Differentiation: Tests of genic and genotypic differentiation

In genepop: Population Genetic Data Analysis Using 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')

genepop documentation built on Jan. 22, 2023, 1:07 a.m.