<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">library<span style="color: #042299">(</span>foreign<span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">AFE_PA_XY<span style="color: #042299"> <- </span>read.dbf<span style="color: #042299">(</span><span style="color: #b0140c">'AFE_PA_XY.dbf'</span><span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal 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-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">bio<span style="color: #042299"> <- </span>paste<span style="color: #042299">(</span>rep<span style="color: #042299">(</span><span style="color: #b0140c">'bio'</span><span style="color: #042299">, </span>times<span style="color: #042299">=</span><span style="color: #2b6fb8">19</span><span style="color: #042299">), </span>seq<span style="color: #042299">(</span><span style="color: #2b6fb8">1</span><span style="color: #042299">:</span><span style="color: #2b6fb8">19</span><span style="color: #042299">), </span>sep<span style="color: #042299">=</span><span style="color: #b0140c">"_"</span><span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); ">library<span style="color: #042299">(</span>raster<span style="color: #042299">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); "><span style="color: #042299">### 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-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(0, 113, 40); "><span style="color: #042299">You can even add a third line to rm the raster/ASCII layer if it is a large dataset, something like: e</span><span class="Apple-style-span" style="color: rgb(4, 34, 153); ">val(parse(text=paste("rm(</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); ">",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-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal 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-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(4, 34, 153); "><span style="color: #db224a">for</span>(<span style="color: #007128">i</span> <span style="color: #db224a">in</span> <span style="color: #007128">bio</span>) </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(176, 20, 12); "><span style="color: #042299"><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #007128">eval</span><span style="color: #042299">(</span><span style="color: #007128">parse</span><span style="color: #042299">(</span><span style="color: #007128">text</span><span style="color: #042299">=</span><span style="color: #007128">paste</span><span style="color: #042299">(</span><span style="color: #007128">i</span><span style="color: #042299">, </span>"<- raster('/Volumes/GIS_Data/Global/Climate/Current/Wordclim/10m/bio/"<span style="color: #042299">, </span><span style="color: #007128">i</span><span style="color: #042299">,</span>"')"<span style="color: #042299">, </span><span style="color: #007128">sep</span><span style="color: #042299">=</span>""<span style="color: #042299">)))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal 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-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal 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" color="#007128" face="Monaco" size="3"><span class="Apple-style-span" style="font-size: 11px;"><br></span></font></span></font></div></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal 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" color="#007128" face="Monaco" size="3"><span class="Apple-style-span" style="font-size: 11px;"><br></span></font></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal 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" color="#007128" face="Monaco" size="3"><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 href="mailto:mspinola@una.ac.cr">mspinola@una.ac.cr</a><br>mspinola10@gmail.com<br>Teléfono: (506) 2277-3598<br>Fax: (506) 2237-7036<br><br>_______________________________________________<br>Biomod-commits mailing list<br>Biomod-commits@lists.r-forge.r-project.org<br>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits<br></div></blockquote></div><br><div>
<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><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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