<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Yes, join will do more or less the same than xyValues.</div><div>I think the xyValues is better as you can also select the type of sampling design (neighbor or bilinear interpolation).</div><div><br></div><div>For Maxent asc files, this is easy to load:</div><div><br></div><div><br></div><div>Compare to what I wrote, it will look like:</div><div><br></div><div>mn6190_ann = raster(mn6190_ann.asc)</div><div>cld6190_ann = raster(cld6190_ann.asc)</div><div>mydata = stack(mn6190_ann, cld6190_ann)</div><div><br></div><div>myXYvariables = xyValues(CoordXY, mydata)</div><div><br></div><div>## you can remove the stack part with a loop as I wrote below in my first email. </div><div><br></div><div>Best</div><div>Wilfried</div><div><br></div><div><br></div><div><br></div><br><div><div>Le 6 sept. 2010 à 01:06, Manuel Spínola a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
Thank you very much Wilfried.<br>
<br>
Yes, I mean ASCII grids.<br>
<br>
For example, I have 2 files: "tmn6190_ann.asc" and "cld6190_ann.asc"
(layers from MAXENT) but I want to bring them to BIOMOD.<br>
<br>
I found a function in the adehabitatMA package called "join" that I
think does what I am looking for but it works only for an object of
class "SpatialPixelsDataFrame" (package sp):<br>
<br>
df <- join(locs, map) # "locs" are animal locations and "map" are
environmental variables. <br>
<br>
The result is a data frame containing the value of the variables at
the speci fied locations.<br>
<br>
Do you think the join function will do the same that you suggested
me.<br>
<br>
Best,<br>
<br>
Manuel<br>
<br>
<br>
On 05/09/2010 02:34 p.m., Wilfried Thuiller wrote:
<blockquote cite="mid:573A46CD-4FB1-47BC-AC38-1A4F0555F2B8@ujf-grenoble.fr" type="cite">Hi Manuel,
<div>What do you mean by ASCII files? Do you mean ASGII grids?
(exprt asc from raster/grid). I guess your variables were on
Arcgis or something like that and you exported them on ASCII
files? </div>
<div><br>
</div>
<div>If this right, this is rather easy.</div>
<div>Make sure your species data (which I guess is a matrix with X
and Y coordinates and then columns with presence-absence) and
ASCII files use the same spatial projection. </div>
<div>Then, load the rgdal and raster package</div>
<div><br>
</div>
<div>then read the ASCII file (one by one) using the raster
function of the raster package, then build a stack of raster,
and then project the values of the variables onto the XY values
of your sites.</div>
<div>I give you below an example (with arcgis grid layers not
ASCII but it works the same way).</div>
<div><br>
</div>
<div>Hope it helps</div>
<div><br>
</div>
<div>Wilfried</div>
<div><br>
</div>
<div><br>
</div>
<div>##### Load my XY data (European data with XY coordinates in
column 2 and 3, and then species. </div>
<div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(0, 113,
40);">library<span style="color: rgb(4, 34, 153);">(</span>foreign<span style="color: rgb(4, 34, 153);">)</span></div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(0, 113,
40);">AFE_PA_XY<span style="color: rgb(4, 34, 153);"> <- </span>read.dbf<span style="color: rgb(4, 34, 153);">(</span><span style="color:
rgb(176, 20, 12);">'AFE_PA_XY.dbf'</span><span style="color:
rgb(4, 34, 153);">)</span></div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(4, 34,
153); min-height: 15px;"><br>
</div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(4, 34,
153); min-height: 15px;">### Create a vector with the names of
the variables I want to load (here the worldclim data for
instance)</div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(0, 113,
40);">bio<span style="color: rgb(4, 34, 153);"> <- </span>paste<span style="color: rgb(4, 34, 153);">(</span>rep<span style="color: rgb(4, 34, 153);">(</span><span style="color:
rgb(176, 20, 12);">'bio'</span><span style="color: rgb(4,
34, 153);">, </span>times<span style="color: rgb(4, 34,
153);">=</span><span style="color: rgb(43, 111, 184);">19</span><span style="color: rgb(4, 34, 153);">), </span>seq<span style="color: rgb(4, 34, 153);">(</span><span style="color:
rgb(43, 111, 184);">1</span><span style="color: rgb(4, 34,
153);">:</span><span style="color: rgb(43, 111, 184);">19</span><span style="color: rgb(4, 34, 153);">), </span>sep<span style="color: rgb(4, 34, 153);">=</span><span style="color:
rgb(176, 20, 12);">"_"</span><span style="color: rgb(4, 34,
153);">)</span></div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(4, 34,
153); min-height: 15px;"><br>
</div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(0, 113,
40);">library<span style="color: rgb(4, 34, 153);">(</span>raster<span style="color: rgb(4, 34, 153);">)</span></div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(0, 113,
40);"><span style="color: rgb(4, 34, 153);">### Create a loop
to load sequentially the raster (the first line in the loop)
and then project the value of the loaded raster onto the XY
coordinates of the original file and store directly in the
dataframe with the name of the loaded raster</span></div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(0, 113,
40);"><span style="color: rgb(4, 34, 153);">You can even add a
third line to rm the raster/ASCII layer if it is a large
dataset, something like: e</span>val(parse(text=paste("rm(<span class="Apple-style-span" style="color: rgb(4, 34, 153);
font-family: Monaco; font-size: 11px;"><span class="Apple-style-span" style="color: rgb(0, 113, 40);">",i,
")"</span></span><span class="Apple-style-span" style="color: rgb(4, 34, 153); font-family: Monaco;
font-size: 11px;"><span class="Apple-style-span" style="color: rgb(0, 113, 40); font-family: Monaco;
font-size: 11px;"><span style="color: rgb(4, 34, 153);">,
sep="")))</span></span></span></div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(0, 113,
40);"><span class="Apple-style-span" style="color: rgb(4, 34,
