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{"Package":"stats19","Title":"Work with Open Road Traffic Casualty Data from Great Britain","Version":"3.3.1","Authors@R":"c(\nperson(\"Robin\", \"Lovelace\", email = \"rob00x@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5679-6536\")),\nperson(\"Malcolm\", \"Morgan\", email = \"m.morgan1@leeds.ac.uk\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-9488-9183\")),\nperson(\"Layik\", \"Hama\", email = \"layik.hama@gmail.com\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-1912-4890\")),\nperson(\"Mark\", \"Padgham\", role=c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-2172-5265\")),\nperson(\"David\", \"Ranzolin\", role=c(\"rev\")),\nperson(\"Adam\", \"Sparks\", role = c(\"rev\", \"ctb\"),\ncomment = c(ORCID = \"0000-0002-0061-8359\")),\nperson(\"Ivo\", \"Wengraf\", role = c(\"ctb\")),\nperson(given = \"RAC Foundation\", role = c(\"fnd\"))\n)","Description":"Tools to help download, process and analyse the UK road\ncollision data collected using the 'STATS19' form. The datasets\nare provided as 'CSV' files with detailed road safety\ninformation about the circumstances of car crashes and other\nincidents on the roads resulting in casualties in Great Britain\nfrom 1979 to present. Tables are available on 'colissions' with\nthe circumstances (e.g. speed limit of road), information about\n'vehicles' involved (e.g. type of vehicle), and 'casualties'\n(e.g. age). The statistics relate only to events on public\nroads that were reported to the police, and subsequently\nrecorded, using the 'STATS19' collision reporting form. See the\nDepartment for Transport website\n<https://www.data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-accidents-safety-data>\nfor more information on these datasets. The package is\ndescribed in a paper in the Journal of Open Source Software\n(Lovelace et al. 2019) <doi:10.21105/joss.01181>. See Gilardi\net al. (2022) <doi:10.1111/rssa.12823>, Vidal-Tortosa et al.\n(2021) <doi:10.1016/j.jth.2021.101291>, and Tait et al. 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{"Package":"biomartr","Title":"Genomic Data Retrieval","Version":"1.0.9","Authors@R":"c(person(\"Hajk-Georg\", \"Drost\",\nrole = c(\"aut\", \"cre\"),\nemail = \"hajk-georg.drost@tuebingen.mpg.de\",\ncomment = c(ORCID = \"http://orcid.org/0000-0002-1567-306X\")),\nperson(\"Haakon\", \"Tjeldnes\",\nemail = \"hauken_heyken@hotmail.com\",\nrole = c(\"aut\", \"ctb\"))\n)","Description":"Perform large scale genomic data retrieval and functional\nannotation retrieval. This package aims to provide users with a\nstandardized way to automate genome, proteome, 'RNA', coding\nsequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI\nRefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases.\nFurthermore, an interface to the 'BioMart' database (Smedley et\nal. (2009) <doi:10.1186/1471-2164-10-22>) allows users to\nretrieve functional annotation for genomic loci. In addition,\nusers can download entire databases such as 'NCBI RefSeq'\n(Pruitt et al. 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{"Type":"Package","Package":"GSODR","Title":"Global Surface Summary of the Day ('GSOD') Weather Data Client","Version":"4.1.3.9000","Authors@R":"c(\nperson(\"Adam H.\", \"Sparks\", , \"adamhsparks@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0061-8359\")),\nperson(\"Tomislav\", \"Hengl\", , \"tom.hengl@isric.org\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-9921-5129\")),\nperson(\"Andrew\", \"Nelson\", , \"dr.andy.nelson@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-7249-3778\")),\nperson(\"Hugh\", \"Parsonage\", , \"hugh.parsonage@gmail.com\", role = c(\"cph\", \"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(\"Curtin University\", role = \"cph\",\ncomment = \"Supported the development of 'GSODR' through\\n        Adam H. 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{"Package":"weatherOz","Title":"An API Client for Australian Weather and Climate Data Resources","Version":"1.0.0.9000","Authors@R":"c(\nperson(\"Rodrigo\", \"Pires\", , \"rodrigo.pires@dpird.wa.gov.au\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7384-6849\")),\nperson(\"Anna\", \"Hepworth\", , \"anna.hepworth@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-0204-6347\")),\nperson(\"Rebecca\", \"O'Leary\", , \"bec.oleary@curtin.edu.au\", role = \"aut\"),\nperson(\"Jonathan\", \"Carroll\", , \"rpkg@jcarroll.com.au\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-1404-5264\")),\nperson(\"James\", \"Goldie\", , \"me@jamesgoldie.dev\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-5024-6207\")),\nperson(\"Dean\", \"Marchiori\", , \"deanmarchiori@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-3430-7225\")),\nperson(\"Paul\", \"Melloy\", , \"paul@melloy.com.au\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-4253-7167\")),\nperson(\"Mark\", \"Padgham\", , \"mark.padgham@email.