{"Type":"Package","Package":"stplanr","Title":"Sustainable Transport Planning","Version":"1.2.0","Authors@R":"c(\nperson(\"Robin\", \"Lovelace\", , \"rob00x@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5679-6536\")),\nperson(\"Richard\", \"Ellison\", role = \"aut\"),\nperson(\"Malcolm\", \"Morgan\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-9488-9183\")),\nperson(\"Barry\", \"Rowlingson\", role = \"ctb\"),\nperson(\"Nick\", \"Bearman\", role = \"ctb\"),\nperson(\"Nikolai\", \"Berkoff\", role = \"ctb\"),\nperson(\"Scott \", \"Chamberlain\", role = \"rev\",\ncomment = \"Scott reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/10\"),\nperson(\"Mark\", \"Padgham\", , \"mark.padgham@email.com\", role = \"ctb\"),\nperson(\"Zhao\", \"Wang\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4054-0533\")),\nperson(\"Andrea\", \"Gilardi\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-9424-7439\")),\nperson(\"Josiah\", \"Parry\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-9910-865X\"))\n)","Maintainer":"Robin Lovelace ","Description":"Tools for transport planning with an emphasis on spatial\ntransport data and non-motorized modes. Create geographic\n\"desire lines\" from origin-destination (OD) data (building on\nthe 'od' package); calculate routes on the transport network\nlocally and via interfaces to routing services such as\n; calculate route segment attributes\nsuch as bearing. The package implements the 'travel flow\naggregration' method described in Morgan and Lovelace (2020)\n. Further information on the\npackage's aim and scope can be found in the vignettes and in a\npaper in the R Journal (Lovelace and Ellison 2018)\n.","License":"MIT + file LICENSE","URL":"https://github.com/ropensci/stplanr,\nhttps://docs.ropensci.org/stplanr/","BugReports":"https://github.com/ropensci/stplanr/issues","VignetteBuilder":"knitr","Encoding":"UTF-8","LazyData":"yes","Roxygen":"list(markdown = TRUE)","RoxygenNote":"7.2.3","SystemRequirements":"GNU make","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/stplanr","RemoteRef":"master","RemoteSha":"394ff900680fd9c44d2e421796aa7bf9e1bcac20","NeedsCompilation":"no","Packaged":{"Date":"2024-04-24 01:20:16 UTC","User":"root"},"Author":"Robin Lovelace [aut, cre] (),\nRichard Ellison [aut],\nMalcolm Morgan [aut] (),\nBarry Rowlingson [ctb],\nNick Bearman [ctb],\nNikolai Berkoff [ctb],\nScott Chamberlain [rev] (Scott reviewed the package for rOpenSci, see\nhttps://github.com/ropensci/onboarding/issues/10),\nMark Padgham [ctb],\nZhao Wang [ctb] (),\nAndrea Gilardi [ctb] (),\nJosiah Parry [ctb] ()","MD5sum":"b5cd5e631db893535cd6529714909a18","_user":"ropensci","_file":"stplanr_1.2.0.tar.gz","_fileid":"b5cd5e631db893535cd6529714909a18","_filesize":2470098,"_created":"2024-04-24T01:20:16.000Z","_published":"2024-04-24T01:25:43.206Z","_upstream":"https://github.com/ropensci/stplanr","_commit":{"id":"394ff900680fd9c44d2e421796aa7bf9e1bcac20","author":"robinlovelace ","committer":"robinlovelace ","message":"Remove dev version of rsgeo, for now\n","time":1713918958},"_maintainer":{"name":"Robin 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representing the spatial bounds of an object","topics":["geo_bb_matrix"]},{"page":"geo_buffer","title":"Perform a buffer operation on a temporary projected CRS","topics":["geo_buffer"]},{"page":"geo_code","title":"Convert text strings into points on the map","topics":["geo_code"]},{"page":"geo_length","title":"Calculate line length of line with geographic or projected CRS","topics":["geo_length"]},{"page":"geo_projected","title":"Perform GIS functions on a temporary, projected version of a spatial object","topics":["geo_projected","gprojected"]},{"page":"geo_select_aeq","title":"Select