IBD {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)