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Tutorial: LEA won't run lfmm sequentially and independently on individual environmental variables when d set to 0
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gravatar for afreedman405
5 weeks ago by
Harvard University, Cambridge, Massachusetts, USA
afreedman4050 wrote:

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.

ADD COMMENTlink modified 5 weeks ago by eric.frichot0 • written 5 weeks ago by afreedman4050

it seems that for LEA, 0 != NULL, but somehow translates into 1. Omitting the -d arg altogether results in lfmm iterating all of the environmental variables. go figure.

ADD REPLYlink written 5 weeks ago by afreedman4050
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gravatar for eric.frichot
5 weeks ago by
France
eric.frichot0 wrote:

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 


 

ADD COMMENTlink written 5 weeks ago by eric.frichot0
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