a custom projected CRS for the area of interest","topics":["geo_select_aeq"]},{"page":"geo_toptail","title":"Clip the first and last n metres of SpatialLines","topics":["geo_toptail","toptail"]},{"page":"gsection","title":"Function to split overlapping SpatialLines into segments","topics":["gsection"]},{"page":"is_linepoint","title":"Identify lines that are 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coords","topics":["line2df"]},{"page":"line2points","title":"Convert a spatial (linestring) object to points","topics":["line2points","line2pointsn","line2vertices"]},{"page":"mats2line","title":"Convert 2 matrices to lines","topics":["mats2line"]},{"page":"n_segments","title":"Vectorised function to calculate number of segments given a max segment length","topics":["n_segments"]},{"page":"n_vertices","title":"Retrieve the number of vertices in sf objects","topics":["n_vertices"]},{"page":"od_aggregate_from","title":"Summary statistics of trips originating from zones in OD data","topics":["od_aggregate_from"]},{"page":"od_aggregate_to","title":"Summary statistics of trips arriving at destination zones in OD data","topics":["od_aggregate_to"]},{"page":"od_coords","title":"Create matrices representing origin-destination coordinates","topics":["od_coords"]},{"page":"od_coords2line","title":"Convert origin-destination coordinates into desire lines","topics":["od_coords2line"]},{"page":"od_data_lines","title":"Example of desire line representations of origin-destination data from UK Census","topics":["od_data_lines"]},{"page":"od_data_routes","title":"Example segment-level route data","topics":["od_data_routes"]},{"page":"od_data_sample","title":"Example of origin-destination data from UK Census","topics":["od_data_sample"]},{"page":"od_id","title":"Combine two ID values to create a single ID number","topics":["od_id","od_id_character","od_id_max_min","od_id_szudzik"]},{"page":"od_id_order","title":"Generate ordered ids of OD pairs so lowest is always first This function is slow on large datasets, see szudzik_pairing for faster alternative","topics":["od_id_order"]},{"page":"od_oneway","title":"Aggregate od pairs they become non-directional","topics":["od_oneway"]},{"page":"od_to_odmatrix","title":"Convert origin-destination data from long to wide format","topics":["od_to_odmatrix"]},{"page":"od2line","title":"Convert origin-destination data to spatial lines","topics":["od2line"]},{"page":"od2odf","title":"Extract coordinates from OD data","topics":["od2odf"]},{"page":"odmatrix_to_od","title":"Convert origin-destination data from wide to long format","topics":["odmatrix_to_od"]},{"page":"onewaygeo","title":"Aggregate flows so they become non-directional (by geometry - the slow way)","topics":["onewaygeo"]},{"page":"osm_net_example","title":"Example of OpenStreetMap road network","topics":["osm_net_example"]},{"page":"overline","title":"Convert series of overlapping lines into a route network","topics":["overline","overline2"]},{"page":"overline_intersection","title":"Convert series of overlapping lines into a route network","topics":["overline_intersection"]},{"page":"points2flow","title":"Convert a series of points into geographical flows","topics":["points2flow"]},{"page":"points2line","title":"Convert a series of points, or a matrix of coordinates, into a line","topics":["points2line"]},{"page":"points2odf","title":"Convert a series of points into a dataframe of origins and destinations","topics":["points2odf"]},{"page":"quadrant","title":"Split a spatial object into quadrants","topics":["quadrant"]},{"page":"read_table_builder","title":"Import and format Australian Bureau of Statistics (ABS) TableBuilder files","topics":["read_table_builder"]},{"page":"rnet_add_node","title":"Add a node to route network","topics":["rnet_add_node"]},{"page":"rnet_boundary_points","title":"Get points at the beginner and end of linestrings","topics":["rnet_boundary_df","rnet_boundary_points","rnet_boundary_points_lwgeom","rnet_boundary_unique","rnet_duplicated_vertices"]},{"page":"rnet_breakup_vertices","title":"Break up an sf object with LINESTRING geometry.","topics":["rnet_breakup_vertices"]},{"page":"rnet_connected","title":"Keep only segments connected to the largest group in a network","topics":["rnet_connected"]},{"page":"rnet_cycleway_intersection","title":"Example of cycleway intersection data showing problems for SpatialLinesNetwork objects","topics":["rnet_cycleway_intersection"]},{"page":"rnet_get_nodes","title":"Extract nodes from route network","topics":["rnet_get_nodes"]},{"page":"rnet_group","title":"Assign segments in a route network to groups","topics":["rnet_group","rnet_group.default","rnet_group.sf","rnet_group.sfc"]},{"page":"rnet_join","title":"Join route networks","topics":["rnet_join"]},{"page":"rnet_merge","title":"Merge route networks, keeping attributes with aggregating functions","topics":["rnet_merge"]},{"page":"rnet_overpass","title":"Example of overpass data showing problems for SpatialLinesNetwork objects","topics":["rnet_overpass"]},{"page":"rnet_roundabout","title":"Example of roundabout data showing problems for SpatialLinesNetwork objects","topics":["rnet_roundabout"]},{"page":"rnet_subset","title":"Subset one route network 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{"Package":"weatherOz","Title":"An API Client for Australian Weather and Climate Data Resources","Version":"1.0.0","Authors@R":"c(\nperson(\ngiven = \"Rodrigo\",\nfamily = \"Pires\",\nrole = c(\"aut\", \"cre\"),\nemail = \"rodrigo.pires@dpird.wa.gov.au\",\ncomment = c(ORCID = \"0000-0001-7384-6849\")\n),\nperson(\ngiven = \"Anna\",\nfamily = \"Hepworth\",\nrole = \"aut\",\nemail = \"anna.hepworth@gmail.com\",\ncomment = c(ORCID = \"0000-0003-0204-6347\")\n),\nperson(\ngiven = \"Rebecca\",\nfamily = \"O'Leary\",\nrole = \"aut\",\nemail = \"bec.oleary@curtin.edu.au\"\n),\nperson(\ngiven = \"Jonathan\",\nfamily = \"Carroll\",\nrole = \"aut\",\nemail = \"rpkg@jcarroll.com.au\",\ncomment = c(ORCID = \"0000-0002-1404-5264\")\n),\nperson(\ngiven = \"James\",\nfamily = \"Goldie\",\nrole = \"aut\",\nemail = \"me@jamesgoldie.dev\",\ncomment = c(ORCID = \"0000-0002-5024-6207\")\n),\nperson(\ngiven = \"Dean\",\nfamily = \"Marchiori\",\nrole = \"aut\",\nemail = \"deanmarchiori@gmail.com\",\ncomment = c(ORCID = \"0000-0002-3430-7225\")\n),\nperson(\ngiven = \"Paul\",\nfamily = \"Melloy\",\nrole = \"aut\",\nemail = \"paul@melloy.com.au\",\ncomment = c(ORCID = \"0000-0003-4253-7167\")\n),\nperson(\ngiven = \"Mark\",\nfamily = \"Padgham\",\nrole = \"aut\",\nemail = \"mark.padgham@email.com\",\ncomment = c(ORCID = \"0000-0003-2172-5265\")\n),\nperson(\ngiven = \"Hugh\",\nfamily = \"Parsonage\",\nrole = \"aut\",\nemail = \"hugh.parsonage@gmail.com\",\ncomment = c(ORCID = \"0000-0003-4055-0835\")\n),\nperson(\ngiven = \"Keith\",\nfamily = \"Pembleton\",\nrole = \"aut\",\nemail = \"keith.pembleton@usq.edu.au\",\ncomment = c(ORCID = \"0000-0002-1896-4516\")\n),\nperson(\ngiven = \"Maëlle\",\nfamily = \"Salmon\",\nrole = \"ctb\",\nemail = \"maelle.salmon@yahoo.se\",\ncomment = c(ORCID = \"0000-0002-2815-0399\",\n\"Contributed to debugging a nasty little bug with CI where\ntimezones caused tests to fail due to vcr not recognising the\nURL when run outside of Australia/Perth TZ! Suggested the use of\n`withr::local_timzeone()`, see\n.