa_ca_in_site" ] }, { "page": "get_qa_ca_in_state", "title": "Get quality assurance collocated assessment data in a state.", "topics": [ "get_qa_ca_in_state" ] }, { "page": "get_qa_fra_in_agency", "title": "Get quality assurance flow rate audit data for a monitoring agency.", "topics": [ "get_qa_fra_in_agency" ] }, { "page": "get_qa_fra_in_county", "title": "Get quality assurance flow rate audit data in a county.", "topics": [ "get_qa_fra_in_county" ] }, { "page": "get_qa_fra_in_pqao", "title": "Get quality assurance flow rate audit data for a primary quality assurance organization.", "topics": [ "get_qa_fra_in_pqao" ] }, { "page": "get_qa_fra_in_site", "title": "Get quality assurance flow rate audit data at a site.", "topics": [ "get_qa_fra_in_site" ] }, { "page": "get_qa_fra_in_state", "title": "Get quality 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"habitat_morphological_type_photo", "perimeter_corner2", "perimeter_corner2_longitude", "perimeter_corner2_latitude", "perimeter_corner2_altitude", "perimeter_corner3", "perimeter_corner3_longitude", "perimeter_corner3_latitude", "perimeter_corner3_altitude", "perimeter_corner4", "perimeter_corner4_longitude", "perimeter_corner4_latitude", "perimeter_corner4_altitude", "perimeter_mudmap_photo", "encounter_end_datetime", "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", "vegetation_stratum_odata_navigation_link", "taxon_encounter_odata_navigation_link", "odata_context" ], "rows": 1, "table": true, "tojson": true }, { "name": "fq_data_strata", "title": "Parsed submission data for a subgroup of an ODK Central form.", "object": "fq_data_strata", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "nvis_level3_broad_floristic_group", "max_height_m", "foliage_cover", "dominant_species_1", "dominant_species_2", "dominant_species_3", "dominant_species_4", "id", "submissions_id", "odata_context.x", "meta_instance_id", "encounter_start_datetime", "reporter", "device_id", "location_area_name", "location_quadrat_photo", "location_corner1", "location_corner1_longitude", "location_corner1_latitude", "location_corner1_altitude", "habitat_morphological_type", "habitat_morphological_type_photo", "perimeter_corner2", "perimeter_corner2_longitude", "perimeter_corner2_latitude", "perimeter_corner2_altitude", "perimeter_corner3", "perimeter_corner3_longitude", "perimeter_corner3_latitude", "perimeter_corner3_altitude", "perimeter_corner4", "perimeter_corner4_longitude", "perimeter_corner4_latitude", "perimeter_corner4_altitude", "perimeter_mudmap_photo", "encounter_end_datetime", "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", "vegetation_stratum_odata_navigation_link", "taxon_encounter_odata_navigation_link", "odata_context.y" ], "rows": 2, "table": true, "tojson": true }, { "name": "fq_data_taxa", "title": "Parsed submission data for a subgroup of an ODK Central form.", "object": "fq_data_taxa", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "field_name", "photo_in_situ", "taxon_encounter_location", "life_form", "voucher_specimen_barcode", "voucher_specimen_label", "id", "submissions_id", "odata_context.x", "meta_instance_id", "encounter_start_datetime", "reporter", "device_id", "location_area_name", "location_quadrat_photo", "location_corner1", "location_corner1_longitude", "location_corner1_latitude", "location_corner1_altitude", "habitat_morphological_type", "habitat_morphological_type_photo", "perimeter_corner2", "perimeter_corner2_longitude", "perimeter_corner2_latitude", "perimeter_corner2_altitude", "perimeter_corner3", "perimeter_corner3_longitude", "perimeter_corner3_latitude", "perimeter_corner3_altitude", "perimeter_corner4", "perimeter_corner4_longitude", "perimeter_corner4_latitude", "perimeter_corner4_altitude", "perimeter_mudmap_photo", "encounter_end_datetime", "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", "vegetation_stratum_odata_navigation_link", "taxon_encounter_odata_navigation_link", "odata_context.y" ], "rows": 