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Thank you very much Wilfried.<br>
Best,<br>
<br>
Manuel<br>
<br>
<br>
On 05/09/2010 11:37 p.m., Wilfried Thuiller wrote:
<blockquote
cite="mid:CB769A95-C57E-49CE-A3B1-8A809A8B7646@ujf-grenoble.fr"
type="cite">
<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 moz-do-not-send="true"
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>
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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>
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</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 moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:mspinola@una.ac.cr">mspinola@una.ac.cr</a>
<a moz-do-not-send="true" 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-indent: 0px; text-transform: none; white-space:
normal; widows: 2; word-spacing: 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;">
<div style="word-wrap: break-word;"><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;">
<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>
</span><br class="Apple-interchange-newline">
</span><br class="Apple-interchange-newline">
</div>
<br>
</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>
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