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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Bruno,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Yes, indeed this is the case. The FDA process produces NA
outputs in the projections, so either removing the Bin, etc. projections or
setting FDA=F clears up the error. Oddly, it only produces NA outputs for some
species and not for others, even though the xyz for the projections points for
all species is all the same (i.e. it produces projections for some species but only
NA for others given the same environmental data, but non consistently, as all species
have at least some valid (numerical) FDA outputs).<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I will re-build the models and try the projections again, but
this takes some time (about a day). Will also look at the enviro data to see if
there’s a pattern in the NA values. Stay tuned...<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks for the help.<o:p></o:p></span></p>
<p class=MsoListParagraph style='margin-left:.5in;text-indent:-.25in;
mso-list:l0 level1 lfo1'><![if !supportLists]><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif";color:#1F497D'><span style='mso-list:Ignore'>-<span
style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>David<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:
"Calibri","sans-serif";color:#1F497D'>________________________<o:p></o:p></span></b></p>
<p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:
"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></b></p>
<p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:
"Calibri","sans-serif";color:#1F497D'>David Roberts<o:p></o:p></span></b></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>PhD Student<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Dept. of Renewable Resources<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>University of Alberta<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>(780) 492-2540<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><a href="mailto:drr3@ualberta.ca"><u><span style='color:blue'>drr3@ualberta.ca</span></u></a><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'> Bruno Lafourcade
[mailto:brunolafourcade@aol.com] <br>
<b>Sent:</b> Thursday, June 17, 2010 6:36 AM<br>
<b>To:</b> drr3@ualberta.ca<br>
<b>Subject:</b> Re : [Biomod-commits] Projection Error (sum (ProbData) !=0)<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>Hum that's funny...<br>
<br>
I see no reasons why the FDA T/F would make any difference. Perhaps the models
built did something funny.<br>
The error you get is to do with NAs somewher in the data, I am guessing it is
in what the FDA produces as <br>
a projection. <br>
<br>
To check this, could you try it with FDA=T and </span><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New";color:black'>BinRoc=F, BinKappa=F,
BinTSS=F, FiltRoc=F, FiltKappa=F, FiltTSS=F</span><span lang=EN-US
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'> </span><span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>(if no conversion of data is needed to binary or filtered there
shouldn't be a problem with having NAs in it) and check what the FDA projection<br>
looks like.<br>
<br>
Thanks !<br>
Bruno<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>-------<br>
Bruno Lafourcade<br>
Statistical tools engineer<br>
<br>
Laboratoire d'Ecologie Alpine, bureau 308<br>
CNRS - UMR 5553, 2233 rue de la piscine<br>
38400 Saint Martin d'Hères<br>
-------<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
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<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'><o:p> </o:p></span></p>
</div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:10.0pt;
font-family:"Arial","sans-serif";color:black'>-----E-mail d'origine-----<br>
De : David Roberts <drr3@ualberta.ca><br>
A : biomod-commits@r-forge.wu-wien.ac.at<br>
Envoyé le : Mercredi, 16 Juin 2010 21:33<br>
Sujet : Re: [Biomod-commits] Projection Error (sum (ProbData) !=0)<o:p></o:p></span></p>
<div id="AOLMsgPart_3_c2168de4-e1fb-413c-8cd0-c73dd92646e3">
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<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'>Update: model projections run smoothly when “FDA=F”. Perhaps I
am missing an FDA setting? Using “MDA=T” instead (on a hunch) returns an unused
argument error on MDA=T. For the record, the model built smoothly with FDA=T.</span><span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'> </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'>Apologies if you know this already and I missed a previous
string. </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'> </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal style='text-indent:-.25in'><span style='font-size:10.0pt;
font-family:"Arial","sans-serif";color:#1F497D'>-</span><span style='font-size:
7.0pt;color:#1F497D'> </span><span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>DR</span><span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'> </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Arial","sans-serif";color:#1F497D'>________________________</span></b><span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Arial","sans-serif";color:#1F497D'> </span></b><span style='font-size:
10.0pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Arial","sans-serif";color:#1F497D'>David Roberts</span></b><span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'>PhD Student</span><span style='font-size:10.0pt;font-family:
"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'>Dept. of Renewable Resources</span><span style='font-size:10.0pt;
font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'>University of Alberta</span><span style='font-size:10.0pt;
