[Biomod-commits] Biomod-commits Digest, Vol 22, Issue 2
Diego Alarcon
chilebosque at gmail.com
Fri Feb 4 14:10:07 CET 2011
Dear Sarah and Wilfried,
I had the same error message before. I didn't know what is it about, but
when I tried to run it in a more powered computer, it ran OK. Also happened
when I tried to run with too many variables, before choosing the more
independent ones.
Thank you
Diego Alarcon
Universidad de Concepcion, Chile.
http://www.udec.cl/~ecobiosis
On Fri, Feb 4, 2011 at 8:00 AM, <
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> 1. Re: "xzfile" error with models function (Wilfried Thuiller)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 3 Feb 2011 20:07:30 +0100
> From: Wilfried Thuiller <wilfried.thuiller at ujf-grenoble.fr>
> Subject: Re: [Biomod-commits] "xzfile" error with models function
> To: Sarah Skikne <skikne at gmail.com>
> Cc: biomod-commits at r-forge.wu-wien.ac.at
> Message-ID: <77CFA348-C41E-4384-90B2-0CBF400DA5A8 at ujf-grenoble.fr>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Sarah,
> Sorry it took me so long to answer. I have no clue about the problem but I
> expect it has something to do with the selection of pseudo-absence.
> Please have a try with using "random" instead and let me know.
>
> In the meantime, you seem to have a very very large number of variables.
> Given the names, I expect that many of them are strongly correlated. Running
> most of these models on correlated data is not a very good practice.
>
> Cheers,
> Wilfried
>
>
> Le 22 janv. 2011 ? 03:34, Sarah Skikne a ?crit :
>
> > Dear BIOMODers,
> >
> > I am having some trouble with the models() function in BIOMOD and was
> hoping to get some help.
> >
> > Here is the relevant info:
> > - R version 2.12.1
> > - I re-downloaded the BIOMOD package a few days ago so it should be up to
> date.
> > - code:
> >
> > TrialDF<-data.frame(XCoord=x, YCoord=y, RAIN1=RAIN1scan, RAIN2=RAIN2scan,
> RAIN3=RAIN3scan, RAIN4=RAIN4scan, RAIN5=RAIN5scan, RAIN6=RAIN6scan,
> RAIN7=RAIN7scan, RAIN8=RAIN8scan, RAIN9=RAIN9scan, RAIN10=RAIN10scan,
> RAIN11=RAIN11scan, RAIN12=RAIN12scan, TMAX1=TMAX1scan, TMAX2=TMAX2scan,
> TMAX3=TMAX3scan, TMAX4=TMAX4scan, TMAX5=TMAX5scan, TMAX6=TMAX6scan,
> TMAX7=TMAX7scan, TMAX8=TMAX8scan, TMAX9=TMAX9scan, TMAX10=TMAX10scan,
> TMAX11=TMAX11scan, TMAX12=TMAX12scan, TMEAN1=TMEAN1scan, TMEAN2=TMEAN2scan,
> TMEAN3=TMEAN3scan, TMEAN4=TMEAN4scan, TMEAN5=TMEAN5scan, TMEAN6=TMEAN6scan,
> TMEAN7=TMEAN7scan, TMEAN8=TMEAN8scan, TMEAN9=TMEAN9scan,
> TMEAN10=TMEAN10scan, TMEAN11=TMEAN11scan, TMEAN12=TMEAN12scan,
> TMIN1=TMIN1scan, TMIN2=TMIN2scan, TMIN3=TMIN3scan, TMIN4=TMIN4scan,
> TMIN5=TMIN5scan, TMIN6=TMIN6scan, TMIN7=TMIN7scan, TMIN8=TMIN8scan,
> TMIN9=TMIN9scan, TMIN10=TMIN10scan, TMIN11=TMIN11scan, TMIN12=TMIN12scan,
> LOCALITY=localityscan)
> >
> > Initial.State(Response=TrialDF[,51], Explanatory=TrialDF[,3:50],
> IndependentResponse=NULL, IndependentExplanatory=NULL, sp.name='spp1')
