IBD: Isolation by distance

In genepop: Population Genetic Data Analysis Using Genepop

Isolation by distance

Description

Estimates isolation by distance by regression of genetic distance to geographical distance. See this section of the Genepop executable documentation for more information on individual-based analyses and this one for group-based analyses.

Usage

ibd(
  inputFile,
  outputFile = "",
  settingsFile = "",
  dataType = "Diploid",
  statistic = "F/(1-F)",
  geographicScale = "2D",
  CIcoverage = 0.95,
  testPoint = 0,
  minimalDistance = 1e-04,
  maximalDistance = 1e+09,
  mantelPermutations = 1000,
  mantelRankTest = FALSE,
  bootstrapMethod = "ABC",
  bootstrapNsim = 999,
  verbose = interactive()
)

Arguments

inputFile	The path of the input file, in Genepop format
outputFile	character: The path of the output file
settingsFile	character: The path of the settings file
dataType	character: 'haploid' or 'diploid'
statistic	character: The pairwise genetic distance, either 'a' or 'e' for diploid individual data, 'a-like' for haploid individual data, and 'F/(1-F)' or 'SingleGeneDiv' for group data (haploid or diploid)
geographicScale	character: gives either the scale transformation 'Log' or 'Linear' for geographic distances, or the shape of the habitat '2D' or '1D'
CIcoverage	numeric: The coverage probability of confidence intervals
testPoint	numeric: Given value of the slope to be tested
minimalDistance	numeric: The minimal geographic distance
maximalDistance	numeric: The maximal geographic distance
mantelPermutations	numeric: The number of permutations may be specified
mantelRankTest	logical: whether to use ranks in the Mantel test
bootstrapMethod	character: which bootstrap method to use (one of "ABC", "BC" or "BCa").
bootstrapNsim	integer: the number of bootstrap simulations to use (has no effect if method is "ABC").
verbose	logical: whether to print some information

Value

The path of the output file is returned invisibly.

Examples

## Not run: 
locinfile <- genepopExample('w2.txt')
outfile <- ibd(locinfile,'w2.txt.ISO', geographicScale = 'Log', statistic='e')
if ( ! interactive()) clean_workdir(otherfiles='w2.txt')

locinfile <- genepopExample('PEL1600withCoord.txt')
outfile <- ibd(locinfile,'PEL1600withCoord.ISO', statistic = 'SingleGeneDiv',
               geographicScale = '1D')
if ( ! interactive()) clean_workdir(otherfiles='PEL1600withCoord.txt')

## End(Not run)

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