Differentiation {genepop}

Tests of genic and genotypic differentiation

Description

Exact conditional contingency-table tests for genic or genotypic differentiation. A single test for all populations, or distinct tests for all pairs of populations, may be computed. See this section of the Genepop executable documentation for more information on the statistical methods.

Usage

test_diff(
  inputFile,
  genic = TRUE,
  pairs = FALSE,
  outputFile = "",
  settingsFile = "",
  dememorization = 10000,
  batches = 100,
  iterations = 5000,
  verbose = interactive()
)

Arguments

inputFile

The path of the input file, in Genepop format

genic

logical: whether to perform genic or genotypic tests

pairs

logical: whether to test differentiation between all pairs of ppulation, or to perform a single global test

outputFile

character: The path of the output file

settingsFile

character: The path of the settings file

dememorization

integer: length of dememorization step of Markov chain algorithm

batches

integer: Number of batches

iterations

integer: Iterations per batch

verbose

logical: whether to print some information

Value

The path of the output file is returned invisibly.

Examples

locinfile <- genepopExample('sample.txt')
test_diff(locinfile,outputFile='sample.txt.GE')
if ( ! interactive()) clean_workdir(otherfiles='sample.txt')