dartR (version 1.9.9.1)

gl.collapse: Collapse a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold

Description

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

Usage

gl.collapse(fd, tpop = 0, tloc = 0, pb = FALSE, verbose = NULL)

Arguments

fd

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

tpop

-- threshold number of fixed differences above which populatons will not be amalgamated [0]

tloc

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

pb

-- if TRUE, show a progress bar on time consuming loops [FALSE]

verbose

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

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]] $expfpos -- NA's, populated by gl.fixed.diff [by simulation] [[7]] $expfpos -- NA's, populated by gl.fixed.diff [by simulation] [[8]] $prob -- NA's, populated by gl.fixed.diff [by simulation]

Details

The script then applies the new population assignments to the genlight object and recalculates the distance and associated matricies.

Examples

# NOT RUN {
fd <- gl.fixed.diff(testset.gl,tloc=0.05)
fd
fd2 <- gl.collapse(fd,tpop=1)
fd2
fd3 <- gl.collapse(fd2,tpop=1)
fd3
# }