2, "table": true, "tojson": true }, { "name": "fq_form_detail", "title": "A tibble of form metadata.", "object": "fq_form_detail", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "name", "fid", "version", "state", "submissions", "created_at", "created_by_id", "created_by", "updated_at", "published_at", "last_submission", "hash" ], "rows": 1, "table": true, "tojson": true }, { "name": "fq_form_list", "title": "A tibble of forms.", "object": "fq_form_list", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "project_id", "xml_form_id", "state", "enketo_id", "enketo_once_id", "created_at", "updated_at", "webforms_enabled", "key_id", "version", "hash", "sha", "sha256", "draft_token", "published_at", "name", "submissions", "entity_related", "review_states_received", "review_states_has_issues", "review_states_edited", "last_submission", "excel_content_type", "public_links", "created_by_id", "created_by_type", "created_by_display_name", "created_by_created_at", "created_by_updated_at", "created_by_deleted_at", "fid" ], "rows": 16, "table": true, "tojson": true }, { "name": "fq_form_schema", "title": "JSON form schema for an ODK Central form.", "object": "fq_form_schema", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "path", "name", "type", "binary", "selectMultiple", "ruodk_name" ], "rows": 33, "table": true, "tojson": true }, { "name": "fq_form_xml", "title": "A nested list of a form definition.", "object": "fq_form_xml", "class": [ "xml_document", "xml_node" ], "fields": [], "table": false, "tojson": false }, { "name": "fq_meta", "title": "OData metadata document for an ODK Central form.", "object": "fq_meta", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "fq_project_detail", "title": "A tibble of project metadata.", "object": "fq_project_detail", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "id", "name", "forms", "app_users", "last_submission", "created_at", "updated_at", "archived", "verbs" ], "rows": 1, "table": false, "tojson": true }, { "name": "fq_project_list", "title": "A tibble of project metadata.", "object": "fq_project_list", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "id", "name", "description", "archived", "key_id", "created_at", "updated_at", "deleted_at", "verbs", "forms", "app_users", "datasets", "last_submission", "last_entity" ], "rows": 3, "table": false, "tojson": true }, { "name": "fq_raw", "title": "OData submission data for an ODK Central form.", "object": "fq_raw", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "fq_raw_strata", "title": "OData submission data for a subgroup of an ODK Central form.", "object": "fq_raw_strata", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "fq_raw_taxa", "title": "OData submission data for a subgroup of an ODK Central form.", "object": "fq_raw_taxa", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "fq_submission_list", "title": "A tibble of submission metadata.", "object": "fq_submission_list", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "instance_id", "submitter_id", "device_id", "created_at", "updated_at", "review_state", "user_agent", "deleted_at", "submitter_id_2", "submitter_type", "submitter_display_name", "submitter_created_at", "submitter_updated_at", "submitter_deleted_at", "current_version" ], "rows": 1, "table": false, "tojson": true }, { "name": "fq_submissions", "title": "A nested list of submission data.", "object": "fq_submissions", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "fq_svc", "title": "OData service document for an ODK Central form.", "object": "fq_svc", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "name", "kind", "url" ], "rows": 3, "table": true, "tojson": true }, { "name": "fq_zip_data", "title": "A tibble of the main data table of records from a test