\")),\nperson(\ngiven = \"Jimmy\",\nfamily = \"Ng\",\nrole = \"ctb\",\nemail = \"jimmy.ng@dpird.wa.gov.au\"\n),\nperson(\ngiven = \"Steve\",\nfamily = \"Collins\",\nrole = \"ctb\",\nemail = \"steve.collins@dpird.wa.gov.au\",\ncomment = c(\"Designed weatherOz's hex logo.\")\n),\nperson(\ngiven = \"Adam H.\",\nfamily = \"Sparks\",\nemail = \"adamhsparks@gmail.com\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-0061-8359\")\n),\nperson(\ngiven = \"Laurens\",\nfamily = \"Geffert\",\nrole = \"rev\",\nemail = \"laurensgeffert@gmail.com\"\n),\nperson(\ngiven = \"Sam\",\nfamily = \"Rogers\",\nrole = \"rev\",\nemail = \"sam.rogers@adelaide.edu.au\"\n),\nperson(given = \"Western Australia Agriculture Authority (WAAA)\",\nrole = c(\"cph\")))","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, agriculture bulletin data, and downloading\nand importing radar and satellite imagery files. DPIRD weather\ndata are accessed through public APIs provided by DPIRD,\n, providing access\nto weather station data from DPIRD's weather station network.\nAustralia-wide weather data are based on data from the\nAustralian Bureau of Meteorology (BOM) data and accessed\nthrough SILO (Scientific Information for Land Owners) (Jeffery\net al., 2001, ). DPIRD\ndata are made available under a Creative Commons Attribution\n3.0 Licence (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\ndetails.","URL":"https://github.com/ropensci/weatherOz/,\nhttps://docs.ropensci.org/weatherOz/","BugReports":"https://github.com/ropensci/weatherOz/issues/","License":"GPL (>= 3)","Encoding":"UTF-8","Roxygen":"list(markdown = TRUE, roclets = c(\"collate\", \"namespace\",\n\"rd\", \"roxyglobals::global_roclet\"))","RoxygenNote":"7.3.1","Config/testthat/edition":"3","Config/testthat/parallel":"true","VignetteBuilder":"knitr","Language":"en-US","LazyData":"true","Config/roxyglobals/filename":"globals.R","Config/roxyglobals/unique":"FALSE","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/weatherOz","RemoteRef":"main","RemoteSha":"b804761a1a8119ef1ca391d6806b9e16929efb54","NeedsCompilation":"no","Packaged":{"Date":"2024-04-19 06:29:48 UTC","User":"root"},"Author":"Rodrigo Pires [aut, cre] (),\nAnna Hepworth [aut] (),\nRebecca O'Leary [aut],\nJonathan Carroll [aut] (),\nJames Goldie [aut] (),\nDean Marchiori [aut] (),\nPaul Melloy [aut] (),\nMark Padgham [aut] (),\nHugh Parsonage [aut] (),\nKeith Pembleton [aut] (),\nMaëlle Salmon [ctb] (,\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\n`withr::local_timzeone()`, see\n.),\nJimmy Ng [ctb],\nSteve Collins [ctb] (Designed weatherOz's hex logo.),\nAdam H. Sparks [aut] (),\nLaurens Geffert [rev],\nSam Rogers [rev],\nWestern Australia Agriculture Authority (WAAA) [cph]","Maintainer":"Rodrigo Pires ","MD5sum":"0e136c49dc70324137870bdd260411bd","_user":"ropensci","_file":"weatherOz_1.0.0.tar.gz","_fileid":"0e136c49dc70324137870bdd260411bd","_filesize":4691752,"_created":"2024-04-19T06:29:48.000Z","_published":"2024-04-19T06:38:32.418Z","_upstream":"https://github.com/ropensci/weatherOz","_commit":{"id":"b804761a1a8119ef1ca391d6806b9e16929efb54","author":"Adam H. Sparks ","committer":"Adam H. 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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_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_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":"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 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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' 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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 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'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 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'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 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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 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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 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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. 