Collapse a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold
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().
gl.collapse(fd, tpop = 0, tloc = 0, pb = FALSE, verbose = NULL)
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] |
The script then applies the new population assignments to the genlight object and recalculates the distance and associated matricies.
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]
Arthur Georges (Post to https://groups.google.com/d/forum/dartr)
fd <- gl.fixed.diff(testset.gl,tloc=0.05) fd fd2 <- gl.collapse(fd,tpop=1) fd2 fd3 <- gl.collapse(fd2,tpop=1) fd3
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