<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear Andreas,</div><div><br></div><div>You made my day! Honestly, I had a good laugh tonight. I will not answer the last part of your email to avoid being rude. </div><div>If you are not able to understand humor from people who tried to help you for free on their spare time, better to keep going outside of the R environment. </div><div><br></div><div>Having say that, I downloaded the Maxent data and now that I had the exact code you used, I simply copy-pasted your code and run BIOMOD. I am sorry to say, it worked pretty well, and the Models folder was full of the models outputs, as the Pred folder was. </div><div><br></div><div>See below the copy-paste from my console.</div><div><br></div><div>In summary, either your computer crashed, or went out of memory but there is nothing wrong about the output BIOMOD can deliver on this species, from the exact code you wrote. </div><div><br></div><div><br></div><div>I want to remind you that besides the manuals, which are so badly written, you have the help files in R. I agree there are probably not the best self-explanatory you can find, but still if you follow them, you should be able to find your way, as many people have done before you. </div><div><br></div><div>For instance, typing </div><div><br></div><div>?Models</div><div><br></div><div>will guide you all the way for building models, analyzing the variable importance and the response curves. </div><div><br></div><div>Same for other functions such as </div><div>?Projections</div><div>?Ensemble.Forecasting</div><div>?Biomod.Turnover</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div>###</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(176, 20, 12); "><span style="color: #042299">setwd(</span>"/Wilfried/0000/Simulations/MISC/Maxent/tutorial-data"<span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(176, 20, 12); "><span style="color: #007128">bradypus</span><span style="color: #042299"><-</span><span style="color: #000000"> </span><span style="color: #042299">read.csv(</span>"/Wilfried/0000/Simulations/MISC/Maxent/tutorial-data/swd/bradypus_swd.csv"<span style="color: #042299">,</span><span style="color: #000000"> </span><span style="color: #007128">header</span><span style="color: #042299">=</span><span style="color: #db224a">TRUE</span><span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(176, 20, 12); "><span style="color: #007128">background</span><span style="color: #042299"><-</span><span style="color: #000000"> </span><span style="color: #042299">read.csv(</span>"/Wilfried/0000/Simulations/MISC/Maxent/tutorial-data/swd/background.csv"<span style="color: #042299">,</span><span style="color: #000000"> </span><span style="color: #007128">header</span><span style="color: #042299">=</span><span style="color: #db224a">TRUE</span><span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); ">names(<span style="color: #007128">bradypus</span>)[<span style="color: #2b6fb8">2</span>]<-paste(<span style="color: #b0140c">"x"</span>)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); ">names(<span style="color: #007128">bradypus</span>)[<span style="color: #2b6fb8">3</span>]<-paste(<span style="color: #b0140c">"y"</span>)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">presence_absence<span style="color: #042299"><-</span><span style="color: #000000"> </span><span style="color: #042299">matrix(</span>nrow<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #042299">(nrow(</span>bradypus<span style="color: #042299">)</span><span style="color: #000000"> </span><span style="color: #042299">+</span><span style="color: #000000"> </span><span style="color: #042299">nrow(</span>background<span style="color: #042299">)),</span><span style="color: #000000"> </span>ncol<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #2b6fb8">1</span><span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); "><span style="color: #db224a">for</span><span style="color: #000000"> </span><span style="color: #042299">(</span>i<span style="color: #000000"> </span><span style="color: #db224a">in</span><span style="color: #000000"> </span><span style="color: #2b6fb8">1</span><span style="color: #042299">:nrow(</span>bradypus<span style="color: #042299">))</span><span style="color: #000000"> </span><span style="color: #042299">{</span>presence_absence<span style="color: #042299">[</span>i<span style="color: #042299">,</span><span style="color: #2b6fb8">1</span><span style="color: #042299">]<-</span><span style="color: #000000"> </span><span style="color: #2b6fb8">1</span><span style="color: #042299">}</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); "><span style="color: #db224a">for</span><span style="color: #000000"> </span><span style="color: #042299">(</span>i<span style="color: #000000"> </span><span style="color: #042299">in</span><span style="color: #000000"> </span><span style="color: #042299">(nrow(</span>bradypus<span style="color: #042299">)</span><span style="color: #2b6fb8">+1</span><span style="color: #042299">):nrow(</span>presence_absence<span style="color: #042299">))</span><span style="color: #000000"> </span><span style="color: #042299">{</span>presence_absence<span style="color: #042299">[</span>i<span style="color: #042299">,</span><span style="color: #2b6fb8">1</span><span style="color: #042299">]<-</span><span style="color: #000000"> </span><span style="color: #2b6fb8">0</span><span style="color: #042299">}</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); "><span style="color: #042299">colnames(</span>presence_absence<span style="color: #042299">)<-</span><span style="color: #000000"> </span><span style="color: #042299">c(</span><span style="color: #b0140c">"Sp1"</span><span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">Sp.Env<span style="color: #042299"><-</span><span style="color: #000000"> </span><span style="color: #042299">rbind(</span>bradypus<span style="color: #042299">,</span><span style="color: #000000"> </span>background<span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">Sp.Env<span style="color: #042299"><-</span><span style="color: #000000"> </span><span style="color: #042299">cbind(</span>Sp.Env<span style="color: #042299">,</span><span style="color: #000000"> </span>presence_absence<span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">Sp.Env<span style="color: #042299">$</span>ecoreg<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #042299">as.factor(</span>Sp.Env<span style="color: #042299">$</span>ecoreg<span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">Resp.Var<span style="color: #042299"><-</span><span style="color: #000000"> </span>Sp.Env<span style="color: #042299">[,</span><span style="color: #2b6fb8">18</span><span style="color: #042299">]</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); "><span style="color: #007128">Resp.Var</span><-<span style="color: #000000"> </span>as.data.frame(<span style="color: #007128">Resp.Var</span>)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">Expl.Var<span style="color: #000000"> </span><span style="color: #042299"><-</span><span style="color: #000000"> </span>Sp.Env<span style="color: #042299">[,</span><span style="color: #2b6fb8">4</span><span style="color: #042299">:</span><span style="color: #2b6fb8">17</span><span style="color: #042299">]</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">LatLong<span style="color: #042299"><-</span><span style="color: #000000"> </span>Sp.Env<span style="color: #042299">[,</span><span style="color: #000000"> </span><span style="color: #2b6fb8">2</span><span style="color: #042299">:</span><span style="color: #2b6fb8">3</span><span style="color: #042299">]</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); ">head(<span style="color: #007128">Sp.Env</span>,<span style="color: #000000"> </span><span style="color: #2b6fb8">10</span>)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); ">summary(<span style="color: #007128">Sp.Env</span>)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); ">library(<span style="color: #007128">BIOMOD</span>)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); "><span style="color: #042299">Initial.State(</span>Response<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span>Resp.Var<span style="color: #042299">,</span><span style="color: #000000"> </span>Explanatory<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span>Expl.Var<span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 11px/normal Monaco; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); "><span style="color: #042299">Models(</span>GLM<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>TypeGLM<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #b0140c">"poly"</span><span style="color: #042299">,</span><span style="color: #000000"> </span>Test<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #b0140c">"AIC"</span><span style="color: #042299">,</span><span style="color: #000000"> </span>GBM<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>No.trees<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #2b6fb8">2000</span><span style="color: #042299">,</span><span style="color: #000000"> </span>GAM<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span>Spline<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #2b6fb8">3</span><span style="color: #042299">,</span><span style="color: #000000"> </span>CTA<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>CV.tree<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #2b6fb8">50</span><span style="color: #042299">,</span><span style="color: #000000"> </span>ANN<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>CV.ann<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #2b6fb8">2</span><span style="color: #042299">,</span><span style="color: #000000"> </span>SRE<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>quant<span style="color: #042299">=</span><span style="color: #2b6fb8">0.025</span><span style="color: #042299">,</span><span style="color: #000000"> </span>FDA<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>MARS<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>RF<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>NbRunEval<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #2b6fb8">1</span><span style="color: #042299">,</span><span style="color: #000000"> </span>DataSplit<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #2b6fb8">80</span><span style="color: #042299">,</span><span style="color: #000000"> </span>Yweights<span style="color: #042299">=</span><span style="color: #db224a">NULL</span><span style="color: #042299">,</span><span style="color: #000000"> </span>Roc<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>Optimized.Threshold.Roc<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>Kappa<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>TSS<span style="color: #042299">=</span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>KeepPredIndependent<span style="color: #000000"> </span><span style="color: #042299">=</span><span style="color: #000000"> </span><span style="color: #db224a">T</span><span style="color: #042299">,</span><span style="color: #000000"> </span>VarImport<span style="color: #042299">=</span><span style="color: #2b6fb8">0</span><span style="color: #042299">,</span>NbRepPA<span style="color: #042299">=</span><span style="color: #2b6fb8">1</span><span style="color: #042299">,</span><span style="color: #000000"> </span>strategy<span style="color: #042299">=</span><span style="color: #b0140c">"circles"</span><span style="color: #042299">,</span><span style="color: #000000"> </span>coor<span style="color: #042299">=</span>LatLong<span style="color: #042299">,</span><span style="color: #000000"> </span>distance<span style="color: #042299">=</span><span style="color: #2b6fb8">2</span><span style="color: #042299">,</span><span style="color: #000000"> </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 13px/normal Arial; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(169, 65, 203); ">#####################</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">MARS<span style="color: #000000"> </span>model<span style="color: #000000"> </span>was<span style="color: #000000"> </span>shut<span style="color: #000000"> </span>down<span style="color: #042299">,</span><span style="color: #000000"> </span>it<span style="color: #000000"> </span>cannot<span style="color: #000000"> </span>run<span style="color: #000000"> </span>on<span style="color: #000000"> </span>factorial<span style="color: #000000"> </span>variables<span style="color: #000000"> </span><span style="color: #042299">:</span><span style="color: #000000"> </span>ecoreg</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">SRE<span style="color: #000000"> </span>model<span style="color: #000000"> </span>was<span style="color: #000000"> </span>shut<span style="color: #000000"> </span>down<span style="color: #042299">,</span><span style="color: #000000"> </span>it<span style="color: #000000"> </span>cannot<span style="color: #000000"> </span>run<span style="color: #000000"> </span>on<span style="color: #000000"> </span>factorial<span style="color: #000000"> </span>variables<span style="color: #000000"> </span><span style="color: #042299">:</span><span style="color: #000000"> </span>ecoreg</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(4, 34, 153); ">-----------------------------------<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">Modelling<span style="color: #000000"> </span>summary<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(4, 34, 153); ">-----------------------------------<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">Number<span style="color: #000000"> </span>of<span style="color: #000000"> </span>species<span style="color: #000000"> </span>modelled<span style="color: #000000"> </span><span style="color: #042299">:</span><span style="color: #000000"> <span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #2b6fb8">1</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">Resp.Var</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">numerical<span style="color: #000000"> </span>variables<span