Package: beastier 2.5.2

Richèl J.C. Bilderbeek

beastier: Call 'BEAST2'

'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is a command-line tool. This package provides a way to call 'BEAST2' from an 'R' function call.

Authors:Richèl J.C. Bilderbeek [aut, cre], Joëlle Barido-Sottani [rev], David Winter [rev], Jason Griffiths [ctb], Olivier Roy [ctb], Thijs Janzen [ctb]

beastier_2.5.2.tar.gz
beastier_2.5.2.zip(r-4.5)beastier_2.5.2.zip(r-4.4)beastier_2.5.2.zip(r-4.3)
beastier_2.5.2.tgz(r-4.4-any)beastier_2.5.2.tgz(r-4.3-any)
beastier_2.5.2.tar.gz(r-4.5-noble)beastier_2.5.2.tar.gz(r-4.4-noble)
beastier_2.5.2.tgz(r-4.4-emscripten)beastier_2.5.2.tgz(r-4.3-emscripten)
beastier.pdf |beastier.html✨
beastier/json (API)
NEWS

# Install 'beastier' in R:
install.packages('beastier', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ropensci/beastier/issues

Pkgdown:https://docs.ropensci.org

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On CRAN:

bayesianbeastbeast2phylogenetic-inferencephylogeneticsopenjdk

7.86 score 11 stars 4 packages 46 scripts 577 downloads 99 exports 50 dependencies

Last updated 1 months agofrom:21474822a6. Checks:OK: 6 ERROR: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 03 2024
R-4.5-winOKDec 03 2024
R-4.5-linuxERRORDec 03 2024
R-4.4-winOKDec 03 2024
R-4.4-macOKDec 03 2024
R-4.3-winOKDec 03 2024
R-4.3-macOKDec 03 2024

Exports:add_quotes_if_has_spacesare_beast2_input_linesare_beast2_input_lines_deepare_beast2_input_lines_fastare_identical_alignmentsbeast2_options_to_tablebeastier_reportcheck_beast2check_beast2_optionscheck_beast2_options_data_typescheck_beast2_options_do_not_overwrite_existing_filescheck_beast2_options_filenames_differcheck_beast2_options_namescheck_beast2_optionsescheck_beast2_pathcheck_can_create_dir_for_state_output_filecheck_can_create_filecheck_can_create_screenlog_filecheck_can_create_state_output_filecheck_can_create_tracelog_filecheck_can_create_treelog_filecheck_empty_beastier_foldercheck_empty_beaustier_folderscheck_input_filenamecheck_input_filename_validitycheck_n_threadscheck_oscheck_rng_seedcontinue_beast2create_beast2_continue_cmd_from_optionscreate_beast2_input_file_foldercreate_beast2_optionscreate_beast2_run_cmdcreate_beast2_run_cmd_from_optionscreate_beast2_screenlog_foldercreate_beast2_state_output_file_foldercreate_beast2_tracelog_foldercreate_beast2_treelog_foldercreate_beast2_validate_cmdcreate_beast2_validate_cmd_bincreate_beast2_validate_cmd_jarcreate_beast2_version_cmdcreate_beast2_version_cmd_bincreate_beast2_version_cmd_jarcreate_beastier_tempfoldercreate_mcbette_beast2_optionscreate_random_alignmentcreate_random_fastacreate_random_phylogenycreate_temp_input_filenamecreate_temp_state_filenamedo_minimal_runextract_screenlog_filename_from_beast2_input_fileextract_tracelog_filename_from_beast2_input_fileextract_treelog_filename_from_beast2_input_fileget_alignment_ids_from_xml_filenameget_beast2_example_filenameget_beast2_example_filenamesget_beast2_main_class_nameget_beast2_options_filenamesget_beast2_versionget_beastier_folderget_beastier_pathget_beastier_pathsget_beastier_tempfilenameget_default_beast2_bin_pathget_default_beast2_download_urlget_default_beast2_download_url_linuxget_default_beast2_download_url_winget_default_beast2_folderget_default_beast2_jar_pathget_default_beast2_pathget_default_beast2_versionget_default_java_pathget_duplicate_param_idsget_java_versionget_trees_filenamesgives_beast2_warninghas_unique_idsinstall_beast2is_alignmentis_beast2_input_fileis_beast2_installedis_bin_pathis_jar_pathis_on_appveyoris_on_ciis_on_travisis_win_bin_pathprint_beast2_optionsremove_beastier_folderremove_beaustier_foldersremove_file_if_presentrename_beast2_options_filenamesrun_beast2run_beast2_from_optionssave_linessave_nexus_as_fastauninstall_beast2

