<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>These are the site coordinates. </div><div><br></div><div>When running the models, BIOMOD do not need the site coordinates as soon as the presence-absence matrix is in the same order than the environment matrix. </div><div>For instance, when you used the Initial.State function, you do not include the site coordinates. It creates the dataBIOMOD data which do not contain the site coordinates. </div><div><br></div><div>However, in the case you need a selection of pseudo-absence based on a minimum distance to the presence data, you need to give to BIOMOD the coordinates to make this selection. See Page 73 of the manual (>Biomod.Manual()). This is for the pseudo-absence function but this is the same in the Models function. </div><div>This is why you can give the site coordinates in the Models function (toward the end in the pseudo-absence issues).</div><div><br></div><div>Therefore, we also gave the CoorXY matrix in order to plot the prediction for instance or the presence-absence data. </div><div>> data(Sp.Env)<br>> ?Sp.Env</div><div><br></div><div>HIH</div><div>Wilfried</div><div><br></div><div><br></div><div><br></div><div><br></div><br><div><div>Le 20 juin 2010 à 16:06, Manuel Spínola a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
Thank you very much Antonio and Wilfried.<br>
<br>
I am sorry but I am still confused.<br>
If BIOMOD do not use site coordinates, what are the X and Y in the
CoorXY file or in the Sp.Env file? <br>
<br>
> CoorXY<br>
X Y<br>
1 -9.28809 38.62282<br>
2 -9.29181 39.52392<br>
3 -9.28993 39.07339<br>
4 -8.71546 37.72158<br>
5 -8.71718 37.27090<br>
6 -8.14814 37.71886<br>
<br>
Best,<br>
<br>
Manuel<br>
<br>
<br>
On 20/06/2010 05:34 a.m., Wilfried Thuiller wrote:
<blockquote cite="mid:876FD497-CC09-4822-A41E-86D835291B09@ujf-grenoble.fr" type="cite">
<div>Dear all,</div>
<div><br>
</div>
<div>No, it simply means that BIOMOD does not keep or use site
coordinates (excepted in the case of selection of pseudo-absence using
minimum distance around the presence and in the Migration routine). </div>
<div>In other words, you need to keep the data in the same order
(species presences and environmental data) to avoid any problem. </div>
<div><br>
</div>
<div>Cheers,</div>
<div>Wilfried</div>
<div><br>
</div>
<div><br>
</div>
<br>
<div>
<div>Le 20 juin 2010 à 13:30, Antonio Canepa a écrit :</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Hi Manuel,
<div>I´m new in BIMOD too, but I think that you need to enter
coordinates without grades, I mean not 32° 54' S, but 32,7334...by
example.</div>
<div>So you will need to transform second (Dividing them by 60).</div>
<div>I hope that it can help you</div>
<div><br>
</div>
<div>Good Luck!</div>
<div><br>
</div>
<div>Antonio</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<br>
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1. Biomod coordinate system (Manuel Sp?nola)<br>
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----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sat, 19 Jun 2010 07:39:43 -0600<br>
From: Manuel Sp?nola <<a moz-do-not-send="true" href="mailto:mspinola10@gmail.com">mspinola10@gmail.com</a>><br>
Subject: [Biomod-commits] Biomod coordinate system<br>
To: <a moz-do-not-send="true" href="mailto:biomod-commits@lists.r-forge.r-project.org">biomod-commits@lists.r-forge.r-project.org</a><br>
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<br>
Dear BIOMOD users,<br>
<br>
I am a new BIOMOD user and I would like to know what type of coordinates<br>
BIOMOD uses.<br>
<br>
In the BIOMOD manual say:<br>
<br>
"BIOMOD does not recognise geographical coordinates"<br>
<br>
What does it mean?<br>
<br>
Best,<br>
<br>
Manuel Sp?nola<br>
<br>
--<br>
Manuel Sp?nola, Ph.D.<br>
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre<br>
Universidad Nacional<br>
Apartado 1350-3000<br>