style="color: #000000"> </span><span style="color: #042299">:</span><span style="color: #000000"> <span class="Apple-tab-span" style="white-space:pre"> </span></span>cld6190_ann<span style="color: #042299">,</span><span style="color: #000000"> </span>dtr6190_ann<span style="color: #042299">,</span><span style="color: #000000"> </span>frs6190_ann<span style="color: #042299">,</span><span style="color: #000000"> </span>h_dem<span style="color: #042299">,</span><span style="color: #000000"> </span>pre6190_ann<span style="color: #042299">,</span><span style="color: #000000"> </span>pre6190_l10<span style="color: #042299">,</span><span style="color: #000000"> </span>pre6190_l1<span style="color: #042299">,</span><span style="color: #000000"> </span>pre6190_l4<span style="color: #042299">,</span><span style="color: #000000"> </span>pre6190_l7<span style="color: #042299">,</span><span style="color: #000000"> </span>tmn6190_ann<span style="color: #042299">,</span><span style="color: #000000"> </span>tmp6190_ann<span style="color: #042299">,</span><span style="color: #000000"> </span>tmx6190_ann<span style="color: #042299">,</span><span style="color: #000000"> </span>vap6190_ann</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">factorial<span style="color: #000000"> </span>variables<span style="color: #000000"> </span><span style="color: #042299">:</span><span style="color: #000000"> <span class="Apple-tab-span" style="white-space:pre"> </span></span>ecoreg</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">number<span style="color: #000000"> </span>of<span style="color: #000000"> </span>evaluation<span style="color: #000000"> </span>repetitions<span style="color: #000000"> </span><span style="color: #042299">:</span><span style="color: #000000"> <span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #2b6fb8">1</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">number<span style="color: #000000"> </span>of<span style="color: #000000"> </span>pseudo<span style="color: #042299">-</span>absences<span style="color: #000000"> </span>runs<span style="color: #000000"> </span><span style="color: #042299">:</span><span style="color: #000000"> <span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #2b6fb8">1</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">models<span style="color: #000000"> </span>selected<span style="color: #000000"> </span><span style="color: #042299">:</span><span style="color: #000000"> <span class="Apple-tab-span" style="white-space:pre"> </span></span>ANN<span style="color: #042299">,</span><span style="color: #000000"> </span>CTA<span style="color: #042299">,</span><span style="color: #000000"> </span>GAM<span style="color: #042299">,</span><span style="color: #000000"> </span>GBM<span style="color: #042299">,</span><span style="color: #000000"> </span>GLM<span style="color: #042299">,</span><span style="color: #000000"> </span>FDA<span style="color: #042299">,</span><span style="color: #000000"> </span>RF</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">total<span style="color: #000000"> </span>number<span style="color: #000000"> </span>of<span style="color: #000000"> </span>model<span style="color: #000000"> </span>runs<span style="color: #000000"> </span><span style="color: #042299">:</span><span style="color: #000000"> <span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #2b6fb8">14</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(4, 34, 153); ">-----------------------------------<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(169, 65, 203); ">#####<span class="Apple-tab-span" style="white-space:pre"> </span> Resp.Var <span class="Apple-tab-span" style="white-space:pre"> </span>#####</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(169, 65, 203); ">#####<span class="Apple-tab-span" style="white-space:pre"> </span> pseudo-absence run 1 <span class="Apple-tab-span" style="white-space:pre"> </span>#####</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">Model<span style="color: #042299">=</span>Artificial<span style="color: #000000"> </span>Neural<span style="color: #000000"> </span>Network<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span> </span><span style="color: #2b6fb8">2</span><span style="color: #000000"> </span>Fold<span style="color: #000000"> </span>Cross<span style="color: #000000"> </span>Validation<span style="color: #000000"> </span><span style="color: #042299">+</span><span style="color: #000000"> </span><span style="color: #2b6fb8">3</span><span style="color: #000000"> </span>Repetitions<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">Calibration<span style="color: #000000"> </span>and<span style="color: #000000"> </span>evaluation<span style="color: #000000"> </span>phase<span style="color: #042299">:</span><span style="color: #000000"> </span>Nb<span style="color: #000000"> </span>of<span style="color: #000000"> </span>cross<span style="color: #042299">-</span>validations<span style="color: #042299">:</span><span style="color: #000000"> </span><span style="color: #2b6fb8">1</span><span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">Model<span style="color: #042299">=</span>Classification<span style="color: #000000"> </span>tree<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span> </span><span style="color: #2b6fb8">50</span><span style="color: #000000"> </span>Fold<span style="color: #000000"> </span>Cross<span style="color: #042299">-</span>Validation<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">Model<span style="color: #042299">=</span>GAM<span style="color: #000000"> </span>spline<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span> </span><span style="color: #2b6fb8">3</span><span style="color: #000000"> </span>Degrees<span style="color: #000000"> </span>of<span style="color: #000000"> </span>smoothing<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">Model<span style="color: #042299">=</span>Generalised<span style="color: #000000"> </span>Boosting<span style="color: #000000"> </span>Regression<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span> </span><span style="color: #2b6fb8">2000</span><span style="color: #000000"> </span>maximum<span style="color: #000000"> </span>different<span style="color: #000000"> </span>trees<span style="color: #000000"> </span>and<span style="color: #000000"> </span>lambda<span style="color: #000000"> </span>Fold<span style="color: #000000"> </span>Cross<span style="color: #042299">-</span>Validation<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">Model<span style="color: #042299">=</span>GLM<span style="color: #000000"> </span>polynomial<span style="color: #000000"> </span><span style="color: #042299">+</span><span style="color: #000000"> </span>quadratic<span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span> </span>Stepwise<span style="color: #000000"> </span>procedure<span style="color: #000000"> </span>using<span style="color: #000000"> </span>AIC<span style="color: #000000"> </span>criteria<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(0, 113, 40); ">Model<span style="color: #042299">=</span>Flexible<span style="color: #000000"> </span>Discriminant<span style="color: #000000"> </span>Analysis<span style="color: #000000"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); "><span style="color: #007128">Model</span><span style="color: #042299">=</span><span style="color: #007128">Breiman</span><span style="color: #000000"> </span><span style="color: #007128">and</span><span style="color: #000000"> </span><span style="color: #007128">Cutler</span>'s random forests for classification and regression </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); ">##############</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); ">> list.files("Models/")</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); "> [1] "rescaling_models" "Resp.Var_ANN_PA1" "Resp.Var_ANN_PA1_rep1" "Resp.Var_CTA_PA1" "Resp.Var_CTA_PA1_rep1" "Resp.Var_FDA_PA1" </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); "> [7] "Resp.Var_FDA_PA1_rep1" "Resp.Var_GAM_PA1" "Resp.Var_GAM_PA1_rep1" "Resp.Var_GBM_PA1" "Resp.Var_GBM_PA1_rep1" "Resp.Var_GLM_PA1" </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); ">[13] "Resp.Var_GLM_PA1_rep1" "Resp.Var_RF_PA1" "Resp.Var_RF_PA1_rep1" </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); ">> list.files("Pred/")</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); ">[1] "Pred_Resp.Var"</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Arial; color: rgb(176, 20, 12); min-height: 15px; "><br></div><div> </div><div><br></div><div><br></div><br><div><div>Le 28 févr. 2012 à 19:25, Andreas Soteriades a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: arial, helvetica, sans-serif; font-size: 10pt; position: static; z-index: auto; "><div><font face="'times new roman', 'new york', times, serif">Hi Wilfried,</font></div><div><font face="'times new roman', 'new york', times, serif"><br></font></div><div><font face="'times new roman', 'new york', times, serif">Here's my code:</font></div><div><font face="'times new roman', 'new york', times, serif"><br></font></div><div><font face="'times new roman', 'new york', times, serif"><div>library(BIOMOD)</div><div>bradypus<- read.csv("bradypus_swd.csv", header=TRUE)</div><div>background<- read.csv("background.csv", header=TRUE)</div><div>names(bradypus)[2]<-paste("x")</div><div>names(bradypus)[3]<-paste("y")</div><div>presence_absence<- matrix(nrow = (nrow(bradypus) + nrow(background)), ncol = 1)</div><div>for (i in 1:nrow(bradypus)) {presence_absence[i,1]<- 1}</div><div>for (i in
