dartR (version 1.1.11)

gl.collapse: Collapse a distance matrix by amalgamating populations

Description

This script takes a the file generated by gl.fixed.diff and generates a population recode table to amalgamate populations with distance less than or equal to a specified threshold The distance matrix is generated by gl.fixed.diff()

Usage

gl.collapse(fd, recode.table = "tmp.csv", tpop = 0, tloc = 0,
  v = 2)

Arguments

fd

-- name of the list of matricies produced by gl.fixed.diff() [required]

recode.table

-- name of the new recode.table to receive the new population reassignments arising from the amalgamation of populations [default tmp.csv]

tpop

-- max number of fixed differences used amalgamating populations [default 0]

tloc

-- threshold defining a fixed difference (e.g. 0.05 implies 95:5 vs 5:95 is fixed) [default 0]

v

-- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2]

Value

A list containing the gl object x and the following square matricies [[1]] $gl -- the new genlight object with populations collapsed; [[2]] $fd -- raw fixed differences; [[3]] $pcfd -- percent fixed differences; [[4]] $nobs -- mean no. of individuals used in each comparison; [[5]] $nloc -- total number of loci used in each comparison; [[6]] $expobs -- if test=TRUE, the expected count of false positives for each comparison [by simulation]; [[7]] $prob -- if test=TRUE, the significance of the count of fixed differences [by simulation])

Details

The script then applies the recode to the genlight object and recalculates the distance and associated matricies.

Examples

# NOT RUN {
fd <- gl.fixed.diff(testset.gl, tloc=0.05)
gl <- gl.collapse(fd, recode.table="testset_recode.csv",tpop=1)
# }