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

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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 reproduciblity of results.

See Also

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

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

Examples

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# 5 Chromosomes with 100 bases each with recombination and mutation
sum_stats <- scrm('5 1 -r 5 100 -t 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

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