R: Simulate the evolution of biological sequences

scrm {scrm} | R Documentation

## 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

[Package scrm version 1.7.2-1 Index]