# [Biomod-commits] average of two scenarios

Jan Sauer Jan.Sauer at senckenberg.de
Mon Oct 18 11:33:12 CEST 2010

```Hi all,
I have some questions to combine greenhouse gas emission scenarios.
But first, what I have done:
I used biomod (6 algorithms) and two climate scenarios each with two
greenhouse gas emission scenarios.  My output is a consensus, based on
weight.method=ROC (see “R” instructions below).
Now, I want to plot the average of the two climate scenarios (HadCM3
and CCCma) for one greenhouse gas emission scenario (A2a), on GIS. To
this, I  calculated the average of both scenarios and used the
prob.mean.weighted as threshold. However, this plot doesn´t look like
the average of the two climate scenarios given from the output.
To this, the probabilities of my 23 modeled species vary from 0 to 800,
but never reach 1000. For example, the probabilities of the average of
both greenhouse gas scenarios for one species vary from 0 to 657, the
prob.mean.weighted is 579. By using this threshold, the species is
nearly extinct to the end of this century, whereas the output of biomod
for the concerning species looks greatly different to the average I
calculated.
What did I do wrong with the threshold?

§  Initial.State(Response=species[, c(4:27)], Explanatory =
data_present[,c(4:15)],
IndependentResponse = NULL, IndependentExplanatory =
NULL)

§  Models(GLM = T, TypeGLM = "poly", Test = "AIC",
GBM = T, No.trees = 3000,
GAM = T, Spline = 4,
CTA = T, CV.tree = 50,
ANN = F, CV.ann = 5,
FDA = F,
SRE = F, quant=0.025,
MARS = T,
RF = T,
NbRunEval = 10, DataSplit = 70,
Yweights=NULL, Roc=TRUE,
Optimized.Threshold.Roc=TRUE,
Kappa=TRUE, TSS=TRUE,
KeepPredIndependent = FALSE, VarImport=5,
NbRepPA=1, strategy="random",
nb.absences=10000)

GLM = T,
GBM = T,
GAM = T,
CTA = T,
ANN = F,
FDA = F,
SRE = F, quant=0.025,
MARS = T,
RF = T,
BinRoc = T, BinKappa =
T, BinTSS = F,
FiltRoc = F, FiltKappa =
F, FiltTSS = F,
repetition.models=T)

weight.method='Roc',
PCA.median=T,
binary=T,
bin.method='Roc',
Test=T,
decay=1.6,
repetition.models=T)
--
Dipl.- Biol. Jan Sauer
Forschungsinstitut und Naturmuseum Senckenberg
Abteilung Limnologie und Naturschutzforschung

Clamecystr. 12
63571 Gelnhausen

Tel.:06051 61954-3117
Fax.:06051 61954-3118

www.senckenberg.de
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