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ID","topics":["lowest_common","lowest_common.default","lowest_common.gbifid","lowest_common.tolid","lowest_common.tsn","lowest_common.uid"]},{"page":"names_list","title":"Get a random vector of species names.","topics":["names_list"]},{"page":"nbn_classification","title":"Search UK National Biodiversity Network database for taxonomic classification","topics":["nbn_classification"]},{"page":"nbn_search","title":"Search UK National Biodiversity Network","topics":["nbn_search"]},{"page":"nbn_synonyms","title":"Return all synonyms for a taxon name with a given id from NBN","topics":["nbn_synonyms"]},{"page":"ncbi_children","title":"Search NCBI for children of a taxon","topics":["ncbi_children"]},{"page":"ncbi_downstream","title":"Retrieve all taxa names downstream in hierarchy for NCBI","topics":["ncbi_downstream"]},{"page":"ncbi_get_taxon_summary","title":"NCBI taxon information from uids","topics":["ncbi_get_taxon_summary"]},{"page":"ping","title":"Ping an API used in taxize to see if it's working.","topics":["bold_ping","col_ping","eol_ping","fg_ping","gbif_ping","ipni_ping","itis_ping","nbn_ping","ncbi_ping","ping","tropicos_ping","vascan_ping"]},{"page":"plantGenusNames","title":"Vector of plant genus names from ThePlantList","topics":["plantGenusNames"]},{"page":"plantminer","title":"Search for taxonomy data from Plantminer.com","topics":["plantminer"]},{"page":"plantNames","title":"Vector of plant species (genus - specific epithet) names from ThePlantList","topics":["plantNames"]},{"page":"pow_lookup","title":"Lookup taxa in Kew's Plants of the World","topics":["pow_lookup"]},{"page":"pow_search","title":"Search Kew's Plants of the World","topics":["pow_search"]},{"page":"pow_synonyms","title":"Lookup synonyms in Kew's Plants of the World","topics":["pow_synonyms"]},{"page":"rank_ref","title":"Lookup-table for IDs of taxonomic ranks","topics":["rank_ref"]},{"page":"rank_ref_zoo","title":"Lookup-table for IDs of taxonomic ranks 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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) ) allows users to\nretrieve functional annotation for genomic loci. In addition,\nusers can download entire databases such as 'NCBI RefSeq'\n(Pruitt et al. (2007) ), 'NCBI nr',\n'NCBI nt', 'NCBI Genbank' (Benson et al. (2013)\n), etc. with only one command.","VignetteBuilder":"knitr","NeedsCompilation":"yes","License":"GPL-2","URL":"https://docs.ropensci.org/biomartr/,\nhttps://github.com/ropensci/biomartr","BugReports":"https://github.com/ropensci/biomartr/issues","RoxygenNote":"7.3.1","Encoding":"UTF-8","Config/pak/sysreqs":"make libicu-dev libpng-dev libxml2-dev libssl-dev\nlibx11-dev","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/biomartr","RemoteRef":"master","RemoteSha":"d9302099ed582f688411e7721cbe43e10a4c4d0e","Packaged":{"Date":"2024-12-12 22:23:05 UTC","User":"root"},"Author":"Hajk-Georg Drost [aut, cre] (),\nHaakon Tjeldnes [aut, ctb]","Maintainer":"Hajk-Georg Drost 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*[Stable]*","topics":["vis_drake_graph"]},{"page":"which_clean","title":"Which targets will 'clean()' invalidate? *[Stable]*","topics":["which_clean"]}],"_pkglogo":"https://github.com/ropensci/drake/raw/main/man/figures/logo.svg","_readme":"https://github.com/ropensci/drake/raw/main/README.md","_rundeps":["backports","base64url","cli","cpp11","digest","filelock","glue","igraph","lattice","lifecycle","magrittr","Matrix","pkgconfig","R6","rlang","storr","tidyselect","txtq","vctrs","withr"],"_score":11.511262326898112,"_indexed":true,"_nocasepkg":"drake","_universes":["ropensci","wlandau"]} {"Package":"jagstargets","Title":"Targets for JAGS Pipelines","Description":"Bayesian data analysis usually incurs long runtimes and\ncumbersome custom code. A pipeline toolkit tailored to Bayesian\nstatisticians, the 'jagstargets' R package is leverages\n'targets' and 'R2jags' to ease this burden. 'jagstargets' makes\nit super easy to set up scalable JAGS pipelines that\nautomatically parallelize the computation and skip expensive\nsteps when the results are already up to date. Minimal custom\ncode is required, and there is no need to manually configure\nbranching, so usage is much easier than 'targets' alone. 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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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