PopGenReport: wassermann – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

wassermann

Partial Mantel tests on costdistance matrices

Description

This function implements the Causal modelling approach as suggested by Wassermann et al. 2010 and Cushman et al. 2010. It tests for the effect of landscape features using a cost distance matrix on the genetic structure of subpopulation/individuals.

Usage

wassermann(gen.mat, cost.mats, eucl.mat = NULL, plot = TRUE,
  nperm = 999)

Arguments

`gen.mat`	pairwise genetic distance matrix
`cost.mats`	pairwise cost distance matrix
`eucl.mat`	pairwise Eukclidean distance matrix
`plot`	switch for control plots of the partial mantel test
`nperm`	number of permutations for the partial mantel test

Details

see landgenreport

Value

A table with the results of the partial mantel test. Using plot=TRUE results in diagnostic plots for the partial mantel tests.

Author(s)

Bernd Gruber (bernd.gruber@canberra.edu.au)

References

Wassermann, T.N., Cushman, S. A., Schwartz, M. K. and Wallin, D. O. (2010). Spatial scaling and multi-model inference in landscape genetics: Martes americana in northern Idaho. Landscape Ecology, 25(10), 1601-1612.

Examples

library(raster)
fric.raster <- readRDS(system.file("extdata","fric.raster.rdata", package="PopGenReport"))
glc <- genleastcost(landgen, fric.raster, "D", NN=8)
wassermann(eucl.mat = glc$eucl.mat, cost.mats = glc$cost.mats, gen.mat = glc$gen.mat)

PopGenReport

A Simple Framework to Analyse Population and Landscape Genetic Data

v3.0.4

GPL

Authors

Bernd Gruber [aut, cre], Aaron Adamack [aut]

Initial release

2019-02-04