gl.costdistances

a raster object coding the resistance of the landscape

landscape

coordinates of the subpopulations. If a genlight object is provided coordinates are taken from @other$latlong and centers for population (pop(gl)) are calculated. In case you want to calculate costdistances between individuals redefine pop(gl) via: <code>pop(gl)&lt;- indNames(gl)</code>.

locs

defines the type of cost distance, types are "least-cost", "rSPDistance" or "commute (Circuitscape type)"

method

number of next neighbours recommendation is 8

calculates a cost distance matrix, to be used with run.popgensim

Functions are provided that facilitate the import and analysis of
SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated
by DarT (Diversity Arrays Technology). However, once SNP or related fragment
presence/absence data from any source is imported into a genlight object many
of the functions can be used. Functions are available for input and output of
SNP and silicodart data, for reporting on and filtering on various criteria
(e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency).
Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions
are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data
between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.

gl.costdistances: Calculates cost distances for a given landscape (resistance matrix)

Description

Usage

Arguments

Value