Dependencies:ade4apebeautierbitbit64clicliprcpp11crayondigestfansigenericsgluehmsigraphlatticelifecyclemagrittrMASSMatrixnlmephangornpillarpixmappkgconfigprettyunitsprogresspurrrquadprogR6rappdirsRcppRcppArmadilloreadrrJavarlangsegmentedseqinrsessioninfospstringistringrtibbletidyselecttzdbutf8vctrsvroomwithrxml2

beastier demo

Richèl J.C. Bilderbeek

Rendered fromdemo.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2022-06-01
Started: 2019-04-25

Readme and manuals

Help Manual

Help pageTopics
Add quotes around the string if it contains spaces.add_quotes_if_has_spaces
Would these lines of text, when written to a file, result in a valid BEAST2 input file?are_beast2_input_lines
Would these lines of text, when written to a file, result in a valid BEAST2 input file?are_beast2_input_lines_deep
Would these lines of text, when written to a file, result in a valid BEAST2 input file?are_beast2_input_lines_fast
Determines if the two alignments are equalare_identical_alignments
Convert a 'beast2_options' to a tablebeast2_options_to_table
Creates a beastier reportbeastier_report
Check if 'BEAST2' is installed properly.check_beast2
Check if the 'beast2_options' is a valid BEAST2 options object.check_beast2_options
Check if the 'beast2_options', which is a list, has all elements of the right data typescheck_beast2_options_data_types
Internal functioncheck_beast2_options_do_not_overwrite_existing_files
Check if the filenames in 'beast2_options' differcheck_beast2_options_filenames_differ
Check if the 'beast2_options', which is a list, has all the elements needed.check_beast2_options_names
Check if the 'beast2_options' is a valid BEAST2 options object.check_beast2_optionses
Checks the BEAST2 '.jar' path. Will stop if there is a problem with the BEAST2 '.jar' path.check_beast2_path
Internal functioncheck_can_create_dir_for_state_output_file
Internal functioncheck_can_create_file
Internal functioncheck_can_create_screenlog_file
Internal functioncheck_can_create_state_output_file
Internal function to check if the MCMC's tracelog file can be created.check_can_create_tracelog_file
Internal functioncheck_can_create_treelog_file
Check there are no files in the default beastier foldercheck_empty_beastier_folder
Check there are no files in the default `beautier` and `beastier` folderscheck_empty_beaustier_folders
Checks the input filename. Will stop if there is a problem with the input filename.check_input_filename
Checks the input filename. Will stop if there is a problem with the input filename.check_input_filename_validity
Check if the input is a valid number of threads.check_n_threads
Checks if the operating system is supportedcheck_os
Check if the input is a valid RNG seed.check_rng_seed
Continue a BEAST2 runcontinue_beast2
Creates the terminal command to run BEAST2 from a 'beast2_options'create_beast2_continue_cmd_from_options
Create the folder where the BEAST2 input file will be createdcreate_beast2_input_file_folder
Function to create a set of BEAST2 options.create_beast2_options
Creates the terminal command to run BEAST2create_beast2_run_cmd
Creates the terminal command to run BEAST2 from a 'beast2_options'create_beast2_run_cmd_from_options
Internal functioncreate_beast2_screenlog_folder
Create the folder where the BEAST2 state output file will be createdcreate_beast2_state_output_file_folder
Internal functioncreate_beast2_tracelog_folder
Internal functioncreate_beast2_treelog_folder
Creates the terminal command to validate a BEAST2 input filecreate_beast2_validate_cmd
Creates the terminal command to validate a BEAST2 input file using a call to the 'launcher.jar' filecreate_beast2_validate_cmd_bin
Creates the terminal command to validate a BEAST2 input file using a call to the 'launcher.jar' filecreate_beast2_validate_cmd_jar
Creates the terminal command to version a BEAST2 input filecreate_beast2_version_cmd
Creates the terminal command to version a BEAST2 input file using a call to the 'launcher.jar' filecreate_beast2_version_cmd_bin
Creates the terminal command to version a BEAST2 input file using a call to the 'launcher.jar' filecreate_beast2_version_cmd_jar
