call_ms: Call MS from R

In vsbuffalo/msr: Call and parse MS from R

Description

Call Hudon's MS from R, returning a string of results (that can be parsed with parse_ms()). Other coalescent simulators are supported as long as they output results in MS format; specify with the argument ms='mspms' (in this example, running msprime here). No argument checking occurs in this function; arguments passed to ... are converted to command line arguments, e.g. r=c(4, 1000) is converted to -r 4 1000 and mutation.rate=1e-5 converted to --mutation-rate 1e-5.

Usage

call_ms(nsam, howmany, cmd = NULL, ..., ms = "ms", verbose = TRUE)

Arguments

nsam	number of samples (gametes) to draw
howmany	how many replicates to run
cmd	the command to pass to MS
...	command line arguments as function arguments (if not using cmd)
ms	the ms-like executable to run, must be in $PATH or path to executable

vsbuffalo/msr documentation built on May 3, 2019, 7:07 p.m.