calc_summary_stats_traces
Calculates the Effective Sample Sizes of the traces of multiple
estimated variables.
Calculates the Effective Sample Sizes of one estimated variable's trace.
Extract the JSON lines out of a .xml.state with
the unparsed BEAST2 MCMC operator acceptances
file with the operators
Documentation of general function arguments.
This function does nothing.
It is intended to inherit function argument documentation.
Deprecated function to parse a BEAST2 .log output file.
Use parse_beast_tracelog_file instead
Parse all BEAST2 output files
parse_beast_state_operators
Parses a BEAST2 state .xml.state output file to get only the operators
acceptances
Get the full paths of files in the inst/extdata folder
Parses BEAST2 output files to a posterior
Removed the burn-in from a trace
Removed the burn-ins from a data frame
Measure if a file a valid BEAST2 .trees file
Calculate the corrected sample standard deviation.
Save the BEAST2 trees as a BEAST2 .log file.
There will be some differences: a BEAST2 .log file also saves
the model as comments and formats the numbers in a way non-standard to R
parse_beast_tracelog_file
Parses a BEAST2 tracelog .log output file
Determines if the input is a BEAST2 posterior,
as parsed by parse_beast_trees
Save the BEAST2 estimates as a BEAST2 .log file.
There will be some differences: a BEAST2 .log file also saves
the model as comments and formats the numbers in a way non-standard to R
Parses a BEAST2 .trees output file
Check if the trace is a valid. Will stop if not Determines if the input is a BEAST2 posterior
get_tracerer_tempfilename
Get a temporary filename
tracerer: A package to parse BEAST2 output files.
Calculate the geometric mean
Calculates the Effective Sample Sizes from a parsed BEAST2 log file
Calculate the auto-correlation time, alternative implementation
Calculate the Highest Probability Density of an MCMC trace that
has its burn-in removed
Calculate the standard error of the mean
calc_std_error_of_mean_cpp
Calculates the standard error of the mean
Calculates the Effective Sample Sizes of one estimated variable's trace.
Calculate the auto-correlation time using only R. Consider using
calc_act instead, as it is orders of magnitude faster
Calculates the Effective Sample Size
Calculate the mode of values
If the distribution is bi or multimodal or uniform, NA is returned
Count the number of trees in a .trees file
Get the full path of a file in the inst/extdata folder