[Biomod-commits] myBiomodModelEval in biomod2

[Damien Georges]

Dear Anne,

Your script seems to be correct and that's weird you don't get the 
evaluation scores. Could you send me (in private) the  
"BIOMOD_envSP_full_data.txt" file for make some tests.

Best,

Damien.

On 07/01/2013 11:23, Anne Blach Overgaard wrote:
> Dear Damien/list
> I have just recently started using biomod2 (newest version with R2.15.2)
> instead of BIOMOD and I am still getting used to the new code. I have run
> into an issue I hope you can assist me with.
> Running biomod2 using the script below runs smoothly and I get no error
> messages. However, when I try to assess the evaluation of the different
> models I get the R output pasted below with NA's for all dimensions.
> With a data split of 80 surely some evaluation should be done or have I
> made a mistake in my script somewhere that I cannot seem to spot?
>
> Thanks,
>
> Anne
>
> PS I have the same issue whether I use the dataframe data as here or a
> rasterstack
>
>
>
> --------------------R input---------------------------------------
> #Load required data
> Data <- read.table("BIOMOD_envSP_full_data.txt", h=T, sep="\t")
> #Read species data file
> Sp.data <- Data[, c(2:3, 34)]
>
> ### Fill 'NAs'
> Sp.data[Sp.data==0] <- NA
>
> #read environmental data
> Env <- Data[, 4:33]
>
>
> #Load the library
> library(biomod2)
>
>
>
> ### definition of data
>
> myResp <- (Sp.data["B_aeth"])
> # get NAs id
> na.id <- which(is.na(Sp.data))
>
> myRespCoord = Sp.data[-na.id, c('X', 'Y')] ## coordinates of the
> presence-only data
> myRespName = "B_aeth"
>
>
> #Format data to biomod2
> myBiomodData <- BIOMOD_FormatingData(resp.var = myResp, expl.var = Env,
> resp.xy = myRespCoord, resp.name = myRespName, PA.nb.rep = 1,
> PA.nb.absences = 10000, PA.strategy = 'random')
>
> #Check input data
> myBiomodData
>
> #View the input data
> plot(myBiomodData)
>
> ### Options definition
> myBiomodOption <- BIOMOD_ModelingOptions(MAXENT = list(path_to_maxent.jar =
> "C:\\Maxent\\", maximumiterations = 500), GBM = list(n.trees = 3000,
> cv.folds = 5))
>
>
> ### Modelling
> myBiomodModelOut <- BIOMOD_Modeling(myBiomodData, models =
> c('MAXENT','GBM'), models.options = myBiomodOption, NbRunEval=1,
> DataSplit=80, Yweights=NULL, VarImport=0, models.eval.meth =
> c('TSS','ROC'), SaveObj = TRUE, rescal.all.models = TRUE)
>
> #model evaluation
> myBiomodModelEval <- getModelsEvaluations(myBiomodModelOut)
> dimnames(myBiomodModelEval)
> myBiomodModelEval
>
> ------------------R output------------------
>
>> myBiomodModelEval
> , , MAXENT, RUN1, PA1
>
>      Testing.data Cutoff Sensitivity Specificity
> TSS           NA     NA          NA          NA
> ROC           NA     NA          NA          NA
>
> , , GBM, RUN1, PA1
>
>      Testing.data Cutoff Sensitivity Specificity
> TSS           NA     NA          NA          NA
> ROC           NA     NA          NA          NA
>
> , , MAXENT, Full, PA1
>
>      Testing.data Cutoff Sensitivity Specificity
> TSS           NA     NA          NA          NA
> ROC           NA     NA          NA          NA
>
> , , GBM, Full, PA1
>
>      Testing.data Cutoff Sensitivity Specificity
> TSS           NA     NA          NA          NA
> ROC           NA     NA          NA          NA
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