form.", "object": "fq_zip_data", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "submission_date", "meta_instance_id", "encounter_start_datetime", "reporter", "device_id", "location_area_name", "location_quadrat_photo", "location_corner1_latitude", "location_corner1_longitude", "location_corner1_altitude", "location_corner1_accuracy", "habitat_morphological_type", "habitat_morphological_type_photo", "perimeter_corner2_latitude", "perimeter_corner2_longitude", "perimeter_corner2_altitude", "perimeter_corner2_accuracy", "perimeter_corner3_latitude", "perimeter_corner3_longitude", "perimeter_corner3_altitude", "perimeter_corner3_accuracy", "perimeter_corner4_latitude", "perimeter_corner4_longitude", "perimeter_corner4_altitude", "perimeter_corner4_accuracy", "perimeter_mudmap_photo", "encounter_end_datetime", "key", "submitter_id", "submitter_name", "attachments_present", "attachments_expected", "status", "review_state", "device_id_2", "edits", "form_version", "id" ], "rows": 1, "table": true, "tojson": true }, { "name": "fq_zip_strata", "title": "A tibble of a repeated sub-group of records from a test form.", "object": "fq_zip_strata", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "nvis_level3_broad_floristic_group", "max_height_m", "foliage_cover", "dominant_species_1", "dominant_species_2", "dominant_species_3", "dominant_species_4", "parent_key", "key.x", "id.x", "submission_date", "encounter_start_datetime", "reporter", "device_id", "location_area_name", "location_quadrat_photo", "location_corner1_latitude", "location_corner1_longitude", "location_corner1_altitude", "location_corner1_accuracy", "habitat_morphological_type", "habitat_morphological_type_photo", "perimeter_corner2_latitude", "perimeter_corner2_longitude", "perimeter_corner2_altitude", "perimeter_corner2_accuracy", "perimeter_corner3_latitude", "perimeter_corner3_longitude", "perimeter_corner3_altitude", "perimeter_corner3_accuracy", "perimeter_corner4_latitude", "perimeter_corner4_longitude", "perimeter_corner4_altitude", "perimeter_corner4_accuracy", "perimeter_mudmap_photo", "encounter_end_datetime", "key.y", "submitter_id", "submitter_name", "attachments_present", "attachments_expected", "status", "review_state", "device_id_2", "edits", "form_version", "id.y" ], "rows": 2, "table": true, "tojson": true }, { "name": "fq_zip_taxa", "title": "A tibble of a repeated sub-group of records from a test form.", "object": "fq_zip_taxa", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "field_name", "photo_in_situ", "taxon_encounter_location_latitude", "taxon_encounter_location_longitude", "taxon_encounter_location_altitude", "taxon_encounter_location_accuracy", "life_form", "voucher_specimen_barcode", "voucher_specimen_label", "parent_key", "key.x", "id.x", "submission_date", "encounter_start_datetime", "reporter", "device_id", "location_area_name", "location_quadrat_photo", "location_corner1_latitude", "location_corner1_longitude", "location_corner1_altitude", "location_corner1_accuracy", "habitat_morphological_type", "habitat_morphological_type_photo", "perimeter_corner2_latitude", "perimeter_corner2_longitude", "perimeter_corner2_altitude", "perimeter_corner2_accuracy", "perimeter_corner3_latitude", "perimeter_corner3_longitude", "perimeter_corner3_altitude", "perimeter_corner3_accuracy", "perimeter_corner4_latitude", "perimeter_corner4_longitude", "perimeter_corner4_altitude", "perimeter_corner4_accuracy", "perimeter_mudmap_photo", "encounter_end_datetime", "key.y", "submitter_id", "submitter_name", "attachments_present", "attachments_expected", "status", "review_state", "device_id_2", "edits", "form_version", "id.y" ], "rows": 2, "table": true, "tojson": true }, { "name": "fs_v7", "title": "The parsed XML form_schema of a form from ODK Central v0.6.", "object": "fs_v7", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "type", "name", "path" ], "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", "shape_location_shape_map", "shape_location_shape_manual_longitude", "shape_location_shape_manual_latitude", "shape_location_shape_manual_altitude", "shape_location_shape_manual", "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": false, "tojson": true }, { "name": "geo_gj_raw", "title": "The unparsed submissions of a form containing geofields in GeoJSON.", "object": "geo_gj_raw", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "geo_gj88", "title": "The parsed submissions of a form containing geofields in GeoJSON with trailing empty coordinates present.", "object": "geo_gj88", "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_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", "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", 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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, xronos.", "Version": "5.2.0", "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", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libssl-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-08-31 12:56:01 UTC", "RemoteUrl": "https://github.com/ropensci/c14bazAAR", "RemoteRef": "master", "RemoteSha": "9f0aa674793138d2224d12969279ea928ff5fb21", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-01 08:16:23 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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\"0000-0002-0077-6074\")),\nperson(\"Abraham\", \"Olvera-Barrios\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-3305-4465\")),\nperson(\"Chuin Ying\", \"Ung\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-8487-4589\")),\nperson(\"Robert\", \"Luben\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-5088-6343\")),\nperson(given = \"Zhian N.\",\nfamily = \"Kamvar\",\nrole = c(\"rev\"),\nemail = \"zkamvar@carpentries.org\",\ncomment = c(ORCID = \"0000-0003-1458-7108\"))\n)", "Description": "A convenient R interface to the Genotype-Tissue Expression\n(GTEx) Portal API. The GTEx project is a comprehensive public\nresource for studying tissue-specific gene expression and\nregulation in human tissues. Through systematic analysis of RNA\nsequencing data from 54 non-diseased tissue sites across nearly\n1000 individuals, GTEx provides crucial insights into the\nrelationship between genetic variation and gene expression.\nThis data is accessible through the GTEx Portal API enabling\nprogrammatic access to human gene expression data. For more\ninformation on the API, see\n.", "License": "MIT + file LICENSE", "URL": "https://docs.ropensci.org/gtexr/,\nhttps://github.com/ropensci/gtexr", "BugReports": "https://github.com/ropensci/gtexr/issues", "Encoding": "UTF-8", "Language": "en-US", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev libssl-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-08-19 08:39:42 UTC", "RemoteUrl": "https://github.com/ropensci/gtexr", "RemoteRef": "main", "RemoteSha": "03abf00ad979023b5377ebdf6dff4a19dc79688c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-01 08:17:10 UTC", "User": "root" }, "Author": "Alasdair Warwick [aut, cre, cph] (ORCID:\n),\nBenjamin Zuckerman [aut] (ORCID:\n),\nAbraham Olvera-Barrios [aut] (ORCID:\n),\nChuin Ying Ung [aut] (ORCID: ),\nRobert Luben [aut] (ORCID: ),\nZhian N. 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Trait Loci", "concept": [ "Dynamic Association Endpoints" ], "topics": [ "calculate_splicing_quantitative_trait_loci" ] }, { "page": "download", "title": "Download", "concept": [ "Biobank Data Endpoints" ], "topics": [ "download" ] }, { "page": "get_annotation", "title": "Get Annotation", "concept": [ "Datasets Endpoints" ], "topics": [ "get_annotation" ] }, { "page": "get_clustered_median_exon_expression", "title": "Get Clustered Median Exon Expression", "concept": [ "Expression Data Endpoints" ], "topics": [ "get_clustered_median_exon_expression" ] }, { "page": "get_clustered_median_gene_expression", "title": "Get Clustered Median Gene Expression", "concept": [ "Expression Data Endpoints" ], "topics": [ "get_clustered_median_gene_expression" ] }, { "page": "get_clustered_median_junction_expression", "title": "Get Clustered Median Junction Expression", "concept": [ "Expression Data Endpoints" ], "topics": [ "get_clustered_median_junction_expression" ] }, { "page": "get_clustered_median_transcript_expression", "title": "Get Clustered Median Transcript Expression", "concept": [ "Expression Data Endpoints" ], "topics": [ "get_clustered_median_transcript_expression" ] }, { "page": "get_collapsed_gene_model_exon", "title": "Get Collapsed Gene Model Exon", "concept": [ "Datasets Endpoints" ], "topics": [ "get_collapsed_gene_model_exon" ] }, { "page": "get_dataset_info", "title": "Get Dataset Info", "concept": [ "Metadata Endpoints" ], "topics": [ "get_dataset_info" ] }, { "page": "get_downloads_page_data", "title": "Get Downloads Page Data", "concept": [ "Datasets Endpoints" ], "topics": [ "get_downloads_page_data" ] }, { "page": "get_eqtl_genes", "title": "Get Eqtl Genes", "concept": [ "Static Association Endpoints" ], "topics": [ "get_eqtl_genes" ] }, { "page": "get_exons", "title": "Get Exons", "concept": [ "Reference Genome Endpoints" ], "topics": [ "get_exons" ] }, { "page": "get_expression_pca", "title": "Get Expression Pca", "concept": [ "Expression Data Endpoints" ], "topics": [ "get_expression_pca" ] }, { "page": "get_file_list", "title": "Get File List", "concept": [ "Datasets Endpoints" ], "topics": [ "get_file_list" ] }, { "page": "get_fine_mapping", "title": "Get Fine Mapping", "concept": [ "Static Association Endpoints" ], "topics": [ "get_fine_mapping" ] }, { "page": "get_full_get_collapsed_gene_model_exon", "title": "Get Full Get Collapsed Gene Model Exon", "concept": [ "Datasets Endpoints" ], "topics": [ "get_full_get_collapsed_gene_model_exon" ] }, { "page": "get_functional_annotation", "title": "Get Functional Annotation", "concept": [ "Datasets Endpoints" ], "topics": [ "get_functional_annotation" ] }, { "page": "get_gene_expression", "title": "Get Gene Expression", "concept": [ "Expression Data Endpoints" ], "topics": [ "get_gene_expression" ] }, { "page": "get_gene_search", "title": "Get Gene Search", "concept": [ "Reference Genome Endpoints" ], "topics": [ "get_gene_search" ] }, { "page": "get_genes", "title": "Get Genes", "concept": [ "Reference Genome Endpoints" ], "topics": [ "get_genes" ] }, { "page": "get_genomic_features", "title": "Get Genomic Features", "concept": [ "Reference Genome Endpoints" ], "topics": [ "get_genomic_features" ] }, { "page": "get_gwas_catalog_by_location", "title": "Get Gwas Catalog By Location", "concept": [ "Reference Genome Endpoints" ], "topics": [ "get_gwas_catalog_by_location" ] }, { "page": "get_image", "title": "Get Image", "concept": [ "Histology Endpoints" ], "topics": [ "get_image" ] }, { "page": "get_independent_eqtl", "title": "Get Independent Eqtl", "concept": [ "Static Association Endpoints" ], "topics": [ "get_independent_eqtl" ] }, { "page": "get_linkage_disequilibrium_by_variant_data", "title": "Get Linkage Disequilibrium By Variant Data", "concept": [ "Datasets Endpoints" ], "topics": [ "get_linkage_disequilibrium_by_variant_data" ] }, { "page": "get_linkage_disequilibrium_data", "title": "Get Linkage Disequilibrium Data", "concept": [ "Datasets Endpoints" ], "topics": [ "get_linkage_disequilibrium_data" ] }, { "page": "get_maintenance_message", "title": "Get Maintenance Message", "concept": [ "Admin Endpoints" ], "topics": [ "get_maintenance_message" ] }, { "page": "get_median_exon_expression", "title": "Get Median Exon Expression", "concept": [ "Expression Data Endpoints" ], "topics": [ "get_median_exon_expression" ] }, { "page": "get_median_gene_expression", "title": "Get Median Gene Expression", "concept": [ "Expression Data Endpoints" ], "topics": [ "get_median_gene_expression" ] }, { "page": "get_median_junction_expression", "title": "Get Median Junction Expression", "concept": [ "Expression Data Endpoints" ], "topics": [ "get_median_junction_expression" ] }, { "page": "get_median_transcript_expression", "title": "Get Median Transcript Expression", "concept": [ "Expression Data Endpoints" ], "topics": [ "get_median_transcript_expression" ] }, { "page": "get_multi_tissue_eqtls", "title": "Get