All functions 


Calculate the autocorrelation time, alternative implementation 

Calculate the auto correlation time from https://github.com/beastdev/beastmcmc/blob/800817772033c13061f026226e41128d21fd14f3/src/dr/inference/trace/TraceCorrelation.java#L159 # nolint 

Calculate the autocorrelation time using only R. Consider using calc_act instead, as it is orders of magnitude faster 

Calculates the Effective Sample Size 

Calculates the Effective Sample Sizes from a parsed BEAST2 log file 

Calculate the Highest Probability Density of an MCMC trace that has its burnin removed 

Calculates the standard error of the mean 

Calculate the standard error of the mean 

Calculates the Effective Sample Sizes of one estimated variable's trace. 

Calculates the Effective Sample Sizes of one estimated variable's trace. 

Calculates the Effective Sample Sizes of the traces of multiple estimated variables. 

Count the number of trees in a 

Calculate the corrected sample standard deviation. 

Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation. 

Extract the JSON lines out of a 

Get the full path of a file in the 

Get the full paths of files in the 

Determines if the input is a BEAST2 posterior 

Measure if a file a valid BEAST2 

Determines if the input is a BEAST2 posterior, as parsed by parse_beast_trees 

Parses a BEAST2 

Parse all BEAST2 output files 

Parses BEAST2 output files to a posterior 

Parses a BEAST2 .xml.state output file to get only the operators acceptances 

Parses a BEAST2 .trees output file 

Removed the burnin from a trace 

Removed the burnins from a data frame 

Save the BEAST2 estimates as a BEAST2 

Save the BEAST2 trees as a BEAST2 

