Call 'BEAST2'
Add quotes around the string if it contains spaces.
Would these lines of text, when written to a file, result in a valid B...
Would these lines of text, when written to a file, result in a valid B...
Would these lines of text, when written to a file, result in a valid B...
Determines if the two alignments are equal
Convert a beast2_options to a table
Creates a beastier report
beastier: A package to call BEAST2.
Check if the beast2_options, which is a list, has all elements of th...
Internal function
Check if the filenames in beast2_options differ
Check if the beast2_options, which is a list, has all the elements n...
Check if the beast2_options is a valid BEAST2 options object.
Check if the beast2_options is a valid BEAST2 options object.
Checks the BEAST2 .jar path. Will stop if there is a problem with th...
Check if BEAST2 is installed properly.
Internal function
Internal function
Internal function
Internal function
Internal function to check if the MCMC's tracelog file can be created.
Internal function
Check there are no files in the default beastier folder
Check there are no files in the default beautier and beastier fold...
Checks the input filename. Will stop if there is a problem with the in...
Checks the input filename. Will stop if there is a problem with the in...
Check if the input is a valid number of threads.
Checks if the operating system is supported
Check if the input is a valid RNG seed.
Continue a BEAST2 run
Creates the terminal command to run BEAST2 from a beast2_options
Create the folder where the BEAST2 input file will be created
Function to create a set of BEAST2 options.
Creates the terminal command to run BEAST2 from a beast2_options
Creates the terminal command to run BEAST2
Internal function
Create the folder where the BEAST2 state output file will be created
Internal function
Internal function
Creates the terminal command to validate a BEAST2 input file using a c...
Creates the terminal command to validate a BEAST2 input file using a c...
Creates the terminal command to validate a BEAST2 input file
Creates the terminal command to version a BEAST2 input file using a ca...
Creates the terminal command to version a BEAST2 input file using a ca...
Creates the terminal command to version a BEAST2 input file
Create the temporary folder as used by beastier
Create a beast2_options structure for the mcbette R package
Create a random alignment
Create a random FASTA file
Create a random phylogeny
Create a temporary filename for the BEAST2 XML filename
Create a temporary file for the BEAST2 XML output file that stores its...
This function does nothing. It is intended to inherit is parameters' d...
Do a minimal BEAST2 run
Internal function to extract the screenlog filename for a BEAST2 input...
Internal function to extract the tracelog filename for a BEAST2 input ...
Internal function to extract the treelog filename for a BEAST2 input f...
Get the alignment ID from a file with one alignment
Get the full path of a BEAST2 example file
Get a list with the full paths of all BEAST2 example filenames
Get the BEAST2 main class name.
Extract the filenames from a beast2_options
Get the BEAST2 version
Get the path to the beastier temporary files folder
Get the full path of a file in the inst/extdata folder
Get the full paths of files in the inst/extdata folder
Get a temporary filename
Get the default BEAST2 binary file (beast, that is) path
Get the BEAST2 download URL for Linux
Get the BEAST2 download URL for Windows
Get the default BEAST2 download URL, which depends on the operating sy...
Get the path to the folder where this package installs BEAST2 by defau...
Get the default BEAST2 jar file's path
Get the default BEAST2 path
Get the default BEAST2 version that is used by beastier
Obtains the default path to the Java executable
Find duplicate RealParameter IDs
Get the Java version
Get the .trees filenames that BEAST2 will produce
Determines if BEAST2 issues a warning when using the BEAST2 XML input ...
Determine if the XML text has unique parameter IDs
Deprecated function to install BEAST2
Determines if the input is an alignment of type DNAbin
Is a file a valid BEAST2 input file?
Checks if BEAST2 is installed
Is the path a path to the BEAST2 binary file? Does not check if the fi...
Is the path a path to the BEAST2 jar file? Does not check if the file ...
Deprecated function, use is_on_appveyor
Deprecated function, use is_on_ci
Deprecated function, use is_on_travis
Is the path a path to the BEAST2 binary file? Does not check if the fi...
Pretty-print a beast2_options
Check there are no files in the default beautier folder
Remove the beautier and beastier temporary folders
Remove a file if it is present, will do nothing if it is not.
Rename the filenames in the BEAST2 options
Run BEAST2
Run BEAST2
Save text (a container of strings) to a file
Save a NEXUS file as a FASTA file
Deprecated function to uninstall BEAST2
Deprecated function to upgrade 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.