<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear Peter,</div><div>I have checked and I am not sure what's happening with your data. BIOMOD does work with factor variables. </div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">library<span style="color: #042299">(</span>BIOMOD<span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">data<span style="color: #042299">(</span>Sp.Env<span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">Cat<span style="color: #042299"> <- </span>c<span style="color: #042299">(</span>rep<span style="color: #042299">(</span><span style="color: #2b6fb8">0</span><span style="color: #042299">, </span>nrow<span style="color: #042299">(</span>Sp.Env<span style="color: #042299">)/</span><span style="color: #2b6fb8">2</span><span style="color: #042299">), </span>rep<span style="color: #042299">(</span><span style="color: #2b6fb8">1</span><span style="color: #042299">, </span>nrow<span style="color: #042299">(</span>Sp.Env<span style="color: #042299">)/</span><span style="color: #2b6fb8">2</span><span style="color: #042299">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">Cat<span style="color: #042299"> <- </span>as.factor<span style="color: #042299">(</span>Cat<span style="color: #042299">[</span>sample<span class="Apple-style-span" style="color: rgb(0, 113, 40); font-family: Monaco; font-size: 11px; "><span style="color: rgb(4, 34, 153); ">(</span></span><span class="Apple-style-span" style="color: rgb(0, 113, 40); font-family: Monaco; font-size: 11px; ">nrow</span><span class="Apple-style-span" style="color: rgb(0, 113, 40); font-family: Monaco; font-size: 11px; "><span style="color: rgb(4, 34, 153); ">(</span></span><span class="Apple-style-span" style="color: rgb(0, 113, 40); font-family: Monaco; font-size: 11px; ">Sp.Env</span><span class="Apple-style-span" style="color: rgb(0, 113, 40); font-family: Monaco; font-size: 11px; "><span style="color: rgb(4, 34, 153); ">))</span></span><span class="Apple-style-span" style="color: rgb(4, 34, 153); ">])</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">Sp.Env<span style="color: #042299">$</span>Cat<span style="color: #042299"> <- </span>Cat</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; color: rgb(0, 113, 40); "><font class="Apple-style-span" color="#042299"><font class="Apple-style-span" color="#007128"><br></font></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; color: rgb(0, 113, 40); ">Initial.State<span style="color: #042299">(</span>Response<span style="color: #042299">=</span>Sp.Env<span style="color: #042299">[,</span><span style="color: #2b6fb8">11</span><span style="color: #042299">:</span><span style="color: #2b6fb8">12</span><span style="color: #042299">], </span>Explanatory<span style="color: #042299">=</span>Sp.Env<span style="color: #042299">[,</span>c<span style="color: #042299">(</span><span style="color: #2b6fb8">4</span><span style="color: #042299">:</span><span style="color: #2b6fb8">6</span><span style="color: #042299">,</span><span style="color: #2b6fb8">19</span><span style="color: #042299">)])<span class="Apple-tab-span" style="white-space:pre"> </span></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; color: rgb(4, 34, 153); min-height: 16px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; color: rgb(0, 113, 40); ">Models<span style="color: #042299">(</span>GLM<span style="color: #042299"> = </span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>TypeGLM<span style="color: #042299"> = </span><span style="color: #b0140c">"quad"</span><span style="color: #042299">, </span>Test<span style="color: #042299"> = </span><span style="color: #b0140c">"AIC"</span><span style="color: #042299">, </span>GBM<span style="color: #042299"> = </span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>No.trees<span style="color: #042299"> = </span><span style="color: #2b6fb8">3000</span><span style="color: #042299">, </span>GAM<span style="color: #042299"> = </span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>CTA<span style="color: #042299"> = </span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>CV.tree<span style="color: #042299"> = </span><span style="color: #2b6fb8">50</span><span style="color: #042299">, </span>ANN<span style="color: #042299"> = </span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>CV.ann<span style="color: #042299"> = </span><span style="color: #2b6fb8">2</span><span style="color: #042299">, </span>SRE<span style="color: #042299"> = </span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>quant<span style="color: #042299">=</span><span style="color: #2b6fb8">0.05</span><span style="color: #042299">, </span>FDA<span style="color: #042299"> = </span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>MARS<span style="color: #042299"> = </span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>RF<span style="color: #042299"> = </span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>NbRunEval<span style="color: #042299"> = </span><span style="color: #2b6fb8">2</span><span style="color: #042299">, </span>DataSplit<span style="color: #042299"> = </span><span style="color: #2b6fb8">80</span><span style="color: #042299">,</span>Yweights<span style="color: #042299">=</span><span style="color: #db224a">NULL</span><span style="color: #042299">, </span>Roc<span style="color: #042299">=</span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>Optimized.Threshold.Roc<span style="color: #042299">=</span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>Kappa<span style="color: #042299">=</span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>TSS<span style="color: #042299">=</span><span style="color: #db224a">TRUE</span><span style="color: #042299">, </span>KeepPredIndependent<span style="color: #042299"> = </span><span style="color: #db224a">FALSE</span><span style="color: #042299">, </span>VarImport<span style="color: #042299">=</span><span style="color: #2b6fb8">5</span><span style="color: #042299">,</span>NbRepPA<span style="color: #042299">=</span><span style="color: #2b6fb8">0</span><span style="color: #042299">, </span>strategy<span style="color: #042299">=</span><span style="color: #b0140c">"circles"</span><span style="color: #042299">, </span>coor<span style="color: #042299">=</span>CoorXY<span style="color: #042299">, </span>distance<span style="color: #042299">=</span><span style="color: #2b6fb8">2</span><span style="color: #042299">, </span>nb.absences<span style="color: #042299">=</span><span style="color: #2b6fb8">1000</span><span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); min-height: 15px; "><br></div></div>It works perfectly fine, excepted MARS and SRE which are turned off because they do not handle factor variables. <div><br></div><div><br></div><div>Do you have the latest version of R and BIOMOD? </div><div><br></div><div>Wilfried</div><div><br></div><div><br></div><div><br><div><div><br></div><div><br></div><div>Le 7 juin 2010 à 18:01, Wilfried Thuiller a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear Peter,</div><div>This is supposed to work indeed. I need to have a look. It seems the GAM function does not work with the categorical variables whereas I thought I had previously removed that problem. </div><div><br></div><div>A sexy alternative is to transform your categorical variable in n-1 binary variables. This is actually what the models do but hidden. </div><div>In your case, you just need one variable GRASS coded in 0 when there is forest and 1 when there is grassland. </div><div>Use this binary variable as continuous into the models. </div><div><br></div><div>HIH</div><div>Wilfried</div><div><br></div><div><br></div><div><div>Le 31 mai 2010 à 13:08, <<a href="mailto:Horchler@bafg.de">Horchler@bafg.de</a>> <<a href="mailto:Horchler@bafg.de">Horchler@bafg.de</a>> a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello,<br><br>I am wondering if I can use factorial vairables in BIOMOD?<br>I want to include type of land-use codes as "grassland" or "forest" in<br>my analysis but get an error message:<br><br>----------------------------------- <br>Modelling summary <br>----------------------------------- <br>Number of species modelled : 6<br>Alopprat, Urtidioi, Glycmaxi, Rubucaes, Crxacuta, Rorisylv<br><br>numerical variables : UFD.n, vmhq, Hum, S<br>factorial variables : Nutzung<br><br>number of evaluation repetitions : 0<br>number of pseudo-absences runs : 0<br>models selected : GAM, GBM, GLM, RF<br>total number of model runs : 24<br>----------------------------------- <br><br><br>##### Alopprat #####<br>Model=GAM spline <br> 3 Degrees of smoothing <br>Fehler in Summary.factor(c(1L, 1L, 1L, 1L, 1L, 3L, 3L, 1L, 1L, 1L, 3L,<br>: <br> sum not meaningful for factors<br><br><br><br>What can I do about this?<br><br>Thnaks in advance!<br>Peter<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><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>
<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; 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><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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<br></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>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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