save_microsimr: Create input files

In andersgs/microsimr: Simulate microsatellite data using Hudson's ms program

Description

Create input files

Usage

save_microsimr(genotypes, filename, n_ind, n_pop, n_loc, format = "migrate-n",
  title = "microsimr simulated data")

Arguments

genotypes	A matrix outputted by sim_microsats function.
filename	A character string indicating the filename to be used for saving the input file.
n_ind	An integer indicating the number of sampled diploid individuals if n_pop = 1, or a vector of integers indicating the number of diploid individuals sampled in each population in n_pop > 1.
n_pop	An integer indicating the number of populations simulated.
n_loc	An integer indicating the number of loci simulated.
format	A character string indicating the format desired. Currently, 'migrate-n' is the only possible option.
title	A character string to be used as the title of the input file, only used if the format allows it.

Examples

#simulate a dataset with theta = 20, 5 loci genotyped at a total of 10
# individuals, with 5 individuals taken from each of 2 populations. The
# populations are connected by 4 migrants/generation (4Nem = 4).

simd_data <- microsimr::sim_microsats(theta = 20,
                                     n_ind = c(5,5),
                                     n_loc = 5,
                                     n_pop = 2,
                                     ms_options = "-I 2 10 10 4")

# write an input file for migrate-n
## Not run: 
microsimr::save_microsimr(genotypes = simd_data,
                         filename = "infile",
                         n_ind = c(5,5),
                         n_pop = 2,
                         n_loc = 5,
                         format = 'migrate-n')

## End(Not run)

## Not run: 
# changing the format to anything else other than 'migrate-n' currently
generates an error
microsimr::save_microsimr(genotypes = simd_data,
                         filename = "infile",
                         n_ind = c(5,5),
                         n_pop = 2,
                         n_loc = 5,
                         format = 'ima2')

## End(Not run)

andersgs/microsimr documentation built on May 12, 2019, 2:42 a.m.