readStatsFile

Read arg-sample stats file

Description

This function will read a .stats file written by arg-sample.

Usage

readStatsFile(file, burnin = NULL, thinVal = 1)

Arguments

Argument	Description
file	A character string, either the name of the stats file or the directory where the stat file can be found. If a directory, there must be only one stat file inside or else an error will occur
burnin	If not NULL, a single numeric value. Any statistics from iterations < burnin will be discarded
thinVal	Remove all iters for which iteration mod thinVal != 0

Value

A data frame containing the data from the stats file. Only MCMC iterations of type “resample” will be retained. In addition to the original columns from the stats file, several statistics may be added to the data frame as follows: “joint2” is the sum of prior2 and likelihood and is an alternative posterior likelihood statistic that is preferred over “joint”, which is the sum of prior and likelihood. Whereas “prior” is the prior probability of the sampled ARG under the model, “prior2” integrates over all possible recombination events that could produce the same series of local trees. “total_recomb” is the sum of “recombs” and “invis_recombs”