batchjacklociArpRANDOM: Remove a random subset of loci from all Arlequin project files (extension .arp) in dir

Description

This function retains a user-specified number of loci from all Arlequin (extension .arp) files in the working directory and creates new input .arp files. The identity of retained markers is chosen randomly for each file. The function also creates a Arlequin batch file (.arb) to allow batch analysis.

Usage

batchjacklociArpRANDOM(n.retain)

Arguments

n.retain

Number of loci to keep in final file (must be between 1 and the number of loci in input file)

Value

New .arp files (with a suffix indicating the number of markers in the filename) and the single batch file (.arb) will be saved in the working directory.

Details

This function relies on jacklociArpRANDOM to jackknife markers in each file. This function is useful to investigate the effect of the number of sampled loci on population genetics parameter estimates, especially in simulations like those that can be performed with the software Easypop. Some .arp files might not be imported correctly depending on which software was used to generate them. If this is the case, start from the Genepop files and convert them first with batchconvert.

References