[Biomod-commits] Question regarding training/testing/evaluating data sets

Kristen Bouska kpitts at siu.edu
Fri May 24 21:32:31 CEST 2013

I wanted to make sure I am understanding my model commands correctly. If I
have the following commands (below), I am calling in a training data set
(expl.var) and an evaluation data set (eval.expl.var), then I am
cross-validating the training data set 10 times, splitting it 75/25 for
each cross-validation. If this is correct, then my evaluation data set
(eval.expl.var) is not used in the BIOMOD_Modeling evaluation step,
correct? Is the evaluation data set only used to evaluate the ensembled

Sorry if this is confusing, I just want to make sure I am doing what I
think I am doing when I am running my models.

myBiomodData <- BIOMOD_FormatingData(resp.var=myResp, resp.xy=myRespXY,
expl.var=myExpl, resp.name=myRespName, eval.resp.var=myEvalpa,
eval.expl.var=myEvalenv, eval.resp.xy=myRespEvalXY)

myBiomodModelOut <- BIOMOD_Modeling(myBiomodData, models = c('GLM', 'GBM',
'CTA', 'RF', 'MARS'), models.options=NULL, NbRunEval=10, DataSplit=75,
Yweights=NULL, Prevalence=NULL, VarImport=3, models.eval.meth =
c('KAPPA','TSS','ROC'),SaveObj = TRUE, rescal.all.models = TRUE,
do.full.models = TRUE, modeling.id = “test_date” )
Kristen Bouska
PhD Candidate
Environmental Resources and Policy Program
Life Sciences II, Room 375 (Mail Code 4325)
Southern Illinois University - Carbondale
Carbondale, IL 62901

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