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(2006).\n\"Globalizing Inequality: 'Centrifugal' and 'Centripetal' Forces\nat Work\". 9. Shannon, C. E. (1948). \"A Mathematical Theory of\nCommunication\". 10. Simpson, E. H. (1949). \"Measurement of\nDiversity\" .","License":"GPL (>= 3)","URL":"https://github.com/ropensci/concstats/,\nhttps://docs.ropensci.org/concstats/(website)","BugReports":"https://github.com/ropensci/concstats/issues/","VignetteBuilder":"knitr, rmarkdown","Encoding":"UTF-8","Language":"en-US","LazyData":"true","Roxygen":"list(markdown = TRUE)","RoxygenNote":"7.3.1","Config/testthat/edition":"3","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/concstats","RemoteRef":"master","RemoteSha":"c450c9e1713c2ce7b9ca44323e462112f6feefd8","NeedsCompilation":"no","Packaged":{"Date":"2024-04-07 07:56:38 UTC","User":"root"},"Author":"Andreas Schneider [aut, cre] (),\nSebastian Wojcik [rev],\nChristopher T. 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c(\n\"matthew.strasiotto@gmail.com\",\n\"mstr3336@uni.sydney.edu.au\"\n)\n),\nperson(\ngiven = \"Ben\",\nfamily = \"Marwick\",\nrole = \"rev\",\nemail = \"bmarwick@uw.edu\"\n),\nperson(\ngiven = \"Peter\",\nfamily = \"Slaughter\",\nrole = \"rev\",\nemail = \"slaughter@nceas.ucsb.edu\"\n),\nperson(\nfamily = \"Eli Lilly and Company\",\nrole = \"cph\"\n))","Description":"A general-purpose computational engine for data analysis,\ndrake rebuilds intermediate data objects when their\ndependencies change, and it skips work when the results are\nalready up to date. Not every execution starts from scratch,\nthere is native support for parallel and distributed computing,\nand completed projects have tangible evidence that they are\nreproducible. Extensive documentation, from beginner-friendly\ntutorials to practical examples and more, is available at the\nreference website and the\nonline manual .","License":"GPL-3","URL":"https://github.com/ropensci/drake,\nhttps://docs.ropensci.org/drake/,\nhttps://books.ropensci.org/drake/","BugReports":"https://github.com/ropensci/drake/issues","Encoding":"UTF-8","Language":"en-US","Roxygen":"list(markdown = TRUE)","RoxygenNote":"7.2.3","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/drake","RemoteRef":"main","RemoteSha":"f5e2391bdb04d9354dd2800cc9386e379c9eff47","NeedsCompilation":"yes","Packaged":{"Date":"2024-04-03 07:26:39 UTC","User":"root"},"Author":"William Michael Landau [aut, cre]\n(),\nAlex Axthelm [ctb],\nJasper Clarkberg [ctb],\nKirill Müller [ctb],\nBen Bond-Lamberty [ctb] (),\nTristan Mahr [ctb] (),\nMiles McBain [ctb] (),\nNoam Ross [ctb] (),\nEllis Hughes [ctb],\nMatthew Mark Strasiotto [ctb],\nBen Marwick [rev],\nPeter Slaughter 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role = \"edt\",\ncomment = \"Mauro was editor for rOpenSci, see https://github.com/ropensci/software-review/issues/485\")\n)","Maintainer":"Alessandro Oggioni ","Description":"ReLTER provides access to DEIMS-SDR (https://deims.org/),\nand allows interaction with data and software implemented by\neLTER Research Infrastructure (RI) thus improving data sharing\namong European LTER projects. 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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 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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? 