> >
> >
> >
> > Models(GLM=T, TypeGLM="poly", Test="AIC", GBM=T, No.trees=2000, GAM=T,
> CTA=T, CV.tree=50, ANN=T, CV.ann=3, SRE=T, MARS=T, RF=T, NbRunEval=3,
> DataSplit=80, NbRepPA=2, strategy="circles", coor=TrialDF[,1:2],
> distance=.5, nb.absences=220, Yweights=NULL, VarImport=T, Roc=T,
> Optimized.Threshold.Roc=T, Kappa=T, TSS=T, KeepPredIndependent=T)
> >
> >
> > From this, I get the following:
> >
> > Modelling summary
> >
> > -----------------------------------
> >
> > Number of species modelled : 1
> >
> > redwood
> >
> > numerical variables : RAIN1, RAIN2, RAIN3, RAIN4,
> RAIN5, RAIN6, RAIN7, RAIN8, RAIN9, RAIN10, RAIN11, RAIN12, TMAX1, TMAX2,
> TMAX3, TMAX4, TMAX5, TMAX6, TMAX7, TMAX8, TMAX9, TMAX10, TMAX11, TMAX12,
> TMEAN1, TMEAN2, TMEAN3, TMEAN4, TMEAN5, TMEAN6, TMEAN7, TMEAN8, TMEAN9,
> TMEAN10, TMEAN11, TMEAN12, TMIN1, TMIN2, TMIN3, TMIN4, TMIN5, TMIN6, TMIN7,
> TMIN8, TMIN9, TMIN10, TMIN11, TMIN12
> >
> >
> > number of evaluation repetitions : 3
> >
> > number of pseudo-absences runs : 2
> >
> > models selected : ANN, CTA, GAM, GBM, GLM, MARS,
> RF, SRE
> >
> > total number of model runs : 64
> >
> > -----------------------------------
> >
> >
> > ##### redwood #####
> >
> > ##### pseudo-absence run 1 #####
> >
> > Model=Artificial Neural Network
> >
> > 3 Fold Cross Validation + 3 Repetitions
> >
> > Calibration and evaluation phase: Nb of cross-validations: 3
> >
> > Error in xzfile(file, "wb", compression = 9) : cannot open the connection
> >
> > In addition: There were 15 warnings (use warnings() to see them)
> >
> >
> >
> > This code used to work for me so not sure what has changed. When I try
> it using the sample data given in the manual, I get the error about 50% of
> the time. When I use my data, I get the error every time.
> >
> >
> >
> > Any help on the "xzfile" error and how to avoid it would be great.
> >
> >
> >
> > Thanks!
> >
> > Sarah
> >
> >
> >
> >
> >
> > Center for Applied Biodiversity Informatics
> >
> > California Academy of Sciences
> >
> >
> >
> >
> > _______________________________________________
> > Biomod-commits mailing list
> > Biomod-commits at lists.r-forge.r-project.org
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits
>
> --------------------------
> Dr. Wilfried Thuiller
> Laboratoire d'Ecologie Alpine, UMR CNRS 5553
> Universit? Joseph Fourier
> BP53, 38041 Grenoble cedex 9, France
> tel: +33 (0)4 76 51 44 97
> fax: +33 (0)4 76 51 42 79
>
> Email: wilfried.thuiller at ujf-grenoble.fr
> Home page: http://www.will.chez-alice.fr
> Website: http://www-leca.ujf-grenoble.fr/equipes/tde.htm
>
> FP6 European MACIS project: http://www.macis-project.net
> FP6 European EcoChange project: http://www.ecochange-project.eu
>
>
>
>
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--
Chilebosque - Conociendo y disfrutando de la Flora Nativa Chilena
http://www.chilebosque.cl
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