153); font-family: Monaco; font-size: 11px;"><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;"><span style="color:
rgb(4, 34, 153);"></span></span></span><span class="Apple-style-span" style="color: rgb(4, 34, 153);
font-family: Monaco; font-size: 11px;"><span class="Apple-style-span" style="color: rgb(0, 113, 40);"> </span></span></div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(4, 34,
153);"><span style="color: rgb(219, 34, 74);">for</span>(<span style="color: rgb(0, 113, 40);">i</span> <span style="color: rgb(219, 34, 74);">in</span> <span style="color: rgb(0, 113, 40);">bio</span>) </div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(176, 20,
12);"><span style="color: rgb(4, 34, 153);"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="color: rgb(0, 113, 40);">eval</span><span style="color: rgb(4, 34, 153);">(</span><span style="color:
rgb(0, 113, 40);">parse</span><span style="color: rgb(4, 34,
153);">(</span><span style="color: rgb(0, 113, 40);">text</span><span style="color: rgb(4, 34, 153);">=</span><span style="color:
rgb(0, 113, 40);">paste</span><span style="color: rgb(4, 34,
153);">(</span><span style="color: rgb(0, 113, 40);">i</span><span style="color: rgb(4, 34, 153);">, </span>"<-
raster('/Volumes/GIS_Data/Global/Climate/Current/Wordclim/10m/bio/"<span style="color: rgb(4, 34, 153);">, </span><span style="color: rgb(0, 113, 40);">i</span><span style="color:
rgb(4, 34, 153);">,</span>"')"<span style="color: rgb(4, 34,
153);">, </span><span style="color: rgb(0, 113, 40);">sep</span><span style="color: rgb(4, 34, 153);">=</span>""<span style="color: rgb(4, 34, 153);">)))</span></div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(4, 34,
153); min-height: 15px;"><span class="Apple-tab-span" style="white-space: pre;"> </span>eval(parse(text=paste("<span class="Apple-style-span" style="color: rgb(0, 113, 40);">AFE_PA_XY$",i,
"</span><span class="Apple-style-span" style="color: rgb(0,
113, 40);">xyValues</span><span class="Apple-style-span" style="color: rgb(0, 113, 40); font-family: Monaco;
font-size: 11px;"><span style="color: rgb(4, 34, 153);">(</span></span><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;">worldclim</span><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;"><span style="color:
rgb(4, 34, 153);">, </span></span><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;">AFE_PA_XY</span><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;"><span style="color:
rgb(4, 34, 153);">[,</span></span><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;"><span style="color:
rgb(43, 111, 184);">2</span></span><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;"><span style="color:
rgb(4, 34, 153);">:</span></span><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;"><span style="color:
rgb(43, 111, 184);">3</span></span><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;"><span style="color:
rgb(4, 34, 153);">],</span></span><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;">method</span><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;"><span style="color:
rgb(4, 34, 153);">=</span></span><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;"><span style="color:
rgb(176, 20, 12);">'bilinear'</span></span><span class="Apple-style-span" style="color: rgb(0, 113, 40);
font-family: Monaco; font-size: 11px;"><span style="color:
rgb(4, 34, 153);">)", sep="")))</span></span><span class="Apple-style-span" style="color: rgb(0, 113, 40);"> </span></div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(0, 113,
40);"><font class="Apple-style-span" color="#042299" face="Helvetica"><span class="Apple-style-span" style="font-size: medium;"><font class="Apple-style-span" size="3" color="#007128" face="Monaco"><span class="Apple-style-span" style="font-size: 11px;"><br>
</span></font></span></font></div>
</div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(0, 113,
40);"><font class="Apple-style-span" color="#042299" face="Helvetica"><span class="Apple-style-span" style="font-size: medium;"><font class="Apple-style-span" size="3" color="#007128" face="Monaco"><span class="Apple-style-span" style="font-size: 11px;"><br>
</span></font></span></font></div>
<div style="margin: 0px; font: 11px Monaco; color: rgb(0, 113,
40);"><font class="Apple-style-span" color="#042299" face="Helvetica"><span class="Apple-style-span" style="font-size: medium;"><font class="Apple-style-span" size="3" color="#007128" face="Monaco"><span class="Apple-style-span" style="font-size: 11px;"><br>
</span></font></span></font></div>
<div><br>
<div>
<div>Le 5 sept. 2010 à 17:12, Manuel Spínola a écrit :</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div> Dear list members,<br>
<br>
I know this is a basic question and not completed related
to BIOMOD.<br>
I want to run an analysis using BIOMOD but I would like to
know the best way to bring bioclimatic and land use
variables from ASCII files to the format that the
environmental variables are presented in the BIOMOD
manual.<br>
Thank you very much in advance.<br>
Best,<br>
<br>
Manuel<br>
<br>
-- <br>
Manuel Spínola, Ph.D.<br>
Instituto Internacional en Conservación 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 class="moz-txt-link-abbreviated" href="mailto:mspinola10@gmail.com">mspinola10@gmail.com</a><br>
Teléfono: (506) 2277-3598<br>
Fax: (506) 2237-7036<br>
<br>
_______________________________________________<br>
Biomod-commits mailing list<br>
<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><br>
<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><br>
</div>
</blockquote>
</div>
<br>
<div>
<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>
</div>
</span></div>
</div>
</span><br class="Apple-interchange-newline">
</div>
<br class="Apple-interchange-newline">
<br class="Apple-interchange-newline">
</div>
<br>
</div>
</blockquote>
<br>
<br>
<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>
</div>
</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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