gl.fdsim {dartR.base}

Estimates the rate of false positives in a fixed difference analysis

Description

This function takes two populations and generates allele frequency profiles for them. It then samples an allele frequency for each, at random, and estimates a sampling distribution for those two allele frequencies. Drawing two samples from those sampling distributions, it calculates whether or not they represent a fixed difference. This is applied to all loci, and the number of fixed differences so generated are counted, as an expectation. The script distinguished between true fixed differences (with a tolerance of delta), and false positives. The simulation is repeated a given number of times (default=1000) to provide an expectation of the number of false positives, given the observed allele frequency profiles and the sample sizes. The probability of the observed count of fixed differences is greater than the expected number of false positives is calculated.

Usage

gl.fdsim(
  x,
  poppair,
  obs = NULL,
  sympatric = FALSE,
  reps = 1000,
  delta = 0.02,
  verbose = NULL
)

Arguments

x

Name of the genlight containing the SNP genotypes [required].

poppair

Labels of two populations for comparison in the form c(popA,popB) [required].

obs

Observed number of fixed differences between the two populations [default NULL].

sympatric

If TRUE, the two populations are sympatric, if FALSE then allopatric [default FALSE].

reps

Number of replications to undertake in the simulation [default 1000].

delta

The threshold value for the minor allele frequency to regard the difference between two populations to be fixed [default 0.02].

verbose

Verbosity: 0, silent, fatal errors only; 1, flag function begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Value

A list containing the following square matrices [[1]] observed fixed differences; [[2]] mean expected number of false positives for each comparison; [[3]] standard deviation of the no. of false positives for each comparison; [[4]] probability the observed fixed differences arose by chance for each comparison.

Author(s)

Custodian: Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

See Also

Other distance: gl.dist.ind(), gl.dist.pop(), utils.dist.ind.snp()

Examples

fd <- gl.fdsim(testset.gl[,1:100],poppair=c('EmsubRopeMata','EmmacBurnBara'),
sympatric=TRUE,verbose=3)