(nrow(bradypus)+1):nrow(presence_absence)) {presence_absence[i,1]<- 0}</div><div>colnames(presence_absence)<- c("Sp1")</div><div>Sp.Env<- rbind(bradypus, background)</div><div>Sp.Env<- cbind(Sp.Env, presence_absence)</div><div>Sp.Env$ecoreg = as.factor(Sp.Env$ecoreg)</div><div>Resp.Var<- Sp.Env[,18]</div><div>Resp.Var<- as.data.frame(Resp.Var)</div><div>Expl.Var <- Sp.Env[,4:17]</div><div>LatLong<- Sp.Env[, 2:3]</div><div>head(Sp.Env, 10)</div><div>summary(Sp.Env)</div><div>Initial.State(Response = Resp.Var, Explanatory = Expl.Var)</div><div><br></div></font></div><div style="font-family: arial, helvetica, sans-serif; "><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; ">>>Perhaps you could copy paste the Initial.State call you made</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; " class="yui_3_2_0_55_133044491230861"><br></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; " class="yui_3_2_0_55_133044491230861">See above<br><br>>>The first ten lines of your observed data (head(MyDate). </div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; " class="yui_3_2_0_55_133044491230861"><br></div><div class="yui_3_2_0_55_133044491230861"><span class="Apple-tab-span" style="white-space:pre"> </span> x y cld6190_ann dtr6190_ann ecoreg<br><div class="yui_3_2_0_55_133044491230861"> 1 -65.4000 <span class="Apple-tab-span" style="white-space:pre"> </span>-10.3833 76 <span class="Apple-tab-span" style="white-space:pre"> </span> 104 10</div><div class="yui_3_2_0_55_133044491230861">2 -65.3833 <span class="Apple-tab-span" style="white-space:pre"> </span>-10.3833 76 104 10</div><div class="yui_3_2_0_55_133044491230861">3 -65.1333 <span class="Apple-tab-span" style="white-space:pre"> </span>-16.8000 57 114 10</div><div class="yui_3_2_0_55_133044491230861">4 -63.6667 <span class="Apple-tab-span" style="white-space:pre"> </span>-17.4500 57 112 10</div><div class="yui_3_2_0_55_133044491230861">5 -63.8500 <span class="Apple-tab-span" style="white-space:pre"> </span>-17.4000
57 113 10</div><div class="yui_3_2_0_55_133044491230861">6 -64.4167<span class="Apple-tab-span" style="white-space:pre"> </span>-16.0000 58 111 10</div><div class="yui_3_2_0_55_133044491230861">7 -63.1667 <span class="Apple-tab-span" style="white-space:pre"> </span>-17.8000 57 110 8</div><div class="yui_3_2_0_55_133044491230861">8 -56.7333 <span class="Apple-tab-span" style="white-space:pre"> </span> -2.6000 77
82 10</div><div class="yui_3_2_0_55_133044491230861">9 -59.1333 <span class="Apple-tab-span" style="white-space:pre"> </span> -3.7000 83 86 10</div><div class="yui_3_2_0_55_133044491230861">10 -60.0833 <span class="Apple-tab-span" style="white-space:pre"> </span> -3.1333 82 85 10</div><div class="yui_3_2_0_55_133044491230861"><br></div><div class="yui_3_2_0_55_133044491230861"><div class="yui_3_2_0_55_133044491230861">frs6190_ann h_dem pre6190_ann pre6190_l10 pre6190_l1 pre6190_l4 pre6190_l7</div><div class="yui_3_2_0_55_133044491230861">1
2 121 46 41 84 54 3</div><div class="yui_3_2_0_55_133044491230861">2 2 121 46 40 84 54 3</div><div class="yui_3_2_0_55_133044491230861">3 1 211
65 56 129 58 34</div><div class="yui_3_2_0_55_133044491230861">4 3 363 36 33 71 27 13</div><div class="yui_3_2_0_55_133044491230861">5 3 303 39 35
77 29 15</div><div class="yui_3_2_0_55_133044491230861">6 0 166 54 48 107 45 23</div><div class="yui_3_2_0_55_133044491230861">7 0 430 33 30 61 29
15</div><div class="yui_3_2_0_55_133044491230861">8 0 12 60 24 69 96 42</div><div class="yui_3_2_0_55_133044491230861">9 0 23 58 30 96 95 25</div><div class="yui_3_2_0_55_133044491230861">10
0 32 62 39 84 98 29</div></div><div class="yui_3_2_0_55_133044491230861"><br></div><div><div> tmn6190_ann tmp6190_ann tmx6190_ann vap6190_ann Sp1</div><div>1 <span class="Apple-tab-span" style="white-space:pre"> </span>192 <span class="Apple-tab-span" style="white-space:pre"> </span>266 <span class="Apple-tab-span" style="white-space:pre"> </span>337 <span class="Apple-tab-span" style="white-space:pre"> </span>279 1</div><div>2
<span class="Apple-tab-span" style="white-space:pre"> </span>192 <span class="Apple-tab-span" style="white-space:pre"> </span>266 <span class="Apple-tab-span" style="white-space:pre"> </span>337 <span class="Apple-tab-span" style="white-space:pre"> </span>279 1</div><div>3 <span class="Apple-tab-span" style="white-space:pre"> </span>140 <span class="Apple-tab-span" style="white-space:pre"> </span>244 <span class="Apple-tab-span" style="white-space:pre"> </span>321 <span class="Apple-tab-span" style="white-space:pre"> </span>221 1</div><div>4 <span class="Apple-tab-span" style="white-space:pre"> </span>135 <span class="Apple-tab-span" style="white-space:pre"> </span>229