font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'>(780) 492-2540</span><span style='font-size:10.0pt;font-family:
"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:blue'>drr3@ualberta.ca</span><span style='font-size:10.0pt;font-family:
"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#1F497D'> </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'><o:p></o:p></span></p>
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<div style='border:none;border-top:solid windowtext 1.0pt;padding:3.0pt 0in 0in 0in;
border-color:-moz-use-text-color -moz-use-text-color'>
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<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif";color:black'>From:</span></b><span lang=EN-US
style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> David
Roberts [mailto:drr3@ualberta.ca] <br>
<b>Sent:</b> Wednesday, June 16, 2010 11:31 AM<br>
<b>To:</b> 'biomod-commits@lists.r-forge.r-project.org'<br>
<b>Subject:</b> Projection Error (sum (ProbData) !=0)</span><span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
</div>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>Greetings all,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>I've been playing with BIOMOD for a while and think I have it all
sorted out, but I see that this error has come up before. I'm running a species
projection with all available model types for a total of 21 species. The first
three species run smoothly, but I hit this familiar error:<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>Input:<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New";
color:black'>Projection(Proj=proj, Proj.name='FIAusa', GLM=T, GBM=T, GAM=T,
CTA=T, ANN=T, SRE=T, FDA=T, MARS=T, RF=T, BinRoc=T, BinKappa=T, BinTSS=T,
FiltRoc=T, FiltKappa=T, FiltTSS=T, repetition.models=T)</span><span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>Output (after listing 3 successful species projections):<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";
color:black'>Error in if (sum(ProbData) != 0) { :</span><span style='font-size:
10.0pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";
color:black'> missing value where TRUE/FALSE needed</span><span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>If there’s a code setting or otherwise that might be generating
this, please do let me know. Just to clarify, I’m not running an ensemble yet,
just a regular projection. I would normally be scouring my data file for an
issue, but since the first few species run fine, I’m confident that it’s clean.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>R is running on a 64-bit Linux machine, if that makes any
difference.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>Thanks everyone!<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'> <o:p></o:p></span></p>
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<p class=MsoNormal style='text-indent:-.25in'><span style='font-size:10.0pt;
font-family:"Arial","sans-serif";color:black'>-</span><span style='font-size:
7.0pt;color:black'> </span><span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>David<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'> </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Arial","sans-serif";color:black'>________________________</span></b><span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Arial","sans-serif";color:black'> </span></b><span style='font-size:10.0pt;
font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
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<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Arial","sans-serif";color:black'>David Roberts</span></b><span
style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
</div>
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<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>PhD Student</span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>Dept. of Renewable Resources</span><span style='font-size:10.0pt;
font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>University of Alberta</span><span style='font-size:10.0pt;
font-family:"Arial","sans-serif";color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>(780) 492-2540</span><span style='font-size:10.0pt;font-family:
"Arial","sans-serif";color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>drr3@ualberta.ca</span><span style='font-size:10.0pt;font-family:
"Arial","sans-serif";color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'> <o:p></o:p></span></p>
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<div id="AOLMsgPart_4_c2168de4-e1fb-413c-8cd0-c73dd92646e3"><pre
style='background:white'><tt><span style='color:black'>_______________________________________________</span></tt><span
style='color:black'><br>
<br>
<tt><o:p></o:p></tt></span></pre><pre style='background:white'><tt><span
style='color:black'><o:p> </o:p></span></tt></pre><pre style='background:
white'><tt><span style='color:black'>Biomod-commits mailing list</span></tt><span
style='color:black'><br>
<br>
<tt><o:p></o:p></tt></span></pre><pre style='background:white'><tt><span
style='color:black'><o:p> </o:p></span></tt></pre><pre style='background:
white'><tt><span style='color:black'>Biomod-commits@lists.r-forge.r-project.org</span></tt><span
style='color:black'><br>
<br>
<tt><o:p></o:p></tt></span></pre><pre style='background:white'><tt><span
style='color:black'><o:p> </o:p></span></tt></pre><pre style='background:
white'><tt><span style='color:black'>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits</span></tt><span
style='color:black'><br>
<br>
<tt><o:p></o:p></tt></span></pre><pre style='background:white'><tt><span
style='color:black'><o:p> </o:p></span></tt></pre></div>
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