<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear Sarah,</div><div>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.</div><div>Please have a try with using "random" instead and let me know.</div><div><br></div><div>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. </div><div><br></div><div>Cheers,</div><div>Wilfried</div><div><br></div><br><div><div>Le 22 janv. 2011 à 03:34, Sarah Skikne a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite">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><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal; font-family: courier new,monospace; margin-left: 40px;"><span style="font-size: 10pt;">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,<span style=""> </span>LOCALITY=localityscan)</span></p>
<div style="margin-left: 40px;"><br style="font-family: courier new,monospace;"></div><p style="font-family: courier new,monospace; margin-left: 40px;" class="MsoNormal">Initial.State(Response=TrialDF[,51],
Explanatory=TrialDF[,3:50], IndependentResponse=NULL,
IndependentExplanatory=NULL, <a href="http://sp.name/">sp.name</a>='spp1')</p><p style="font-family: courier new,monospace; margin-left: 40px;" class="MsoNormal"><br></p><p style="font-family: courier new,monospace; margin-left: 40px;" class="MsoNormal">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)</p>
<br>From this, I get the following:<br><br><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">Modelling
summary </span></p><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">-----------------------------------
</span></p><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">Number
of species modelled :<span style=""> </span>1</span></p><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">redwood</span></p><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">numerical
variables :<span style=""> </span>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</span></p><div style="margin-left: 0.5in; "><span style="font-family: "Courier New";"> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">number
of evaluation repetitions :<span style=""> </span>3</span></p><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">number
of pseudo-absences runs :<span style=""> </span>2</span></p><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">models
selected :<span style=""> </span>ANN,
CTA, GAM, GBM, GLM, MARS, RF, SRE</span></p><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">total
number of model runs :<span style=""> </span>64</span></p><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">-----------------------------------
</span></p><div style="margin-left: 0.5in; "><span style="font-family: "Courier New";"> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">#####<span style=""> </span>redwood<span style=""> </span><span style=""> </span>#####</span></p><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">#####<span style=""> </span>pseudo-absence run 1<span style=""> </span>#####</span></p><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">Model=Artificial
Neural Network </span></p><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";"><span style=""> </span>3 Fold Cross Validation + 3
Repetitions </span></p><p class="MsoNormal" style="margin-left: 0.5in;"><span style="font-family: "Courier New";">Calibration
and evaluation phase: Nb of cross-validations:<span style="">
</span>3 </span></p><p class="MsoNormal" style="margin-left: 0.5in;"><b><span style="font-family: "Courier New";">Error
in xzfile(file, "wb", compression = 9) : cannot open the connection</span></b></p><p class="MsoNormal" style="margin-left: 0.5in;"><b><span style="font-family: "Courier New";">In
addition: There were 15 warnings (use warnings() to see them)</span></b></p><p class="MsoNormal" style="margin-left: 0.5in;"><br><span style="font-family: "Courier New";"></span></p><p class="MsoNormal" style="margin-left: 0.0866in; font-family: arial,helvetica,sans-serif;">
<font size="2">This code used to work for me so not sure what has changed. </font><font size="2">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.</font></p><p class="MsoNormal" style="margin-left: 0.0866in; font-family: arial,helvetica,sans-serif;"><font size="2"><br></font></p><p class="MsoNormal" style="margin-left: 0.0866in; font-family: arial,helvetica,sans-serif;">
<font size="2">Any help on the "xzfile" error and how to avoid it would be great. <br></font></p><p class="MsoNormal" style="margin-left: 0.0866in; font-family: arial,helvetica,sans-serif;"><font size="2"><br></font></p><p class="MsoNormal" style="margin-left: 0.0866in; font-family: arial,helvetica,sans-serif;"><font size="2">Thanks!</font></p><p class="MsoNormal" style="margin-left: 0.0866in; font-family: arial,helvetica,sans-serif;"><font size="2">Sarah<br>
</font></p><p class="MsoNormal" style="margin-left: 0.0866in; font-family: arial,helvetica,sans-serif;"><font size="2"><br></font></p><p class="MsoNormal" style="margin-left: 0.0866in; font-family: arial,helvetica,sans-serif;">
<span style="font-family: "Courier New";"><font style="font-family: arial,helvetica,sans-serif;" size="2"><br></font></span></p><p class="MsoNormal" style="margin-left: 0.0866in; font-family: arial,helvetica,sans-serif;">
<span style="font-family: "Courier New";"><font style="font-family: arial,helvetica,sans-serif;" size="2">Center for Applied Biodiversity Informatics</font></span></p><p class="MsoNormal" style="margin-left: 0.0866in; font-family: arial,helvetica,sans-serif;">
<span style="font-family: "Courier New";"></span><font size="2">California Academy of Sciences</font></p><p class="MsoNormal" style="margin-left: 0.0866in;"><span style="font-family: "Courier New";"><br>
</span></p>
<br>
_______________________________________________<br>Biomod-commits mailing list<br><a href="mailto:Biomod-commits@lists.r-forge.r-project.org">Biomod-commits@lists.r-forge.r-project.org</a><br>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits<br></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><span class="Apple-style-span" style="font-size: 12px; "><div>--------------------------</div><div>Dr. Wilfried Thuiller</div><div>Laboratoire d'Ecologie Alpine, UMR CNRS 5553</div><div>Université Joseph Fourier</div><div>BP53, 38041 Grenoble cedex 9, France</div><div>tel: +33 (0)4 76 51 44 97</div><div>fax: +33 (0)4 76 51 42 79</div><div><br></div><div>Email: <a href="mailto:wilfried.thuiller@ujf-grenoble.fr">wilfried.thuiller@ujf-grenoble.fr</a><br>Home page: <a href="http://www.will.chez-alice.fr/">http://www.will.chez-alice.fr</a><br>Website: <a href="http://www-leca.ujf-grenoble.fr/equipes/tde.htm">http://www-leca.ujf-grenoble.fr/equipes/tde.htm</a><br><br>FP6 European MACIS project: <a href="http://www.macis-project.net/">http://www.macis-project.net</a><br>FP6 European EcoChange project: <a href="http://www.ecochange-project.eu/">http://www.ecochange-project.eu</a></div><div><br></div></span></div></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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