Dear Sarah and Wilfried,<div>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. </div>
<div>Thank you</div><div><br></div><div>Diego Alarcon</div><div>Universidad de Concepcion, Chile.</div><div><a href="http://www.udec.cl/~ecobiosis">http://www.udec.cl/~ecobiosis</a></div><div><div><br><div class="gmail_quote">
On Fri, Feb 4, 2011 at 8:00 AM, <span dir="ltr"><<a href="mailto:biomod-commits-request@r-forge.wu-wien.ac.at">biomod-commits-request@r-forge.wu-wien.ac.at</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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1. Re: "xzfile" error with models function (Wilfried Thuiller)<br>
<br>
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Message: 1<br>
Date: Thu, 3 Feb 2011 20:07:30 +0100<br>
From: Wilfried Thuiller <<a href="mailto:wilfried.thuiller@ujf-grenoble.fr">wilfried.thuiller@ujf-grenoble.fr</a>><br>
Subject: Re: [Biomod-commits] "xzfile" error with models function<br>
To: Sarah Skikne <<a href="mailto:skikne@gmail.com">skikne@gmail.com</a>><br>
Cc: <a href="mailto:biomod-commits@r-forge.wu-wien.ac.at">biomod-commits@r-forge.wu-wien.ac.at</a><br>
Message-ID: <<a href="mailto:77CFA348-C41E-4384-90B2-0CBF400DA5A8@ujf-grenoble.fr">77CFA348-C41E-4384-90B2-0CBF400DA5A8@ujf-grenoble.fr</a>><br>
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<br>
Dear Sarah,<br>
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.<br>
Please have a try with using "random" instead and let me know.<br>
<br>
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.<br>
<br>
Cheers,<br>
Wilfried<br>
<br>
<br>
Le 22 janv. 2011 ? 03:34, Sarah Skikne a ?crit :<br>
<br>
> Dear BIOMODers,<br>
><br>
> I am having some trouble with the models() function in BIOMOD and was hoping to get some help.<br>
><br>
> Here is the relevant info:<br>
> - R version 2.12.1<br>
> - I re-downloaded the BIOMOD package a few days ago so it should be up to date.<br>
> - code:<br>
><br>
> 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)<br>
><br>
> Initial.State(Response=TrialDF[,51], Explanatory=TrialDF[,3:50], IndependentResponse=NULL, IndependentExplanatory=NULL, <a href="http://sp.name" target="_blank">sp.name</a>='spp1')<br>
><br>
><br>
><br>
> 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)<br>
><br>
><br>
> From this, I get the following:<br>
><br>
> Modelling summary<br>
><br>
> -----------------------------------<br>
><br>
> Number of species modelled : 1<br>
><br>
> redwood<br>
><br>
> 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<br>
><br>
><br>
> number of evaluation repetitions : 3<br>
><br>
> number of pseudo-absences runs : 2<br>
><br>
> models selected : ANN, CTA, GAM, GBM, GLM, MARS, RF, SRE<br>
><br>
> total number of model runs : 64<br>
><br>
> -----------------------------------<br>
><br>
><br>
> ##### redwood #####<br>
><br>
> ##### pseudo-absence run 1 #####<br>
><br>
> Model=Artificial Neural Network<br>
><br>
> 3 Fold Cross Validation + 3 Repetitions<br>
><br>
> Calibration and evaluation phase: Nb of cross-validations: 3<br>
><br>
> Error in xzfile(file, "wb", compression = 9) : cannot open the connection<br>
><br>
> In addition: There were 15 warnings (use warnings() to see them)<br>
><br>
><br>
><br>
> 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.<br>
><br>
><br>
><br>
> Any help on the "xzfile" error and how to avoid it would be great.<br>
><br>
><br>
><br>
> Thanks!<br>
><br>
> Sarah<br>
><br>
><br>
><br>
><br>
><br>
> Center for Applied Biodiversity Informatics<br>
><br>
> California Academy of Sciences<br>
><br>
><br>
><br>
><br>
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--------------------------<br>
Dr. Wilfried Thuiller<br>
Laboratoire d'Ecologie Alpine, UMR CNRS 5553<br>
Universit? Joseph Fourier<br>
BP53, 38041 Grenoble cedex 9, France<br>
tel: +33 (0)4 76 51 44 97<br>
fax: +33 (0)4 76 51 42 79<br>
<br>
Email: <a href="mailto:wilfried.thuiller@ujf-grenoble.fr">wilfried.thuiller@ujf-grenoble.fr</a><br>
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Website: <a href="http://www-leca.ujf-grenoble.fr/equipes/tde.htm" target="_blank">http://www-leca.ujf-grenoble.fr/equipes/tde.htm</a><br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Chilebosque - Conociendo y disfrutando de la Flora Nativa Chilena<br><a href="http://www.chilebosque.cl">http://www.chilebosque.cl</a><br><br>
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