Heredia<br>
COSTA RICA<br>
<a moz-do-not-send="true" href="mailto:mspinola@una.ac.cr">mspinola@una.ac.cr</a><br>
<a moz-do-not-send="true" href="mailto:mspinola10@gmail.com">mspinola10@gmail.com</a><br>
Tel?fono: (506) 2277-3598<br>
Fax: (506) 2237-7036<br>
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<br>
-- <br>
Antonio Canepa Oneto<br>
Biólogo Marino<br>
MSc (c) Global Change<br>
Consejo Superior de Investigaciones Científicas (CSIC)<br>
Universidad I. Menéndez Pelayo (UIMP)<br>
Móvil: +34628320778<br>
E-Mail: <a moz-do-not-send="true" href="mailto:ajcanepa@gmail.com">ajcanepa@gmail.com</a><br>
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<div style="word-wrap: break-word;"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; ">
<div style="word-wrap: break-word;">
<div><span class="Apple-style-span" style="font-size: 12px;">
<div>--------------------------</div>
<div>Dr. Wilfried Thuiller</div>
<div>Laboratoire d'Ecologie Alpine, UMR CNRS 5553</div>
<div>Université Joseph Fourier</div>
<div>BP53, 38041 Grenoble cedex 9, France</div>
<div>tel: +33 (0)4 76 51 44 97</div>
<div>fax: +33 (0)4 76 51 42 79</div>
<div><br>
</div>
<div>Email: <a moz-do-not-send="true" href="mailto:wilfried.thuiller@ujf-grenoble.fr">wilfried.thuiller@ujf-grenoble.fr</a><br>
Home page: <a moz-do-not-send="true" href="http://www.will.chez-alice.fr/">http://www.will.chez-alice.fr</a><br>
Website: <a moz-do-not-send="true" href="http://www-leca.ujf-grenoble.fr/equipes/tde.htm">http://www-leca.ujf-grenoble.fr/equipes/tde.htm</a><br>
<br>
FP6 European MACIS project: <a moz-do-not-send="true" href="http://www.macis-project.net/">http://www.macis-project.net</a><br>
FP6 European EcoChange project: <a moz-do-not-send="true" href="http://www.ecochange-project.eu/">http://www.ecochange-project.eu</a></div>
<div><br>
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<pre class="moz-signature" cols="72">--
Manuel Spínola, Ph.D.
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
<a class="moz-txt-link-abbreviated" href="mailto:mspinola@una.ac.cr">mspinola@una.ac.cr</a>
<a class="moz-txt-link-abbreviated" href="mailto:mspinola10@gmail.com">mspinola10@gmail.com</a>
Teléfono: (506) 2277-3598
Fax: (506) 2237-7036</pre>
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_______________________________________________<br>Biomod-commits mailing list<br><a href="mailto:Biomod-commits@lists.r-forge.r-project.org">Biomod-commits@lists.r-forge.r-project.org</a><br>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits<br></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; 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; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: 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; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: 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><span class="Apple-style-span" style="font-size: 12px; "><div>--------------------------</div><div>Dr. Wilfried Thuiller</div><div>Laboratoire d'Ecologie Alpine, UMR CNRS 5553</div><div>Université Joseph Fourier</div><div>BP53, 38041 Grenoble cedex 9, France</div><div>tel: +33 (0)4 76 51 44 97</div><div>fax: +33 (0)4 76 51 42 79</div><div><br></div><div>Email: <a href="mailto:wilfried.thuiller@ujf-grenoble.fr">wilfried.thuiller@ujf-grenoble.fr</a><br>Home page: <a href="http://www.will.chez-alice.fr/">http://www.will.chez-alice.fr</a><br>Website: <a href="http://www-leca.ujf-grenoble.fr/equipes/tde.htm">http://www-leca.ujf-grenoble.fr/equipes/tde.htm</a><br><br>FP6 European MACIS project: <a href="http://www.macis-project.net/">http://www.macis-project.net</a><br>FP6 European EcoChange project: <a href="http://www.ecochange-project.eu/">http://www.ecochange-project.eu</a></div><div><br></div></span></div></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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