Create the temporary folder as used by beastiercreate_beastier_tempfolder
Create a `beast2_options` structure for the `mcbette` R packagecreate_mcbette_beast2_options
Create a random alignmentcreate_random_alignment
Create a random FASTA filecreate_random_fasta
Create a random phylogenycreate_random_phylogeny
Create a temporary filename for the BEAST2 XML filenamecreate_temp_input_filename
Create a temporary file for the BEAST2 XML output file that stores its state.create_temp_state_filename
This function does nothing. It is intended to inherit is parameters' documentation.default_params_doc
Do a minimal BEAST2 rundo_minimal_run
Internal function to extract the screenlog filename for a BEAST2 input fileextract_screenlog_filename_from_beast2_input_file
Internal function to extract the tracelog filename for a BEAST2 input fileextract_tracelog_filename_from_beast2_input_file
Internal function to extract the treelog filename for a BEAST2 input fileextract_treelog_filename_from_beast2_input_file
Get the alignment ID from a file with one alignmentget_alignment_ids_from_xml_filename
Get the full path of a BEAST2 example fileget_beast2_example_filename
Get a list with the full paths of all BEAST2 example filenamesget_beast2_example_filenames
Get the BEAST2 main class name.get_beast2_main_class_name
Extract the filenames from a `beast2_options`get_beast2_options_filenames
Get the BEAST2 versionget_beast2_version
Get the path to the beastier temporary files folderget_beastier_folder
Get the full path of a file in the 'inst/extdata' folderget_beastier_path
Get the full paths of files in the 'inst/extdata' folderget_beastier_paths
Get a temporary filenameget_beastier_tempfilename
Get the default BEAST2 binary file ('beast', that is) pathget_default_beast2_bin_path
Get the default BEAST2 download URL, which depends on the operating systemget_default_beast2_download_url
Get the BEAST2 download URL for Linuxget_default_beast2_download_url_linux
Get the BEAST2 download URL for Windowsget_default_beast2_download_url_win
Get the path to the folder where this package installs BEAST2 by defaultget_default_beast2_folder
Get the default BEAST2 jar file's pathget_default_beast2_jar_path
Get the default BEAST2 pathget_default_beast2_path
Get the default BEAST2 version that is used by beastierget_default_beast2_version
Obtains the default path to the Java executableget_default_java_path
Find duplicate 'RealParameter' IDsget_duplicate_param_ids
Get the Java versionget_java_version
Get the .trees filenames that BEAST2 will produceget_trees_filenames
Determines if BEAST2 issues a warning when using the BEAST2 XML input filegives_beast2_warning
Determine if the XML text has unique parameter IDshas_unique_ids
Deprecated function to install BEAST2install_beast2
Determines if the input is an alignment of type DNAbinis_alignment
Is a file a valid BEAST2 input file?is_beast2_input_file
Checks if BEAST2 is installedis_beast2_installed
Is the path a path to the BEAST2 binary file? Does not check if the file at that path is presentis_bin_path
Is the path a path to the BEAST2 jar file? Does not check if the file at that path is presentis_jar_path
Deprecated function, use is_on_appveyoris_on_appveyor
Deprecated function, use is_on_ciis_on_ci
Deprecated function, use is_on_travisis_on_travis
Is the path a path to the BEAST2 binary file? Does not check if the file at that path is presentis_win_bin_path
Pretty-print a `beast2_options`print_beast2_options
Check there are no files in the default beautier folderremove_beastier_folder
Remove the `beautier` and `beastier` temporary foldersremove_beaustier_folders
Remove a file if it is present, will do nothing if it is not.remove_file_if_present
Rename the filenames in the BEAST2 optionsrename_beast2_options_filenames
Run BEAST2run_beast2
Run BEAST2run_beast2_from_options
Save text (a container of strings) to a filesave_lines
Save a NEXUS file as a FASTA filesave_nexus_as_fasta
Deprecated function to uninstall BEAST2uninstall_beast2
Deprecated function to upgrade BEAST2.upgrade_beast2