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<p>Thank you for the quick response Damien. I understand what you mean about the coordinates now.
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<p> </p>
<p>Regarding the error I did what you proposed do to, but I'm still getting the same error. I think I cleaned my data rather well and I'm<a></a> able to model both these datasets successfully when I don't<a></a> use independent data. Is there perhaps another package<a></a>
that I should load into my library that I am unaware of? </p>
<p> </p>
<p>Many thanx</p>
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<div><font color="#000080" size="2" face="Euphemia"></font> </div>
<div><font color="#000080" size="2" face="Euphemia">Enelge Gildenhuys</font></div>
<div><font color="#000080" size="2" face="Euphemia">MSc student</font></div>
<div><font color="#000080" size="2" face="Euphemia">Department of Botany & Zoology</font><font color="#000080" size="2" face="Euphemia">
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<div><font face="Euphemia"><font size="2"><font color="#000080"><font color="#000080">Centre of Excellence for Invasion Biology</font><br>
Universiteit Stellenbosch University</font><font color="#000080"> </font></font></font><font color="#000080"><br>
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<div style="DIRECTION: ltr" id="divRpF160842"><font color="#000000" size="2" face="Tahoma"><b>From:</b> Damien Georges [damien.georges2@gmail.com]<br>
<b>Sent:</b> 26 October 2012 03:08 PM<br>
<b>To:</b> biomod-commits@lists.r-forge.r-project.org; Gildenhuys, E, Mej <egil@sun.ac.za><br>
<b>Subject:</b> Re: [Biomod-commits] Using independent data to evaluate a model<br>
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<div class="moz-cite-prefix">Dear <span style="FONT-FAMILY: 'Euphemia','sans-serif'; COLOR: navy; FONT-SIZE: 10pt">
</span>Enelge,<br>
<br>
First of all, you have to know that an updated version of BIOMOD package called biomod2 is able on R-Forge since a while. I strongly encourage you to switch to this package version if you just began your study.<br>
<br>
That being said, all models developed in BIOMOD (the version you are working with) are not spacial based models (they don't need points coordinates to work) so you don't have to give such information for your independent data. For "calibrating data", the coordinates
are optional and only used for results plotting.<br>
<br>
Concerning the error you have.. could you check first that no NA's occurs in your dataset.<br>
<br>
## Check if some NA's occurs<br>
summary(<span>alldata5)</span><br>
summary(<span>alldataH</span><span>)</span><br>
<br>
## If some NA's.. do someting like<br>
<span>alldata5 <- na.omit(alldata5)</span><br>
<span>alldataH</span> <- na.omit(<span>alldataH)</span><br>
## and run your script again..<br>
<br>
Does it helps?<br>
<br>
Best,<br>
<br>
Damien<br>
<br>
On 26/10/2012 13:12, Gildenhuys, E, Mej <a class="moz-txt-link-rfc2396E" href="mailto:egil@sun.ac.za" target="_blank">
<egil@sun.ac.za></a> wrote:<br>
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<p class="MsoNormal">Good day,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I hope this email finds you well. I am currently trying to evaluate my species modelling using independent data. I have followed the tutorial and manual, however, in the manual the same data is used for the independent data as the modelling
data and consequently has the same name, where they differ in mine. The problem is that I do not know where/how to read in the coordinates of my independent data from which my model will be evaluated. I suppose in the tutorial example there is no need to read
it in twice as it has the same name?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span>Initial.State(Response = alldata5[,1], Explanatory = alldata5[,2:7], IndependentResponse = alldataH[,1], IndependentExplanatory = alldataH[,2:7], sp.name="halicacabum")</span></p>
<p class="MsoNormal"><span>ls()</span></p>
<p class="MsoNormal"><span>Models(GBM = T, No.trees = 2000,</span></p>
<p class="MsoNormal"><span> NbRepPA=2,</span></p>
<p class="MsoNormal"><span> strategy="random",</span></p>
<p class="MsoNormal"><span> coor=alldata5[,8:9], </span></p>
<p class="MsoNormal"><span> nb.absences=10000, </span></p>
<p class="MsoNormal"><span> DataSplit = 70,</span></p>
<p class="MsoNormal"><span> NbRunEval = 4,</span></p>
<p class="MsoNormal"><span> KeepPredIndependent=T, </span></p>
<p class="MsoNormal"><span> Roc = T,</span></p>
<p class="MsoNormal"><span> Optimized.Threshold.Roc=T,</span></p>
<p class="MsoNormal"><span> TSS=T,</span></p>
<p class="MsoNormal"><span> VarImport=T</span></p>
<p class="MsoNormal"><span>)</span></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">If I run this model I get the following error:</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span>----------------------------------- </span></p>
<p class="MsoNormal"><span>Modelling summary </span></p>
<p class="MsoNormal"><span>----------------------------------- </span></p>
<p class="MsoNormal"><span>Number of species modelled : 1</span></p>
<p class="MsoNormal"><span>halicacabum</span></p>
<p class="MsoNormal"><span></span> </p>
<p class="MsoNormal"><span>numerical variables : mtcoldm, mtwarmm, pcoldq, pdrym, pwarmq, ts</span></p>
<p class="MsoNormal"><span></span> </p>
<p class="MsoNormal"><span></span> </p>
<p class="MsoNormal"><span>number of evaluation repetitions : 4</span></p>
<p class="MsoNormal"><span>number of pseudo-absences runs : 2</span></p>
<p class="MsoNormal"><span>models selected : GBM</span></p>
<p class="MsoNormal"><span>total number of model runs : 10</span></p>
<p class="MsoNormal"><span>----------------------------------- </span></p>
<p class="MsoNormal"><span></span> </p>
<p class="MsoNormal"><span></span> </p>
<p class="MsoNormal"><span>##### halicacabum #####</span></p>
<p class="MsoNormal"><span>##### pseudo-absence run 1 #####</span></p>
<p class="MsoNormal"><span>Model=Generalised Boosting Regression </span></p>
<p class="MsoNormal"><span> 2000 maximum different trees and lambda Fold Cross-Validation
</span></p>
<p class="MsoNormal"><span>Error in TSS.Stat(Misc) : subscript out of bounds</span></p>
<p class="MsoNormal"><span>In addition: Warning message:</span></p>
<p class="MsoNormal"><span>In rbind(Misc, a) :</span></p>
<p class="MsoNormal"><span> number of columns of result is not a multiple of vector length (arg 1)<span style="BACKGROUND: #e1e2e5"></span></span></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Thanx!</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Euphemia','sans-serif'; COLOR: navy; FONT-SIZE: 10pt">Enelge</span><span></span></p>
<p class="MsoNormal"> </p>
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