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.

Indeed, the LEA documentation and LEA behaviour is not clear about this subject !

Let me clarify:

• If you do not specify a "-d" value, it will fit lfmm with each variable from environment.file sequentially and independently.
• If you specify a d value below 0 (d=0, d=-1, ...), it will set d=1. LEA should at least raise a warning (or even an error about it).
• If you specify a d value strictly upper 0 (d=1, d=2, ...), it will fit the model with the d-th variable only.

Thanks for pointing it out