Tracer from R
Calculate the auto-correlation time, alternative implementation
Calculate the auto correlation time from [https://github.com/beast-dev...
Calculate the auto-correlation time using only R. Consider using calc_...
Calculates the Effective Sample Size
Calculates the Effective Sample Sizes from a parsed BEAST2 log file
Calculate the geometric mean
Calculate the Highest Probability Density of an MCMC trace that has it...
Calculate the mode of values If the distribution is bi or multimodal o...
Calculates the standard error of the mean
Calculate the standard error of the mean
Calculates the Effective Sample Sizes of one estimated variable's trac...
Calculates the Effective Sample Sizes of one estimated variable's trac...
Calculates the Effective Sample Sizes of the traces of multiple estima...
Check if the trace is a valid. Will stop if not
Count the number of trees in a .trees file
Calculate the corrected sample standard deviation.
Documentation of general function arguments. This function does nothin...
Extract the JSON lines out of a .xml.state with the unparsed BEAST2 ...
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
Determines if the input is a BEAST2 posterior
Measure if a file a valid BEAST2 .trees file
Determines if the input is a BEAST2 posterior, as parsed by parse_beas...
Deprecated function to parse a BEAST2 .log output file. Use parse_be...
Parse all BEAST2 output files
Parses BEAST2 output files to a posterior
Parses a BEAST2 state .xml.state output file to get only the operato...
Parses a BEAST2 tracelog .log output file
Parses a BEAST2 .trees output file
Removed the burn-in from a trace
Removed the burn-ins from a data frame
Save the BEAST2 estimates as a BEAST2 .log file. There will be some ...
Save the BEAST2 trees as a BEAST2 .log file. There will be some diff...
tracerer: A package to parse BEAST2 output files.
'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. 'Tracer' (<https://github.com/beast-dev/tracer/>) is a GUI tool to parse and analyze the files generated by 'BEAST2'. This package provides a way to parse and analyze 'BEAST2' input files without active user input, but using R function calls instead.