scrm: Simulate the evolution of biological sequences

In scrm: Simulating the Evolution of Biological Sequences

Simulate the evolution of biological sequences

Description

This function provides an interface for calling scrm from R. The command line options are passed via the args argument. The vignette 'scrm-Arguments' contains details about the available options. Summary statistics are converted into an R format. Additionally, there is an option to write the original command line output into a file.

Usage

scrm(args, file = "")

Arguments

args	A string containing the command-line arguments for scrm. Look at scrms vignette for a description of available arguments.
file	If provided, scrm will additionally write it is output into a file with the given file, using an ms-like text output.

Value

A named list of summary statistics. Most summary statistics are again a list, where each entry contains the value for one locus. For the site frequency spectrum, the summary statistic is a matrix, where each row contains the spectrum for one locus.

Seeding

The R version of scrm uses random number from R's random generator. Therefore, the '-seed' argument of the command-line version will be ignored, and no seed is given in the output. Use the R function set.seed prior to calling this function to ensure reproducibility of results.

See Also

• vignette('scrm-Arguments') for an overview of command line arguments and

• vignette('scrm-TreesForApe') for an example on using genealogies simulated with scrm with package 'ape'.

Examples

set.seed(789)
# 5 Chromosomes with 100 bases each with recombination and mutation
sum_stats <- scrm('5 1 -r 3.1 100 -t 1.5 -T -L')
str(sum_stats)

# Simulate the site frequency spectrum at 3 loci. For each locus
# 10 Chromosomes of 1Mb length are sampled from two populations with
# migration inbetween.
scrm('10 3 -r 400 1000000 -l 100000 -I 2 4 6 0.5 -t 300 -oSFS')$sfs

scrm documentation built on May 29, 2024, 2:30 a.m.