Package: beastier 2.5.3

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_2.5.3.tar.gz
beastier_2.5.3.zip(r-4.7)beastier_2.5.3.zip(r-4.6)beastier_2.5.3.zip(r-4.5)
beastier_2.5.3.tgz(r-4.6-any)beastier_2.5.3.tgz(r-4.5-any)
beastier_2.5.3.tar.gz(r-4.7-any)beastier_2.5.3.tar.gz(r-4.6-any)
beastier_2.5.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
beastier/json (API)

# Install 'beastier' in R:

install.packages('beastier', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org'))

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

Pkgdown/docs site:https://docs.ropensci.org

Uses libs:

openjdk– OpenJDK Java runtime, using Hotspot JIT

On CRAN:

bayesian beast beast2 phylogenetic-inference phylogenetics openjdk

7.64 score 11 stars 4 packages 55 scripts 438 downloads 99 exports 50 dependencies

Last updated from:fb20b891a5 (on main). Checks:2 ERROR, 8 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	160
pkgdown docs	OK	138
source / vignettes	OK	217
linux-release-x86_64	ERROR	155
macos-release-arm64	OK	127
macos-oldrel-arm64	OK	158
windows-devel	OK	87
windows-release	OK	102
windows-oldrel	OK	101
wasm-release	OK	166

Dependencies:ade4 ape beautier bit bit64 cli clipr cpp11 crayon digest fastmatch generics glue hms igraph lattice lifecycle magrittr MASS Matrix nlme phangorn pillar pixmap pkgconfig prettyunits progress purrr quadprog R6 rappdirs Rcpp RcppArmadillo readr rJava rlang segmented seqinr sessioninfo sp stringi stringr tibble tidyselect tzdb utf8 vctrs vroom withr xml2

beastier demo

Introduction

Rendered fromdemo.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 equal	are_identical_alignments
Convert a 'beast2_options' to a table	beast2_options_to_table
Creates a beastier report	beastier_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 types	check_beast2_options_data_types
Internal function	check_beast2_options_do_not_overwrite_existing_files
Check if the filenames in 'beast2_options' differ	check_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 function	check_can_create_dir_for_state_output_file
Internal function	check_can_create_file
Internal function	check_can_create_screenlog_file
Internal function	check_can_create_state_output_file
Internal function to check if the MCMC's tracelog file can be created.	check_can_create_tracelog_file
Internal function	check_can_create_treelog_file
Check there are no files in the default beastier folder	check_empty_beastier_folder
Check there are no files in the default `beautier` and `beastier` folders	check_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 supported	check_os
Check if the input is a valid RNG seed.	check_rng_seed
Continue a BEAST2 run	continue_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 created	create_beast2_input_file_folder
Function to create a set of BEAST2 options.	create_beast2_options
Creates the terminal command to run BEAST2	create_beast2_run_cmd
Creates the terminal command to run BEAST2 from a 'beast2_options'	create_beast2_run_cmd_from_options
Internal function	create_beast2_screenlog_folder
Create the folder where the BEAST2 state output file will be created	create_beast2_state_output_file_folder
Internal function	create_beast2_tracelog_folder
Internal function	create_beast2_treelog_folder
Creates the terminal command to validate a BEAST2 input file	create_beast2_validate_cmd
Creates the terminal command to validate a BEAST2 input file using a call to the 'launcher.jar' file	create_beast2_validate_cmd_bin
Creates the terminal command to validate a BEAST2 input file using a call to the 'launcher.jar' file	create_beast2_validate_cmd_jar
Creates the terminal command to version a BEAST2 input file	create_beast2_version_cmd
Creates the terminal command to version a BEAST2 input file using a call to the 'launcher.jar' file	create_beast2_version_cmd_bin
Creates the terminal command to version a BEAST2 input file using a call to the 'launcher.jar' file	create_beast2_version_cmd_jar
Create the temporary folder as used by beastier	create_beastier_tempfolder
Create a `beast2_options` structure for the `mcbette` R package	create_mcbette_beast2_options
Create a random alignment	create_random_alignment
Create a random FASTA file	create_random_fasta
Create a random phylogeny	create_random_phylogeny
Create a temporary filename for the BEAST2 XML filename	create_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 run	do_minimal_run
Internal function to extract the screenlog filename for a BEAST2 input file	extract_screenlog_filename_from_beast2_input_file
Internal function to extract the tracelog filename for a BEAST2 input file	extract_tracelog_filename_from_beast2_input_file
Internal function to extract the treelog filename for a BEAST2 input file	extract_treelog_filename_from_beast2_input_file
Get the alignment ID from a file with one alignment	get_alignment_ids_from_xml_filename
Get the full path of a BEAST2 example file	get_beast2_example_filename
Get a list with the full paths of all BEAST2 example filenames	get_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 version	get_beast2_version
Get the path to the beastier temporary files folder	get_beastier_folder
Get the full path of a file in the 'inst/extdata' folder	get_beastier_path
Get the full paths of files in the 'inst/extdata' folder	get_beastier_paths
Get a temporary filename	get_beastier_tempfilename
Get the default BEAST2 binary file ('beast', that is) path	get_default_beast2_bin_path
Get the default BEAST2 download URL, which depends on the operating system	get_default_beast2_download_url
Get the BEAST2 download URL for Linux	get_default_beast2_download_url_linux
Get the BEAST2 download URL for Windows	get_default_beast2_download_url_win
Get the path to the folder where this package installs BEAST2 by default	get_default_beast2_folder
Get the default BEAST2 jar file's path	get_default_beast2_jar_path
Get the default BEAST2 path	get_default_beast2_path
Get the default BEAST2 version that is used by beastier	get_default_beast2_version
Obtains the default path to the Java executable	get_default_java_path
Find duplicate 'RealParameter' IDs	get_duplicate_param_ids
Get the Java version	get_java_version
Get the .trees filenames that BEAST2 will produce	get_trees_filenames
Determines if BEAST2 issues a warning when using the BEAST2 XML input file	gives_beast2_warning
Determine if the XML text has unique parameter IDs	has_unique_ids
Deprecated function to install BEAST2	install_beast2
Determines if the input is an alignment of type DNAbin	is_alignment
Is a file a valid BEAST2 input file?	is_beast2_input_file
Checks if BEAST2 is installed	is_beast2_installed
Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present	is_bin_path
Is the path a path to the BEAST2 jar file? Does not check if the file at that path is present	is_jar_path
Deprecated function, use is_on_appveyor	is_on_appveyor
Deprecated function, use is_on_ci	is_on_ci
Deprecated function, use is_on_travis	is_on_travis
Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present	is_win_bin_path
Pretty-print a `beast2_options`	print_beast2_options
Check there are no files in the default beautier folder	remove_beastier_folder
Remove the `beautier` and `beastier` temporary folders	remove_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 options	rename_beast2_options_filenames
Run BEAST2	run_beast2
Run BEAST2	run_beast2_from_options
Save text (a container of strings) to a file	save_lines
Save a NEXUS file as a FASTA file	save_nexus_as_fasta
Deprecated function to uninstall BEAST2	uninstall_beast2
Deprecated function to upgrade BEAST2.	upgrade_beast2