<html><head><base href="x-msg://90/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear Brenna,</div><div>Sorry we modified some functions recently notably 'Biomod.Models' called by the Models function. There was a mistake in the neural nets when providing independent weights. it seems another bug percolated from that.</div><div>Anyway, we uploaded a new version 3 hours ago which works perfectly fine. I just run the example. R-Forge should compile the package as binary in the next 24h.</div><div>You can also load the package as source and compile it yourself it is urgent:</div><div><br></div><div>install.packages("BIOMOD", repos="<a href="http://R-Forge.R-project.org">http://R-Forge.R-project.org</a>", type="source")</div><div><br></div><div>Sorry for the inconvenience,</div><div><br></div><div>Best</div><div>Wilfried</div><div><br></div><div><br></div><div><br></div><br><div><div>Le 7 oct. 2010 à 19:39, Brenna Forester a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite"><div ocsi="0" fpstyle="1"><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 13px; ">Hello, I'm trying to run BIOMOD on a fresh install of R and the example code in ?Models is not executing. I'm running BIOMOD version 1.1-5 installed via<span class="Apple-converted-space"> </span><span style="font-family: 'Courier New'; ">install.packages("BIOMOD", repos="<a href="http://R-Forge.R-project.org">http://R-Forge.R-project.org</a>")</span><br><br>and all packages are up-to-date using<span class="Apple-converted-space"> </span><span style="font-family: 'Courier New'; ">update.packages()</span><br><br>When running the example from Models I get:<br><br><span style="font-family: 'Courier New'; ">> data(Sp.Env)</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">> data(CoorXY)</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">> #use fix(Sp.Env) to visualise the dataset</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">></span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">> #This command is necessary for the run of BIOMOD as a new dataframe is produced for the Models function</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">> Initial.State(Response=Sp.Env[,12:14], Explanatory=Sp.Env[,4:10],</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">+ IndependentResponse=NULL, IndependentExplanatory=NULL)</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">></span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">> #Here are done 2 PA runs and 2 repetitions for each run. Here we will have 36 runs per species. This will hence take several minutes.</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">> Models(GLM = TRUE, TypeGLM = "quad", Test = "AIC", GBM = TRUE, No.trees = 3000, GAM = TRUE, CTA = TRUE, CV.tree = 50,</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">+ ANN = TRUE, CV.ann = 2, SRE = TRUE, quant=0.05, FDA = TRUE, MARS = TRUE, RF = TRUE, NbRunEval = 2, DataSplit = 80,</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">+ Yweights=NULL, Roc=TRUE, Optimized.Threshold.Roc=TRUE, Kappa=TRUE, TSS=TRUE, KeepPredIndependent = FALSE, VarImport=5,</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">+ NbRepPA=2, strategy="circles", coor=CoorXY, distance=2, nb.absences=1000)</span><br style="font-family: 'Courier New'; "><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">-----------------------------------</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">Modelling summary</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">-----------------------------------</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">Number of species modelled : 3</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">Sp290, Sp277, Sp164</span><br style="font-family: 'Courier New'; "><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">numerical variables : Var1, Var2, Var3, Var4, Var5, Var6, Var7</span><br style="font-family: 'Courier New'; "><br style="font-family: 'Courier New'; "><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">number of evaluation repetitions : 2</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">number of pseudo-absences runs : 2</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">models selected : ANN, CTA, GAM, GBM, GLM, MARS, FDA, RF, SRE</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">total number of model runs : 162</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">-----------------------------------</span><br style="font-family: 'Courier New'; "><br style="font-family: 'Courier New'; "><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">##### Sp290 #####</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">##### pseudo-absence run 1 #####</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">Model=Artificial Neural Network</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; "> 2 Fold Cross Validation + 3 Repetitions</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">Calibration and evaluation phase: Nb of cross-validations: 2</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">Error in Rescaler4(as.numeric(TempArray), ref = DataBIOMOD[PA.samp, NbVar + :</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; "> object 'TempArray' not found</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">></span><br><br><br>My version information is:<br><br><span style="font-family: 'Courier New'; ">> version</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; "> _</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">platform i386-pc-mingw32</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">arch i386</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">os mingw32</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">system i386, mingw32</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">status</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">major 2</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">minor 11.1</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">year 2010</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">month 05</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">day 31</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">svn rev 52157</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">language R</span><br style="font-family: 'Courier New'; "><span style="font-family: 'Courier New'; ">version.string R version 2.11.1 (2010-05-31)</span><br><br>Thank you!<br>Brenna<br>_______________________________________<br><div><div style="font-family: Tahoma; font-size: 13px; "><div style="font-family: Tahoma; font-size: 13px; "><br>Brenna Forester<br><br>M.Sc. Candidate<br>Huxley College of the Environment<br>Western Washington University<br>Bellingham, WA<br><br><a href="mailto:forestb@students.wwu.edu">forestb@students.wwu.edu</a><br>360-738-0711<br><div style="font-family: Tahoma; font-size: 13px; "></div></div></div></div></div>_______________________________________________<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><a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits</a><br></div></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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