<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>307 <span class="Apple-tab-span" style="white-space:pre"> </span>202 1</div><div>5 <span class="Apple-tab-span" style="white-space:pre"> </span>134 <span class="Apple-tab-span" style="white-space:pre"> </span>229 <span class="Apple-tab-span" style="white-space:pre"> </span>306 <span class="Apple-tab-span" style="white-space:pre"> </span>202 1</div><div>6 <span class="Apple-tab-span" style="white-space:pre"> </span>156 <span class="Apple-tab-span" style="white-space:pre"> </span>252 <span class="Apple-tab-span" style="white-space:pre"> </span>326
<span class="Apple-tab-span" style="white-space:pre"> </span>235 1</div><div>7 <span class="Apple-tab-span" style="white-space:pre"> </span>153 <span class="Apple-tab-span" style="white-space:pre"> </span>245 <span class="Apple-tab-span" style="white-space:pre"> </span>326 <span class="Apple-tab-span" style="white-space:pre"> </span>217 1</div><div>8 <span class="Apple-tab-span" style="white-space:pre"> </span>229 <span class="Apple-tab-span" style="white-space:pre"> </span>275 <span class="Apple-tab-span" style="white-space:pre"> </span> 335 <span class="Apple-tab-span" style="white-space:pre"> </span>306 1</div><div>9 <span class="Apple-tab-span" style="white-space:pre"> </span>220 <span class="Apple-tab-span" style="white-space:pre"> </span>271 <span class="Apple-tab-span" style="white-space:pre"> </span>328 <span class="Apple-tab-span" style="white-space:pre"> </span>301 1</div><div>10 <span class="Apple-tab-span" style="white-space:pre"> </span>224 <span class="Apple-tab-span" style="white-space:pre"> </span>272 <span class="Apple-tab-span" style="white-space:pre"> </span>328 <span class="Apple-tab-span" style="white-space:pre"> </span>300 1</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div></div><br><font size="3">>>summary( MyData)</font><br><font size="3">>>I doubt there are in the good
format.</font></div><div class="yui_3_2_0_55_133044491230861"><br></div><div class="yui_3_2_0_55_133044491230861"><div class="yui_3_2_0_55_133044491230861"> x y cld6190_ann </div><div class="yui_3_2_0_55_133044491230861">Min. :-94.72 Min. :-55.025 Min. :32.00 </div><div class="yui_3_2_0_55_133044491230861">1st Qu.:-69.92 1st Qu.:-24.538 1st Qu.:54.00 </div><div class="yui_3_2_0_55_133044491230861">Median :-62.98 Median :-11.825 Median :64.00 </div><div class="yui_3_2_0_55_133044491230861">Mean :-62.05 Mean :-13.560 Mean :63.15 </div><div class="yui_3_2_0_55_133044491230861">3rd Qu.:-54.12 3rd Qu.: -2.425 3rd Qu.:74.00 </div><div class="yui_3_2_0_55_133044491230861">Max. :-34.92 Max.
: 23.125 Max. :84.00 </div><div class="yui_3_2_0_55_133044491230861"> </div><div class="yui_3_2_0_55_133044491230861"> dtr6190_ann ecoreg frs6190_ann h_dem </div><div class="yui_3_2_0_55_133044491230861"> Min. : 49.0 10 :4590 Min. : 0.00 Min. : 0 </div><div class="yui_3_2_0_55_133044491230861"> 1st Qu.: 98.0 9 :1781 1st Qu.: 0.00 1st Qu.: 101 </div><div class="yui_3_2_0_55_133044491230861"> Median :110.0 5
:1232 Median : 1.00 Median : 249 </div><div class="yui_3_2_0_55_133044491230861"> Mean :112.4 8 : 790 Mean : 21.04 Mean : 579 </div><div class="yui_3_2_0_55_133044491230861"> 3rd Qu.:125.0 2 : 620 3rd Qu.: 11.00 3rd Qu.: 598 </div><div class="yui_3_2_0_55_133044491230861"> Max. :178.0 12 : 495 Max. :235.00 Max. :5610 </div><div class="yui_3_2_0_55_133044491230861"> (Other): 608 </div><div class="yui_3_2_0_55_133044491230861"> pre6190_ann pre6190_l10 pre6190_l1 pre6190_l4
</div><div class="yui_3_2_0_55_133044491230861"> Min. : 0.00 Min. : 0.00 Min. : 0.00 Min. : 0.00 </div><div class="yui_3_2_0_55_133044491230861"> 1st Qu.: 23.00 1st Qu.: 16.00 1st Qu.: 23.00 1st Qu.: 21.00 </div><div class="yui_3_2_0_55_133044491230861"> Median : 41.00 Median : 37.00 Median : 47.00 Median : 38.00 </div><div class="yui_3_2_0_55_133044491230861"> Mean : 41.43 Mean : 38.96 Mean : 50.99 Mean : 46.93 </div><div class="yui_3_2_0_55_133044491230861"> 3rd Qu.: 58.00 3rd Qu.: 55.00 3rd Qu.: 81.00 3rd Qu.: 73.00 </div><div class="yui_3_2_0_55_133044491230861"> Max. :204.00 Max. :250.00 Max. :185.00 Max. :188.00 </div><div class="yui_3_2_0_55_133044491230861"> </div><div class="yui_3_2_0_55_133044491230861"> pre6190_l7 tmn6190_ann tmp6190_ann tmx6190_ann </div><div class="yui_3_2_0_55_133044491230861"> Min. : 0.00 Min. :-110.0 Min. : 1.0 Min. :101.0 </div><div class="yui_3_2_0_55_133044491230861"> 1st Qu.: 4.00 1st Qu.: 74.0 1st Qu.:183.0 1st Qu.:296.0 </div><div class="yui_3_2_0_55_133044491230861"> Median : 14.00 Median : 159.0 Median :246.0 Median :320.0 </div><div class="yui_3_2_0_55_133044491230861"> Mean : 29.75 Mean : 128.3 Mean :214.9 Mean :301.6 </div><div class="yui_3_2_0_55_133044491230861"> 3rd Qu.: 45.00 3rd Qu.: 196.0 3rd Qu.:261.0 3rd Qu.:331.0 </div><div class="yui_3_2_0_55_133044491230861"> Max. :222.00 Max. : 229.0 Max. :282.0 Max. :362.0 </div><div class="yui_3_2_0_55_133044491230861"> </div><div class="yui_3_2_0_55_133044491230861"> vap6190_ann Sp1 </div><div class="yui_3_2_0_55_133044491230861"> Min. : 1.0 Min. :0.00000
