according to the package doc, when running lfmm in LEA, the def for -d is
"An integer corresponding to the fit of lfmm model with the d-th variable only
from environment.file. By default (if NULL and all is FALSE), fit lfmm with
each variable from environment.file sequentially and independently."
however, if I run it in the following fashion:
project = lfmm("oneperrad_trachylepis_RAD.geno", "taff_lea.env", iteration = 10000, burnin = 5000,d = 0,missing.data = TRUE, CPU = 8,K = 5, repetitions = 5, project = "new")
LEA exits without errors after finishing with the first variable. the logging indicates it is analyzing the first variable
as the default behavior is all=FALSE, I'm not sure why it isn't starting for the next variable. Incidentally, I'm running variable 2 right now using d=2, and it is chugging along just fine.