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Hi again,<br>
<br>
Another possibility for plotting your predictions (without setting the independent data) is to run the Projection() function on your original<br>
dataset. This will work with any calibration procedure. As long as the model exists, simply make a prediction on the whole dataset.<br>
It avoids struggling with getting the right lines to only get a partial map.<br>
<br>
Bruno.<br>
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<div style="clear: both;">-------<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>
-------</div>
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<div style="font-family: arial,helvetica; font-size: 10pt; color: black;">-----E-mail d'origine-----<br>
De : Bruno Lafourcade <brunolafourcade@aol.com><br>
A : lailaliana78@yahoo.com; biomod-commits@lists.r-forge.r-project.org<br>
Envoyé le : Mercredi, 9 Juin 2010 23:13<br>
Sujet : [Biomod-commits] Re : Biomod question<br>
<br>
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Hi Liliana,<br>
<br>
<br>
Q.1<br>
--------<br>
The reason why the level.plot is used using independent data is because we use pseudo-absences.<br>
In that case, the predictions of the models are only produced for the PA data, i.e. a partial sample<br>
of the original dataset. By entering independent data, the predictions are done on the full dataset<br>
given as independent data which : in our case we gave the full original dataset to obtain full predictions<br>
and the correspondant maps.<br>
I hear you are using PA data as well which is why you bump into data length dissimilarities. You can <br>
however obtain a map of your predictions using PA data by selecting only the coordinates which correspond<br>
to the PA data used. An object called "Biomod.PA.data" is produced when running the Models() function.<br>
It will give the lines that have been sampled from the original data for each run. You are thus able to reenact <br>
the correspondant data and associated coordinates. But you will only have a partial map of your original data.<br>
<br>
<br>
Q.2<br>
--------<br>
I will check on that. There are multiple raster formats available. You can always try to convert them before <br>
exporting them to GIS.<br>
<br>
<br>
</font><font color="black" face="arial" size="2"><font face="Arial, Helvetica, sans-serif">Q.3<br>
--------</font></font><br>
<font face="Arial, Helvetica, sans-serif">The Ensemble.Forecasting.raster() function has lately been added to the package and takes the outputs from <br>
Projection.raster() to run. As for the ProjectionBestModel(), the adaptation to rasters hasen't been done yet.<br>
Will soon be done.<br>
<br>
<br>
</font><font><font color="black" face="arial" size="2"><font color="black" face="arial" size="2"><font face="Arial, Helvetica, sans-serif">Q.4<br>
--------</font></font></font></font><br>
<font face="Arial, Helvetica, sans-serif">I don't really get your question ? What do you mean by Raster Calculator ?<br>
<br>
<br>
<br>
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Hoping to answer your queries.<br>
Bruno<br>
<br>
<br>
<div style="clear: both;">-------<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>
-------</div>
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<div style="font-family: arial,helvetica; font-size: 10pt; color: black;">-----E-mail d'origine-----<br>
De : Claudia liliana Ballesteros Mejia <<a href="mailto:lailaliana78@yahoo.com">lailaliana78@yahoo.com</a>><br>
A : <a href="mailto:biomod-commits@lists.r-forge.r-project.org">biomod-commits@lists.r-forge.r-project.org</a><br>
Envoyé le : Mercredi, 9 Juin 2010 15:20<br>
Sujet : [Biomod-commits] Biomod question<br>
<br>