Multi Tissue 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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", "Packaged": { "Date": "2026-07-01 08:27:15 UTC", "User": "root" }, "Author": "Ronald Visser [aut, cre] (ORCID:\n),\nAngelino Salentino [ctb] (ORCID:\n),\nAndy Bunn [ctb] (ORCID: ),\nKaija Gahm [rev] (Kaija Gahm reviewed the package for rOpenSci, see\nhttps://github.com/ropensci/software-review/issues/627#issuecomment-1993235710),\nZachary Gajewski [rev] (Zachary Gajewski reviewed the package for\nrOpenSci, see\nhttps://github.com/ropensci/software-review/issues/627#issuecomment-2037644081)", "_user": "ropensci", "_type": "src", "_file": "dendroNetwork_0.5.5.tar.gz", "_fileid": "https://r2.ropensci.org/d55aceb0f520daef24c1e45d1588d8e3977df6880d620514f1623d01ae889b68", "_filesize": 1710972, "_sha256": "d55aceb0f520daef24c1e45d1588d8e3977df6880d620514f1623d01ae889b68", "_expires": "2026-10-09T08:51:03.000Z", "_created": "2026-07-01T08:27:15.000Z", "_published": "2026-07-01T08:51:03.810Z", "_jobs": [ { "job": 84488346267, "time": 173, "config": "linux-devel-x86_64", "r": "4.7.0", "check": 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More complex classes are provided to store\ntaxonomic trees and user-defined data associated with them.", "Version": "0.4.4", "Authors@R": "c(\nperson(\"Scott\", \"Chamberlain\", role = \"aut\",\nemail = \"myrmecocystus+r@gmail.com\", comment = c(ORCID = \"0000-0003-1444-9135\")),\nperson(\"Zachary\", \"Foster\", role = c(\"aut\", \"cre\"),\nemail = \"zacharyfoster1989@gmail.com\", comment = c(ORCID = \"0000-0002-5075-0948\"))\n)", "LazyLoad": "yes", "Encoding": "UTF-8", "License": "MIT + file LICENSE", "URL": "https://docs.ropensci.org/taxa/, https://github.com/ropensci/taxa", "BugReports": "https://github.com/ropensci/taxa/issues", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-07-28 20:21:36 UTC", "RemoteUrl": "https://github.com/ropensci/taxa", "RemoteRef": "master", "RemoteSha": "f8cc3ab7084d86e983c075e22f48a425205eae57", "NeedsCompilation": "no", "Packaged": 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object to a '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", 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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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\"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'. (2010) ().", "License": "MIT + file LICENSE", "URL": "https://github.com/ropensci/waywiser,\nhttps://docs.ropensci.org/waywiser/", "BugReports": "https://github.com/ropensci/waywiser/issues", "VignetteBuilder": "knitr", "Config/Needs/website": "kableExtra", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibssl-dev libproj-dev libsqlite3-dev libudunits2-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2025-04-15 23:57:33 UTC", "RemoteUrl": "https://github.com/ropensci/waywiser", "RemoteRef": "main", "RemoteSha": "fb05c6eada91a3503f6393e250b79ed2df9af608", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-01 08:17:04 UTC", "User": "root" }, "Author": "Michael Mahoney [aut, cre] (ORCID:\n),\nLucas Johnson [ctb] (ORCID: ),\nVirgilio 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"extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/ritis.html", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/ropensci/ritis", "_realowner": "ropensci", "_cranurl": true, "_releases": [ { "version": "0.0.1", "date": "2012-10-17" }, { "version": "0.0.2", "date": "2012-11-06" }, { "version": "0.0.3", "date": "2012-12-05" }, { "version": "0.5.0", "date": "2016-06-23" }, { "version": "0.5.4", "date": "2016-10-12" }, { "version": "0.6.0", "date": "2017-09-27" }, { "version": "0.7.0", "date": "2017-11-03" }, { "version": "0.7.2", "date": "2018-05-20" }, { "version": "0.7.6", "date": "2018-12-18" }, { "version": "0.8.0", "date": "2019-10-29" }, { "version": "0.9.0", "date": "2020-04-17" }, { "version": "1.0.0", "date": "2021-02-02" } ], "_exports": [ "accepted_names", "any_match_count", "comment_detail", "common_names", "core_metadata", "coverage", "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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A pipeline toolkit tailored to Bayesian\nstatisticians, the 'jagstargets' R package is leverages\n'targets' and 'R2jags' to ease this burden. 