Man pages for richelbilderbeek/beastier
Call 'BEAST2'

are_beast2_input_linesWould these lines of text, when written to a file, result in...
are_beast2_input_lines_deepWould these lines of text, when written to a file, result in...
are_beast2_input_lines_fastWould these lines of text, when written to a file, result in...
are_identical_alignmentsDetermines if the two alignments are equal
beast2_internal_filenames_to_tableConvert a 'beast2_internal_filenames' to a table
beast2_options_to_tableConvert a 'beast2_options' to a table
beastier'beastier': A package to call BEAST2.
check_beast2Check if 'BEAST2' is installed properly.
check_beast2_internal_filenamesCheck if the 'beast2_internal_filenames' is a valid BEAST2...
check_beast2_optionsCheck if the 'beast2_options' is a valid BEAST2 options...
check_beast2_optionsesCheck if the 'beast2_options' is a valid BEAST2 options...
check_beast2_pathChecks the BEAST2 '.jar' path. Will stop if there is a...
check_can_create_fileCheck that a file can be created at a certain path.
check_input_filenameChecks the input filename. Will stop if there is a problem...
check_n_threadsCheck if the input is a valid number of threads.
check_osChecks if the operating system is supported
check_rng_seedCheck if the input is a valid RNG seed.
create_beast2_internal_filenamesCreate a list with the internally used BEAST2 filenames
create_beast2_optionsFunction to create a set of BEAST2 options.
create_beast2_run_cmdCreates the terminal command to run BEAST2
create_beast2_validate_cmdCreates the terminal command to validate a BEAST2 input file
create_beast2_validate_cmd_binCreates the terminal command to validate a BEAST2 input file...
create_beast2_validate_cmd_jarCreates the terminal command to validate a BEAST2 input file...
create_beast2_version_cmdCreates the terminal command to version a BEAST2 input file
create_beast2_version_cmd_binCreates the terminal command to version a BEAST2 input file...
create_beast2_version_cmd_jarCreates the terminal command to version a BEAST2 input file...
create_temp_input_filenameCreate a temporary filename for the BEAST2 XML filename
create_temp_output_state_filenameCreate a temporary file for the BEAST2 XML output file that...
default_params_docThis function does nothing. It is intended to inherit is...
do_minimal_runDo a minimal BEAST2 run
get_alignment_ids_from_xml_filenameGet the alignment ID from a file with one alignment
get_beast2_example_filenameGet the full path of a BEAST2 example file
get_beast2_example_filenamesGet a list with the full paths of all BEAST2 example...
get_beast2_main_class_nameGet the BEAST2 main class name.
get_beast2_options_filenamesExtract the filenames from a 'beast2_options'
get_beast2_versionGet the BEAST2 version
get_beastier_pathGet the full path of a file in the 'inst/extdata' folder
get_beastier_pathsGet the full paths of files in the 'inst/extdata' folder
get_default_beast2_bin_pathGet the default BEAST2 binary file ('beast', that is) path
get_default_beast2_download_urlGet the default BEAST2 download URL, which depends on the...
get_default_beast2_download_url_linuxGet the BEAST2 download URL for Linux
get_default_beast2_download_url_winGet the BEAST2 download URL for Windows
get_default_beast2_folderGet the path to the folder where this package installs BEAST2...
get_default_beast2_jar_pathGet the default BEAST2 jar file's path
get_default_beast2_pathGet the default BEAST2 path
get_default_java_pathObtains the default path to the Java executable
get_duplicate_param_idsFind duplicate 'RealParameter' IDs
get_java_versionGet the Java version
get_trees_filenamesGet the .trees filenames that BEAST2 will produce
gives_beast2_warningDetermines if BEAST2 issues a warning when using the BEAST2...
has_unique_idsDetermine if the XML text has unique parameter IDs
install_beast2Install BEAST2
is_alignmentDetermines if the input is an alignment of type DNAbin
is_beast2_input_fileIs a file a valid BEAST2 input file?
is_beast2_installedChecks if BEAST2 is installed
is_bin_pathIs the path a path to the BEAST2 binary file? Does not check...
is_jar_pathIs the path a path to the BEAST2 jar file? Does not check if...
is_on_appveyorDetermines if the environment is AppVeyor
is_on_ciDetermines if the environment is a continuous integration...
is_on_travisDetermines if the environment is Travis CI
print_beast2_internal_filenamesPrint a 'beast2_internal_filenames' as a table
print_beast2_optionsPretty-print a 'beast2_options'
remove_file_if_presentRemove a file if it is present
run_beast2Run BEAST2
run_beast2_from_optionsRun BEAST2
save_linesSave text (a container of strings) to a file
uninstall_beast2Uninstall BEAST2
update_beastierUpdate all beastier dependencies, by installing their latest...
upgrade_beast2Upgrade BEAST2.
richelbilderbeek/beastier documentation built on Nov. 6, 2019, 10:24 a.m.