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-2172-5265\")),\nperson(\"Hugh\", \"Parsonage\", , \"hugh.parsonage@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-4055-0835\")),\nperson(\"Keith\", \"Pembleton\", , \"keith.pembleton@unisq.edu.au\", role = \"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\", , \"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\\n                URL when run outside of Australia/Perth TZ! Suggested the use of `withr::local_timzeone()`, see <https://github.com/ropensci/weatherOz/commit/b052bf91973b8d7e147a39e8938405a64622634b>.\")),\nperson(\"Max\", \"Moldovan\", , \"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(\"Jimmy\", \"Ng\", , \"jimmy.ng@dpird.wa.gov.au\", role = \"ctb\"),\nperson(\"Steve\", \"Collins\", , \"steve.collins@dpird.wa.gov.au\", role = \"ctb\",\ncomment = \"Designed the hex logo for 'weatherOz' hex logo.\"),\nperson(\"Adam H.\", \"Sparks\", , \"adamhsparks@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-0061-8359\")),\nperson(\"Laurens\", \"Geffert\", , \"laurensgeffert@gmail.com\", role = \"rev\"),\nperson(\"Sam\", \"Rogers\", , \"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\nTechnology Division of the Queensland Government's Department\nof Environment 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'\nweather data are accessed through public 'APIs' provided by\n'DPIRD', <https://www.agric.wa.gov.au/weather-api-20>,\nproviding access to weather station data from the 'DPIRD'\nweather station network.  Australia-wide weather data are based\non data from the Australian Bureau of Meteorology ('BOM') data\nand accessed through 'SILO' (Scientific Information for Land\nOwners) Jeffrey et al. (2001)\n<doi:10.1016/S1364-8152(01)00008-1>.  'DPIRD' data are made\navailable under a Creative Commons Attribution 3.0 Licence (CC\nBY 3.0 AU) license\n<https://creativecommons.org/licenses/by/3.0/au/deed.en>. SILO\ndata are released under a Creative Commons Attribution 4.0\nInternational licence (CC BY 4.0)\n<https://creativecommons.org/licenses/by/4.0/>. '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<http://www.bom.gov.au/other/copyright.shtml> for further\ndetails.","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":"7.3.2","Config/pak/sysreqs":"libgdal-dev gdal-bin libgeos-dev libxml2-dev\nlibssl-dev libproj-dev libsqlite3-dev","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/weatherOz","RemoteRef":"main","RemoteSha":"c0133d2fb913c098068792e3cdce10c64e4d550a","NeedsCompilation":"no","Packaged":{"Date":"2024-12-27 05:45:24 UTC","User":"root"},"Author":"Rodrigo Pires [aut, cre] (<https://orcid.org/0000-0001-7384-6849>),\nAnna Hepworth [aut] (<https://orcid.org/0000-0003-0204-6347>),\nRebecca O'Leary [aut],\nJonathan Carroll [aut] (<https://orcid.org/0000-0002-1404-5264>),\nJames Goldie [aut] (<https://orcid.org/0000-0002-5024-6207>),\nDean Marchiori [aut] (<https://orcid.org/0000-0002-3430-7225>),\nPaul Melloy [aut] (<https://orcid.org/0000-0003-4253-7167>),\nMark Padgham [aut] (<https://orcid.org/0000-0003-2172-5265>),\nHugh Parsonage [aut] (<https://orcid.org/0000-0003-4055-0835>),\nKeith Pembleton [ctb] (<https://orcid.org/0000-0002-1896-4516>,\nContributed code and ideas for original 'bomrang' package that was\nused in the creation of 'weatherOz'.),\nMaëlle Salmon [ctb] (<https://orcid.org/0000-0002-2815-0399>,\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<https://github.com/ropensci/weatherOz/commit/b052bf91973b8d7e147a39e8938405a64622634b>.),\nMax Moldovan [ctb] (<https://orcid.org/0000-0001-9680-8474>,\nContributed valuable feedback on package usage leading to\nimprovements in the package structure and functionality.),\nJimmy Ng [ctb],\nSteve Collins [ctb] (Designed the hex logo for 'weatherOz' hex logo.),\nAdam H. 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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 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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? 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/master/README.md","_rundeps":["ade4","ape","beautier","bit","bit64","cli","clipr","cpp11","crayon","digest","fansi","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":[{"package":"openjdk-21-jre-headless","headers":"openjdk-21-jre-headless","source":"openjdk","version":"21.0.5+11-1ubuntu1~24.04","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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