'jagstargets' makes\nit super easy to set up scalable JAGS pipelines that\nautomatically parallelize the computation and skip expensive\nsteps when the results are already up to date. Minimal custom\ncode is required, and there is no need to manually configure\nbranching, so usage is much easier than 'targets' alone. 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McLean ", "committer": "GitHub ", "message": "Improve encoding non-ASCII characters to LaTeX in toBiblatex (#113)\n\n* Remove appveyor CI\n\nSigned-off-by: Mathew W. McLean \n\n* Avoid msg about page numbers in ReadPDFs for 1page PDFs\n\n* Always use pdfinfo to determine number of pages in each PDF in ReadPDFs\neven when use.metadata is FALSE\n* This avoids a message from pdftotext about incorrect pages\n* Refactor test-readPDF.R to make it clearer when tests are skipped\nif poppler is not installed\n\nSigned-off-by: Mathew W. McLean \n\n* Fix pkg documentation for latest roxygen2\n\nSigned-off-by: Mathew W. McLean \n\n* Fixes for non-ASCII name list fields in toBiblatex and toBibtex\n\n* Add latexify() from dplR instead of tools::encoded_text_to_latex\nto improve conversion of non-ASCII characters to valid latex\n* Fixes #102, #105, #106\n\nSigned-off-by: Mathew W. McLean \n\n* Update documentation for latexify author\n\nSigned-off-by: Mathew W. McLean \n\n* Add website to DESCRIPTION\n\nSigned-off-by: Mathew W. McLean \n\n* Use default value for rettype in ReadPubMed\n\n* c.f. https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/\n* Add mock response for one GetPubMedByID test\n\nSigned-off-by: Mathew W. McLean \n\n* Add more sleep for PubMed/Entrez test\n\nSigned-off-by: Mathew W. McLean \n\n---------\n\nSigned-off-by: Mathew W. McLean ", "time": 1731998236 }, "_maintainer": { "name": "Mathew W. 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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": "master", "RemoteSha": "0d4097e9a3e87dd790c59230801356a0b8faf9da", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-01 08:26:33 UTC", "User": "root" }, "Author": "Matthew Leonawicz [aut, cre] (ORCID:\n)", "Maintainer": "Matthew 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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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"Plot unnormalized Cq data", "Normalized data: delta Cq", "Normalize Cq to 5S rRNA, within Sample only", "Plot normalized data, all reps", "Calculate a summary value for each sample-target 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": 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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 the plate plan", "Display the plate plan", "Analyse Cq (quantification cycle count) data", "Load and summarize data", "Visualise Cq values for each well.", "Plot unnormalized data shows that -RT and NT controls are low", "Dilution series is linear for all probes", "Calculate primer efficiencies for all probes", "Dilution series for nice probes only shows linearity clearly", "Analyse amplification and melt curve data", "Load raw data for amplification and melt curves.", "Plot de-baseline'd raw data for single well", "Plot all amplification curves", "Plot melt curve for single well", "Plot all melt curves", "Plot zoomed melt curves", "Plot only zoomed melt curves for nice probes", "Conclude acceptable primer sets" ], "created": "2019-09-25 09:30:21", "modified": "2022-06-08 12:31:06", "commits": 23 } 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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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