[Biomod-commits] Biomod-commits Digest, Vol 14, Issue 7

Wilfried Thuiller wilfried.thuiller at ujf-grenoble.fr
Sun Jun 20 16:19:43 CEST 2010 

These are the site coordinates. 

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. 
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. 

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. 
This is why you can give the site coordinates in the Models function (toward the end in the pseudo-absence issues).

Therefore, we also gave the CoorXY matrix in order to plot the prediction for instance or the presence-absence data. 
> data(Sp.Env)
> ?Sp.Env

HIH
Wilfried





Le 20 juin 2010 à 16:06, Manuel Spínola a écrit :

> Thank you very much Antonio and Wilfried.
> 
> I am sorry but I am still confused.
> If BIOMOD do not use site coordinates, what are the X and Y in the CoorXY file or in the Sp.Env file? 
> 
> > CoorXY
>              X        Y
> 1     -9.28809 38.62282
> 2     -9.29181 39.52392
> 3     -9.28993 39.07339
> 4     -8.71546 37.72158
> 5     -8.71718 37.27090
> 6     -8.14814 37.71886
> 
> Best,
> 
> Manuel
> 
> 
> On 20/06/2010 05:34 a.m., Wilfried Thuiller wrote:
>> 
>> Dear all,
>> 
>> 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). 
>> In other words, you need to keep the data in the same order (species presences and environmental data) to avoid any problem. 
>> 
>> Cheers,
>> Wilfried
>> 
>> 
>> 
>> Le 20 juin 2010 à 13:30, Antonio Canepa a écrit :
>> 
>>> Hi Manuel,
>>> 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.
>>> So you will need to transform second (Dividing them by 60).
>>> I hope that it can help you
>>> 
>>> Good Luck!
>>> 
>>> Antonio
>>> 
>>> 
>>> 
>>> 
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>>>   1. Biomod coordinate system (Manuel Sp?nola)
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>>> 
>>> ----------------------------------------------------------------------
>>> 
>>> Message: 1
>>> Date: Sat, 19 Jun 2010 07:39:43 -0600
>>> From: Manuel Sp?nola <mspinola10 at gmail.com>
>>> Subject: [Biomod-commits] Biomod coordinate system
>>> To: biomod-commits at lists.r-forge.r-project.org
>>> Message-ID: <4C1CC89F.3030604 at gmail.com>
>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>> 
>>> Dear BIOMOD users,
>>> 
>>> I am a new BIOMOD user and I would like to know what type of coordinates
>>> BIOMOD uses.
>>> 
>>> In the BIOMOD manual say:
>>> 
>>> "BIOMOD does not recognise geographical coordinates"
>>> 
>>> What does it mean?
>>> 
>>> Best,
>>> 
>>> Manuel Sp?nola
>>> 
>>> --
>>> Manuel Sp?nola, Ph.D.
>>> Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
>>> Universidad Nacional
>>> Apartado 1350-3000
>>> Heredia
>>> COSTA RICA
>>> mspinola at una.ac.cr
>>> mspinola10 at gmail.com
>>> Tel?fono: (506) 2277-3598
>>> Fax: (506) 2237-7036
>>> 
>>> 
>>> 
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>>> End of Biomod-commits Digest, Vol 14, Issue 7
>>> *********************************************
>>> 
>>> 
>>> 
>>> -- 
>>> Antonio Canepa Oneto
>>> Biólogo Marino
>>> MSc (c) Global Change
>>> Consejo Superior de Investigaciones Científicas (CSIC)
>>> Universidad I. Menéndez Pelayo (UIMP)
>>> Móvil: +34628320778
>>> E-Mail: ajcanepa at gmail.com
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>> 
>> --------------------------
>> Dr. Wilfried Thuiller
>> Laboratoire d'Ecologie Alpine, UMR CNRS 5553
>> Université Joseph Fourier
>> BP53, 38041 Grenoble cedex 9, France
>> tel: +33 (0)4 76 51 44 97
>> fax: +33 (0)4 76 51 42 79
>> 
>> Email: wilfried.thuiller at ujf-grenoble.fr
>> Home page: http://www.will.chez-alice.fr
>> Website: http://www-leca.ujf-grenoble.fr/equipes/tde.htm
>> 
>> FP6 European MACIS project: http://www.macis-project.net
>> FP6 European EcoChange project: http://www.ecochange-project.eu
>> 
>> 
>> 
>> 
>> 
>> 
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>>   
> 
> 
> -- 
> Manuel Spínola, Ph.D.
> Instituto Internacional en Conservación y Manejo de Vida Silvestre
> Universidad Nacional
> Apartado 1350-3000
> Heredia
> COSTA RICA
> mspinola at una.ac.cr
> mspinola10 at gmail.com
> Teléfono: (506) 2277-3598
> Fax: (506) 2237-7036
> _______________________________________________
> Biomod-commits mailing list
> Biomod-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits

--------------------------
Dr. Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR CNRS 5553
Université Joseph Fourier
BP53, 38041 Grenoble cedex 9, France
tel: +33 (0)4 76 51 44 97
fax: +33 (0)4 76 51 42 79

Email: wilfried.thuiller at ujf-grenoble.fr
Home page: http://www.will.chez-alice.fr
Website: http://www-leca.ujf-grenoble.fr/equipes/tde.htm

FP6 European MACIS project: http://www.macis-project.net
FP6 European EcoChange project: http://www.ecochange-project.eu





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