<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<div class="moz-cite-prefix">Dear <span
style="font-size:10.0pt;font-family:"Euphemia","sans-serif";color:navy;mso-fareast-language:EN-ZA"></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 style="font-size:10.0pt;font-family:"Lucida
Sans Typewriter"">alldata5)</span><br>
summary(<span style="font-size:10.0pt;font-family:"Lucida
Sans Typewriter"">alldataH</span><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter"">)</span><br>
<br>
## If some NA's.. do someting like<br>
<span style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter"">alldata5 <- na.omit(alldata5)</span><br>
<span style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter"">alldataH</span> <- na.omit(<span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter"">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"><egil@sun.ac.za></a>
wrote:<br>
</div>
<blockquote
cite="mid:66C7754B20055449B1BE81AAFE8B87991828EF00@STBEXMB03.stb.sun.ac.za"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 14 (filtered
medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:Euphemia;
panose-1:2 11 5 3 4 1 2 2 1 4;}
@font-face
{font-family:"Lucida Console";
panose-1:2 11 6 9 4 5 4 2 2 4;}
@font-face
{font-family:"Lucida Sans Typewriter";
panose-1:2 11 5 9 3 5 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<p class="MsoNormal">Good day,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></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?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter"">Initial.State(Response = alldata5[,1],
Explanatory = alldata5[,2:7], IndependentResponse =
alldataH[,1], IndependentExplanatory = alldataH[,2:7],
sp.name="halicacabum")<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter"">ls()<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter"">Models(GBM = T, No.trees = 2000,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter""> NbRepPA=2,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter""> strategy="random",<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter""> coor=alldata5[,8:9],
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter""> nb.absences=10000, <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter""> DataSplit = 70,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter""> NbRunEval = 4,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter""> KeepPredIndependent=T,
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter""> Roc = T,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter""> Optimized.Threshold.Roc=T,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter""> TSS=T,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter""> VarImport=T<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida Sans
Typewriter"">)<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If I run this model I get the following
error:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">-----------------------------------
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">Modelling
summary
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">-----------------------------------
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">Number
of species modelled : 1<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">halicacabum<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">numerical
variables : mtcoldm, mtwarmm, pcoldq, pdrym,
pwarmq, ts<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">number
of evaluation repetitions : 4<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">number
of pseudo-absences runs : 2<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">models
selected : GBM<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">total
number of model runs : 10<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">-----------------------------------
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">#####
halicacabum #####<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">#####
pseudo-absence run 1 #####<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">Model=Generalised
Boosting Regression
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;background:#E1E2E5;mso-fareast-language:EN-ZA">
2000 maximum different trees and lambda Fold
Cross-Validation
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;mso-fareast-language:EN-ZA">Error
in TSS.Stat(Misc) : subscript out of bounds<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;mso-fareast-language:EN-ZA">In
addition: Warning message:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;mso-fareast-language:EN-ZA">In
rbind(Misc, a) :<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Lucida
Console";color:black;mso-fareast-language:EN-ZA">
number of columns of result is not a multiple of vector
length (arg 1)<span style="background:#E1E2E5"><o:p></o:p></span></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanx!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Euphemia","sans-serif";color:navy;mso-fareast-language:EN-ZA">Enelge</span><span
style="mso-fareast-language:EN-ZA"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Biomod-commits mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Biomod-commits@lists.r-forge.r-project.org">Biomod-commits@lists.r-forge.r-project.org</a>
<a class="moz-txt-link-freetext" 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></pre>
</blockquote>
<br>
</body>
</html>