<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><font class="Apple-style-span" face="Arial">Dear all,</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">I recently had a BIOMOD run crash mid-stream after 20+ species appear to have run successfully. The error message is pasted below. Any ideas or workarounds? </font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><div><span class="Apple-style-span" style="font-family: Arial; "><i>...</i></span></div><div><font class="Apple-style-span" face="Arial"><i>#####<span class="Apple-tab-span" style="white-space: pre; "> </span> ERFA2 <span class="Apple-tab-span" style="white-space: pre; "> </span>#####</i></font></div><div><font class="Apple-style-span" face="Arial"><i>#####<span class="Apple-tab-span" style="white-space: pre; "> </span> pseudo-absence run 1 <span class="Apple-tab-span" style="white-space: pre; "> </span>#####</i></font></div><div><font class="Apple-style-span" face="Arial"><i>Model=Artificial Neural Network </i></font></div><div><font class="Apple-style-span" face="Arial"><i><span class="Apple-tab-span" style="white-space: pre; "> </span> 3 Fold Cross Validation + 3 Repetitions </i></font></div><div><font class="Apple-style-span" face="Arial"><i>Calibration and evaluation phase: Nb of cross-validations: 3 </i></font></div><div><font class="Apple-style-span" face="Arial"><i>Evaluating Predictor Contributions in ANN ... </i></font></div><div><font class="Apple-style-span" face="Arial"><i>Model=Classification tree </i></font></div><div><font class="Apple-style-span" face="Arial"><i><span class="Apple-tab-span" style="white-space: pre; "> </span> 50 Fold Cross-Validation </i></font></div><div><font class="Apple-style-span" face="Arial"><i>Error in newx$cptable[max(keep), 1L] <- cp : subscript out of bounds</i></font></div></div><div><font class="Apple-style-span" face="Arial"><i><div>> warnings()</div><div>Warning messages:</div><div>1: In predict.lm(object, newdata, se.fit, scale = 1, type = ifelse(type == ... :</div><div> prediction from a rank-deficient fit may be misleading</div></i></font><span class="Apple-style-span" style="font-family: Arial; "><i><div style="display: inline !important; ">2: In cor(g.pred[, ], as.integer(.Rescaler4(as.numeric(predict(model.sp, ... :</div></i></span><font class="Apple-style-span" face="Arial"><i><div> the standard deviation is zero</div><div>...</div></i></font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">FYI, not sure if this matters, but my starting conditions were set as follows:</font></div><div><div style="color: rgb(12, 32, 153); font-size: 12px; "><font class="Apple-style-span" face="Arial"><br></font></div><div style="font-size: 12px; "><font class="Apple-style-span" color="#000001" face="Arial"><i>Initial.State(<span class="Apple-style-span" style="font-size: 12px; ">Response</span><span class="Apple-style-span" style="font-size: 12px; ">=</span><span class="Apple-style-span" style="font-size: 12px; ">SP.ENV</span><span class="Apple-style-span" style="font-size: 12px; ">[,</span><span class="Apple-style-span" style="font-size: 12px; ">12</span><span class="Apple-style-span" style="font-size: 12px; ">:</span><span class="Apple-style-span" style="font-size: 12px; ">75</span><span class="Apple-style-span" style="font-size: 12px; ">],</span><span class="Apple-style-span" style="font-size: 12px; "> Explanatory</span><span class="Apple-style-span" style="font-size: 12px; ">=</span><span class="Apple-style-span" style="font-size: 12px; ">SP.ENV</span><span class="Apple-style-span" style="font-size: 12px; ">[,</span><span class="Apple-style-span" style="font-size: 12px; ">4</span><span class="Apple-style-span" style="font-size: 12px; ">:</span><span class="Apple-style-span" style="font-size: 12px; ">11</span><span class="Apple-style-span" style="font-size: 12px; ">],</span><span class="Apple-style-span" style="font-size: 12px; "> IndependentResponse</span><span class="Apple-style-span" style="font-size: 12px; ">=</span><span class="Apple-style-span" style="font-size: 12px; ">NULL</span><span class="Apple-style-span" style="font-size: 12px; ">,</span><span class="Apple-style-span" style="font-size: 12px; "> </span></i></font></div><div style="font-size: 12px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><font class="Apple-style-span" color="#000001" face="Arial"><i><span class="Apple-tab-span" style="white-space: pre; "> </span>IndependentExplanatory=NULL)</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><font class="Apple-style-span" color="#000001" face="Arial"><i><br></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><font class="Apple-style-span" color="#000001" face="Arial"><i>Models(GLM = FALSE, GAM = TRUE, Spline=4, GBM = TRUE, No.trees = 3000, CTA = TRUE, CV.tree = 50, ANN = TRUE, CV.ann = 3, </i></font></div></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; font-size: 12px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><font class="Apple-style-span" color="#000001" face="Arial"><i><span class="Apple-tab-span" style="white-space: pre; "> </span>SRE = TRUE, quant = 0.025, FDA = TRUE, MARS = TRUE, RF = TRUE, NbRunEval = 3, DataSplit = 70, </i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><font class="Apple-style-span" color="#000001" face="Arial"><i><span class="Apple-tab-span" style="white-space: pre; "> </span>Yweights = NULL, Roc = TRUE, Optimized.Threshold.Roc = TRUE, Kappa = TRUE, TSS = TRUE, </i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><font class="Apple-style-span" color="#000001" face="Arial"><i><span class="Apple-tab-span" style="white-space: pre; "> </span>KeepPredIndependent = FALSE, VarImport = 5, NbRepPA = 2, strategy = "sre", nb.absences = 1000)</i></font></div><div style="color: rgb(12, 32, 153); margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><span style="color: rgb(12, 32, 153); "><font class="Apple-style-span" face="Arial"><br></font></span></div></div></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">Thanks in advance for any help!</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">Cheers, </font></div><div><font class="Apple-style-span" face="Arial">Jason</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; text-indent: -4px; font: normal normal normal 12px/normal Monaco; "><div style="text-indent: 0px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; font: normal normal normal 12px/normal Monaco; "><span class="Apple-style-span" style="color: rgb(92, 92, 92); font-size: medium; "><font class="Apple-style-span" face="Arial"><br></font></span></div><div style="text-indent: 0px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; font: normal normal normal 12px/normal Monaco; "><span class="Apple-style-span" style="color: rgb(92, 92, 92); font-size: medium; "><font class="Apple-style-span" face="Arial"><br></font></span></div><div style="text-indent: 0px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 4px; font: normal normal normal 12px/normal Monaco; "><span class="Apple-style-span" style="color: rgb(92, 92, 92); font-size: medium; "><font class="Apple-style-span" face="Arial">--</font></span></div></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><font class="Apple-style-span" face="Arial"><span class="Apple-style-span" style="border-collapse: separate; font-size: medium; font-variant: 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; "><span class="Apple-style-span" style="border-collapse: separate; font-size: medium; font-variant: 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 style="color: rgb(0, 0, 0); "><br></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" color="#5C5C5C">jason b mackenzie</font></div><div><font class="Apple-style-span" color="#5c5c5c">80 banambila street</font></div><div><font class="Apple-style-span" color="#5c5c5c">aranda, act 2614</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" color="#5C5C5C"><br></font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" color="#5C5C5C">0447 002 629 [mobile]</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" color="#5C5C5C">jasonbmackenzie [skype]</font></div><div style="color: rgb(0, 0, 0); "><br></div></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></font></div></div></div><font class="Apple-style-span" face="Arial">
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