Check if the input is a valid number of threads.
Checks if the operating system is supported
check_beast2_options_data_types
Check if the beast2_options, which is a list,
has all elements of the right data types
check_input_filename_validity
Checks the input filename.
Will stop if there is a problem with the input filename.
Checks the input filename.
Will stop if there is a problem with the input filename.
Creates the terminal command to run BEAST2
Internal function
Function to create a set of BEAST2 options.
check_can_create_tracelog_file
Internal function to check if the MCMC's tracelog file can be created.
check_can_create_treelog_file
Internal function
check_can_create_dir_for_state_output_file
Internal function
Checks the BEAST2 .jar path.
Will stop if there is a problem with the BEAST2 .jar path.
create_beast2_treelog_folder
Internal function
Continue a BEAST2 run
Check if the input is a valid RNG seed.
create_beast2_validate_cmd
Creates the terminal command to validate a BEAST2 input file
check_can_create_screenlog_file
Internal function
check_can_create_state_output_file
Internal function
create_beast2_state_output_file_folder
Create the folder where the BEAST2 state output file will be created
Create a random FASTA file
create_beast2_input_file_folder
Create the folder where the BEAST2 input file will be created
create_beast2_continue_cmd_from_options
Creates the terminal command to run BEAST2 from a beast2_options
create_beast2_tracelog_folder
Internal function
create_mcbette_beast2_options
Create a `beast2_options` structure for the `mcbette` R package
check_beast2_options_do_not_overwrite_existing_files
Internal function
create_beast2_version_cmd
Creates the terminal command to version a BEAST2 input file
get_default_beast2_download_url_linux
Get the BEAST2 download URL for Linux
check_empty_beastier_folder
Check there are no files in the default beastier folder
Create a random phylogeny
get_beast2_example_filenames
Get a list with the full paths of all
BEAST2 example filenames
get_default_beast2_download_url
Get the default BEAST2 download URL,
which depends on the operating system
get_beast2_example_filename
Get the full path of a BEAST2 example file
create_temp_input_filename
Create a temporary filename for the BEAST2 XML filename
create_temp_state_filename
Create a temporary file for the BEAST2 XML output file that
stores its state.
create_beast2_version_cmd_bin
Creates the terminal command to version a BEAST2 input file
using a call to the launcher.jar file
get_default_beast2_download_url_win
Get the BEAST2 download URL for Windows
Find duplicate RealParameter IDs
get_beastier_tempfilename
Get a temporary filename
get_default_beast2_bin_path
Get the default BEAST2 binary file (beast, that is) path
Get the Java version
check_empty_beaustier_folders
Check there are no files in the default
`beautier` and `beastier` folders
Get the .trees filenames that BEAST2 will produce
create_beast2_screenlog_folder
Internal function
extract_screenlog_filename_from_beast2_input_file
Internal function to extract the screenlog filename for a BEAST2 input file
create_beast2_run_cmd_from_options
Creates the terminal command to run BEAST2 from a beast2_options
extract_tracelog_filename_from_beast2_input_file
Internal function to extract the tracelog filename for a BEAST2 input file
Determines if BEAST2 issues a warning
when using the BEAST2 XML input file
Deprecated function, use is_on_ci
get_default_beast2_folder
Get the path to the folder where this package installs
BEAST2 by default
Save a NEXUS file as a FASTA file
Save text (a container of strings) to a file
Determines if the input is an alignment of type DNAbin
Check there are no files in the default beautier folder
Checks if BEAST2 is installed
Create a random alignment
Is the path a path to the BEAST2 binary file?
Does not check if the file at that path is present
get_beast2_options_filenames
Extract the filenames from a `beast2_options`
get_beast2_main_class_name
Get the BEAST2 main class name.
Remove the `beautier` and `beastier` temporary folders
Is a file a valid BEAST2 input file?
Is the path a path to the BEAST2 binary file?
Does not check if the file at that path is present
Pretty-print a `beast2_options`
create_beast2_validate_cmd_bin
Creates the terminal command to validate a BEAST2 input file
using a call to the launcher.jar file
Deprecated function, use is_on_travis
Deprecated function to upgrade BEAST2.
rename_beast2_options_filenames
Rename the filenames in the BEAST2 options
Deprecated function to uninstall BEAST2
Remove a file if it is present,
will do nothing if it is not.
extract_treelog_filename_from_beast2_input_file
Internal function to extract the treelog filename for a BEAST2 input file
create_beast2_validate_cmd_jar
Creates the terminal command to validate a BEAST2 input file
using a call to the launcher.jar file
create_beastier_tempfolder
Create the temporary folder as used by beastier
create_beast2_version_cmd_jar
Creates the terminal command to version a BEAST2 input file
using a call to the launcher.jar file
Get the full paths of files in the inst/extdata folder
Get the full path of a file in the inst/extdata folder
Obtains the default path to the Java executable
get_alignment_ids_from_xml_filename
Get the alignment ID from a file with one alignment
get_default_beast2_version
Get the default BEAST2 version that is used by beastier
Determine if the XML text has unique parameter IDs
Deprecated function to install BEAST2
Run BEAST2
Run BEAST2
This function does nothing. It is intended to inherit is parameters'
documentation.
Do a minimal BEAST2 run
Get the BEAST2 version
Get the path to the beastier temporary files folder
get_default_beast2_jar_path
Get the default BEAST2 jar file's path
Get the default BEAST2 path
Deprecated function, use is_on_appveyor
Is the path a path to the BEAST2 jar file?
Does not check if the file at that path is present
beastier: A package to call BEAST2.
Creates a beastier report
Check if the beast2_options is a valid BEAST2 options object.
are_beast2_input_lines_fast
Would these lines of text, when written to a file,
result in a valid BEAST2 input file?
Add quotes around the string if it contains spaces.
are_beast2_input_lines_deep
Would these lines of text, when written to a file,
result in a valid BEAST2 input file?
Would these lines of text, when written to a file,
result in a valid BEAST2 input file?
Determines if the two alignments are equal
Check if BEAST2 is installed properly.
Convert a beast2_options to a table
check_beast2_options_filenames_differ
Check if the filenames in beast2_options differ
check_beast2_options_names
Check if the beast2_options, which is a list,
has all the elements needed.
Check if the beast2_options is a valid BEAST2 options object.