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<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top"><style>#AOLMsgPart_3_3a1d0936-aa52-4615-9163-6fa5772d86bf td{color: black;} #AOLMsgPart_3_3a1d0936-aa52-4615-9163-6fa5772d86bf #AOLMsgPart_3_86d3db1c-f19a-47e8-b482-afb4e001f9e9 td{color: black;} #AOLMsgPart_3_3a1d0936-aa52-4615-9163-6fa5772d86bf #AOLMsgPart_3_86d3db1c-f19a-47e8-b482-afb4e001f9e9 p.MsoNormal,#AOLMsgPart_3_3a1d0936-aa52-4615-9163-6fa5772d86bf #AOLMsgPart_3_86d3db1c-f19a-47e8-b482-afb4e001f9e9 li.MsoNormal,#AOLMsgPart_3_3a1d0936-aa52-4615-9163-6fa5772d86bf #AOLMsgPart_3_86d3db1c-f19a-47e8-b482-afb4e001f9e9 div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman"; mso-ansi-language:EN-GB;}#AOLMsgPart_3_3a1d0936-aa52-4615-9163-6fa5772d86bf #AOLMsgPart_3_86d3db1c-f19a-47e8-b482-afb4e001f9e9 span.yshortcuts {mso-style-name:yshortcuts;}@page Section1 {size:612.0pt 792.0pt; margin:72.0pt 90.0pt 72.0pt 90.0pt; mso-header-margin:35.4pt; mso-footer-margin:35.4pt; mso-paper-source:0;}#AOLMsgPart_3_3a1d0936-aa52-4615-9163-6fa5772d86bf #AOLMsgPart_3_86d3db1c-f19a-47e8-b482-afb4e001f9e9 div.Section1 {page:Section1;}</style>
<div class="MsoNormal"><span lang="EN-GB">Dear R-forge-List,<br>
<br>
I'm using the package biomod to identify areas of potential distribution of a
butterfly. I don't have independent data to test, so I'm using a partition of
the data 80/20. Maybe I should say as well that I chose to run the Models with
only 1 repetitions but 2 runs of Pseudo-absences, and also that I'm running this models under R-2.9.2 linux. But I have also tried to run it under windows R-2.11. (without much success because of the memory limit issue)<br>
<br>
I have 4 questions.<br>
1. In the tutorial for this package is described the function level.plot. It is
useful to plot the results of every model but in the tutorial they ran the
Models with "independent data", Is there any possibility to use this
function without having to run the models with independent data?<br>
<br>
load("pred/Pred_Ag_cing")<br>
level.plot(Pred_Ag_cing[,"RF",1,1],coorxy,title='Ag_cingulata RF')<br>
<br>
Error in level.plot(Pred_Ag_cing[, "RF", 1, 1], coorxy, title =
"Ag_cingulata RF") : <br>
<br>
data and coordinates should be of the same length <br>
<br>
length(coorxy$Longitude)<br>
[1] 2697182<br>
<br>
length(Pred_Ag_cing[,"RF",1,1])<br>
[1] 1350<br>
<br>
It gives me an error saying that the coordinates and the data must be the same
length, (the truth is I don't get why without running the models with
independent data it doesn't get the same length but with independent it does.) <br>
<br>
<br>
2. Is there any possibility to export the data to make<br>
the plots as an ascii files so can be imported into GIS? I know there is the function Projection.raster (under windows R.2.11) but when I try to imported into GIS it doesn't show anything (does it also exist in Linux?) <br>
</span></div>
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<span lang="EN-GB"></span></div>
<div class="MsoNormal"><span lang="EN-GB">3. When using Projection.raster function, it doesn't produce the output that the functions Ensemble.forecasting and ProjectionBestModel requires to work. But if I use the function Projection is not possible to export them as ascii files. Is it true?, Is there anyway to solve this? <br>
</span></div>
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</span></div>
<div class="MsoNormal"><span lang="EN-GB"><br>
</span></div>
<div class="MsoNormal"><span lang="EN-GB">
4. If the only way to plot the outputs of the models in GIS is by extracting the
model and using Raster <span class="yshortcuts"><span id="lw_1276088743_0">Calculator</span></span>, how do I get the final models of RandomForest, MARS and GAM?<br>
<br>
Any help would be very much appreciated, <br>
<br>
Thanks a lot in advanced,<br>
<br>
Liliana Ballesteros<br>
PhD Student<br>
University of Basel</span></div>
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