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R.\",\nfamily = \"Press\",\nrole = \"aut\",\nemail = \"epress12@gmail.com\",\ncomment = c(ORCID = \"0000-0002-1944-3755\")),\nperson(given = \"Anne-Sophie\",\nfamily = \"Bonnet-Lebrun\",\nrole = \"rev\"),\nperson(given = \"Marco\",\nfamily = \"Sciaini\",\nrole = \"rev\")\n)","Description":"Tools to import, clean, and visualize movement data,\nparticularly from motion capture systems such as Optitrack's\n'Motive', the Straw Lab's 'Flydra', or from other sources. We\nprovide functions to remove artifacts, standardize tunnel\nposition and tunnel axes, select a region of interest, isolate\nspecific trajectories, fill gaps in trajectory data, and\ncalculate 3D and per-axis velocity. For experiments of visual\nguidance, we also provide functions that use subject position\nto estimate perception of visual stimuli.","Maintainer":"Vikram B. Baliga ","License":"GPL-3","Encoding":"UTF-8","Roxygen":"list(markdown = TRUE)","RoxygenNote":"7.2.3","VignetteBuilder":"knitr","URL":"https://github.com/ropensci/pathviewr/,\nhttps://docs.ropensci.org/pathviewr/","BugReports":"https://github.com/ropensci/pathviewr/issues/","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/pathviewr","RemoteRef":"master","RemoteSha":"e591cb88815bc706e6415472d2c6846cf639ad8c","NeedsCompilation":"no","Packaged":{"Date":"2024-03-02 06:11:49 UTC","User":"root"},"Author":"Vikram B. Baliga [aut, cre] (),\nMelissa S. Armstrong [aut] (),\nEric R. 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object","topics":["get_header_viewr"]},{"page":"get_sf","title":"Estimate the spatial frequency of visual stimuli from the subject's perspective in an experimental tunnel.","topics":["get_sf"]},{"page":"get_traj_velocities","title":"Recompute trajectory-specific velocities","topics":["get_traj_velocities"]},{"page":"get_velocity","title":"Get instantaneous velocity for subjects","topics":["get_velocity"]},{"page":"get_vis_angle","title":"Estimate visual angles from a subject's perspective in an experimental tunnel","topics":["get_vis_angle"]},{"page":"import_and_clean_batch","title":"Batch import and clean files","topics":["import_and_clean_batch"]},{"page":"import_and_clean_viewr","title":"Import + clean_viewr()","topics":["import_and_clean_viewr"]},{"page":"import_batch","title":"Batch import of files for either Motive or Flydra (but not a mix of both)","topics":["import_batch"]},{"page":"insert_treatments","title":"Inserts treatment and experiment 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height","topics":["relabel_viewr_axes"]},{"page":"remove_duplicate_frames","title":"Remove any duplicates or aliased frames within trajectories","topics":["remove_duplicate_frames"]},{"page":"remove_vel_anomalies","title":"Remove any rows which show sharp shifts in velocity that are likely due to tracking errors","topics":["remove_vel_anomalies"]},{"page":"rename_viewr_characters","title":"Rename subjects in the data via pattern detection","topics":["rename_viewr_characters"]},{"page":"rescale_tunnel_data","title":"Rescale position data within a 'viewr' object","topics":["rescale_tunnel_data"]},{"page":"rm_by_trajnum","title":"Remove subjects by trajectory number","topics":["rm_by_trajnum"]},{"page":"rotate_tunnel","title":"Rotate a tunnel so that perches are approximately aligned","topics":["rotate_tunnel"]},{"page":"section_tunnel_by","title":"Bin data along a specified axis","topics":["section_tunnel_by"]},{"page":"select_x_percent","title":"Select a region of interest within the 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