</div><div class="yui_3_2_0_55_133044491230861"> 1st Qu.:155.0 1st Qu.:0.00000 </div><div class="yui_3_2_0_55_133044491230861"> Median :225.0 Median :0.00000 </div><div class="yui_3_2_0_55_133044491230861"> Mean :205.3 Mean :0.01147 </div><div class="yui_3_2_0_55_133044491230861"> 3rd Qu.:269.0 3rd Qu.:0.00000 </div><div class="yui_3_2_0_55_133044491230861"> Max. :310.0 Max. :1.00000 </div><br><font size="3">>If you also fear this is because of the categorical variable, try without it.</font></div><div class="yui_3_2_0_55_133044491230861"><br></div><div class="yui_3_2_0_55_133044491230861">But since some models in BIOMOD can handle categorical variables, then would it be wise to exclude it? Doesn't that alter the results?<br><br><font size="3">> First of all, does someone have to go through the whole procedure of typing the
code above for each model >and for each variable, and to use the predict() function each time? According to the tutorial ?once the models >are trained (i.e. calibrated), a standard prediction is made. Then, one of the variables is randomized and a >new prediction is made.? I thought that BIOMOD was following this procedure automatically. If yes, how? If >not, how can I load CTA, ANN (and all the rest of the models in general) the same way glm is loaded in the >code above (i.e. glm(Sp281 ~ Var1 + Var2 + Var3 + Var4 + Var5 + Var6 + Var7, data=Sp.Env))?</font><br><br><font size="3">>>Obviously not, or I will not have spent ten years coding BIOMOD?</font></div><div class="yui_3_2_0_55_133044491230861"><br></div><div class="yui_3_2_0_55_133044491230861">Ok, but this unfairly ironic reply does not answer my question: what should I do instead of following the procedure described above? You might have spent ten years coding BIOMOD but
how much time have you actually spent writing the manuals? I am afraid they are quite badly written! I first tried to learn BIOMOD a year ago by reading the 2008 manuals; I struggled for 2-3 weeks before giving up. I switched to WEKA and learned how to operate the software through the command line in one day by using the manual, even though I had never programmed in Java before. Three weeks ago I downloaded MaxEnt together with the manual and it just took me some days to learn how to analyse the outputs, not to mention that it was a piece of cake to run the models.</div><div class="yui_3_2_0_55_133044491230861"><br></div><div class="yui_3_2_0_55_133044491230861">BIOMOD is such a powerful and innovative tool, and I have always found very exciting the idea of mastering it so as to have a series of different models running my predictions silmuntaneously. I truly believe that it is much better than MaxEnt and WEKA. I have been following your
scientific work since the day I found out about BIOMOD but I still haven't managed to make it work properly. The 2012 manual is as bad as those of 2008... </div><div class="yui_3_2_0_55_133044491230861"><br></div><div class="yui_3_2_0_55_133044491230861">There is only one simple thing I'm asking for: if you aren't really willing to upgrade the manuals, then can I please ask you to be more supportive in the mailing list? I have received incomplete answers in the past as well and that does not help neither the users nor you.</div><div class="yui_3_2_0_55_133044491230861"><br></div><div class="yui_3_2_0_55_133044491230861">Cheers,</div><div class="yui_3_2_0_55_133044491230861"><br></div><div class="yui_3_2_0_55_133044491230861">Andreas<br><br> </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>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits</blockquote></div><br><div apple-content-edited="true">
<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; "><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>Personal website: <a href="http://www.will.chez-alice.fr/">http://www.will.chez-alice.fr</a><br>Team website: <a href="http://www-leca.ujf-grenoble.fr/equipes/emabio.htm">http://www-leca.ujf-grenoble.fr/equipes/emabio.htm</a><br><br>ERC Starting Grant TEEMBIO project: <a href="http://www.will.chez-alice.fr/Research.html">http://www.will.chez-alice.fr/Research.html</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"></div></span><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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