<div dir="ltr">This is great Sandra. Now I am curious to see final ecological relationships you are searching for!<br>D<br></div><div class="gmail_extra"><br><div class="gmail_quote">2014-09-30 3:24 GMT+02:00 Sandra MacFadyen <span dir="ltr"><<a href="mailto:sandramf@live.co.za" target="_blank">sandramf@live.co.za</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div link="blue" vlink="purple" lang="EN-ZA"><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Dear Vaclav,<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I did a quick manual test to see if the results were correct for a few 5x5 windows and yes, everything appears 100%:<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"># Example data from one 5x5 window<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">test1 = c(572,617,661,638,616,<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> 662,617,593,638,616,<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> 662,639,572,661,616,<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> 662,662,639,662,616,<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> 594,572,594,639,593)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"># Calculate info needed for diversity indices<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">freq1 = as.data.frame(table(test1)) # Calculate frequency table<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">S = length(unique(test1)) # Total number of species (S) <u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">N = length(test1) # Total number of individuals (N)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">ln.S = log(S) #Natural log of species (ln S)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">ln.N = log(N) # Natural log of individuals (ln N)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Pi = freq1$Freq/N # Proportion of individuals that belong to each species<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Pi2 = (Pi ^ 2)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">ln.pi = log(Pi)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">pi.ln.pi = Pi * ln.pi<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">pi.ln.pi2 = (ln.pi^2)*Pi<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"># Calculate different diversity indices<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">(M = (S-1)/ln.N) # Margalef's index (M) <u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">(i.Di = 1/sum(Pi2)) # Simpson's index [Inverse] (i.Di)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">(i.Dc = 1 - (sum(Pi2))) # Simpson's index [Complement] (i.Dc) * This one calculated with r.diversity<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">(H = sum(pi.ln.pi)*-1) # Shannon-Wiener index (H') <u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">(J = H/ln.S) # Pielou's index (J) <u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thanks again<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Cheers<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Sandra<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"" lang="EN-US">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"" lang="EN-US"> Vaclav Petras [<a href="mailto:wenzeslaus@gmail.com" target="_blank">mailto:wenzeslaus@gmail.com</a>] <br><b>Sent:</b> 18 September 2014 02:46 AM<br><b>To:</b> Sandra MacFadyen<br><b>Cc:</b> Markus Neteler; GRASS user list; Duccio Rocchini; Luca Delucchi<br><b>Subject:</b> Re: [GRASS-user] Solved: execGRASS("r.diversity") Done. No rasters created (Large rasters)<u></u><u></u></span></p><div><div class="h5"><p class="MsoNormal"><u></u> <u></u></p><div><p class="MsoNormal"><u></u> <u></u></p><div><p class="MsoNormal"><u></u> <u></u></p><div><p class="MsoNormal">On Wed, Sep 17, 2014 at 7:40 PM, Sandra MacFadyen <<a href="mailto:sandramf@live.co.za" target="_blank">sandramf@live.co.za</a>> wrote:<u></u><u></u></p><p class="MsoNormal" style="margin-bottom:12.0pt">Dear Markus,<br><br>Excellent! Thanks to everyone for their help.<br>I tested r.diversity in the new revision (61840) on a raster with 12933032 cells and it took under 3 minutes to complete r.li.simpson, r.li.shannon, r.li.pielou and r.li.renyi outputs.<br>Amazing :)<br><br>> execGRASS("r.diversity",flags="overwrite", parameters=list(input="flow", prefix="flow_div", alpha=0.5, size=3))<br>> r.li.simpson complete. Raster map <flow_div_simpson_size_3.0> created.<br>> r.li.shannon complete. Raster map <flow_div_shannon_size_3.0> created.<br>> r.li.pielou complete. Raster map <flow_div_pielou_size_3.0> created.<br>> r.li.renyi complete. Raster map <flow_div_renyi_size_3.0_alpha_0.5><br>> created.<br>> Done.<br><br>Thanks again and keep well.<u></u><u></u></p><div><p class="MsoNormal">Good to hear that. Can you say if the results are correct? I computed difference of one map before and after and it was OK. But it would be great to have more tests. Let's start with: does the result make sense?<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Vaclav<br> <u></u><u></u></p></div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><p class="MsoNormal">Cheers<br>Sandra<br><br>-----Original Message-----<br>From: <a href="mailto:neteler.osgeo@gmail.com" target="_blank">neteler.osgeo@gmail.com</a> [mailto:<a href="mailto:neteler.osgeo@gmail.com" target="_blank">neteler.osgeo@gmail.com</a>] On Behalf Of Markus Neteler<br>Sent: 06 September 2014 05:15 AM<br>To: Sandra MacFadyen<br>Cc: GRASS user list; Duccio Rocchini; Luca Delucchi<br>Subject: Re: [GRASS-user] execGRASS("r.diversity") Done. No rasters created (Large rasters)<br><br>Dear Sandra,<br><br>On Fri, Jun 20, 2014 at 7:49 AM, Markus Neteler <<a href="mailto:neteler@osgeo.org" target="_blank">neteler@osgeo.org</a>> wrote:<br>> On Sat, Jun 14, 2014 at 9:21 AM, Sandra MacFadyen <<a href="mailto:sandramf@live.co.za" target="_blank">sandramf@live.co.za</a>> wrote:<br>>> I am using r.diversity (GRASS GIS 7.0.0svn build 60785 win32) through<br>>> R (R version 3.0.2 win32) on Windows 7 64bit.<br>...<br>>> However, when running the same code on a larger image (cells=6746328)<br>>> from my own location, although it reports Done, no rasters are<br>>> created. If I subset the image<br>>> (cells=1632830) and run it again its works (see # sub2Kruger # code and results below).<br>>> So I'm guessing it is a memory issue?<br>...<br>> ... it consumes a lot of memory... will check on a bigger machine,<br>> perhaps a memory leak.<br><br>The assumption turned out to be right and I think we got it today!<br><br>Vaclav Petras checked it and discovered an "unfortunate" memory allocation which he fixed in r.li.* in revision <a href="http://trac.osgeo.org/grass/changeset/61812" target="_blank">http://trac.osgeo.org/grass/changeset/61812</a> ("<a href="http://r.li" target="_blank">r.li</a>: fix memory handling (memory leak in avl_to_array function))".<br><br>Now <a href="http://r.li" target="_blank">r.li</a> has become very fast, on my laptop:<br><br>GRASS 7.1.svn (nc_spm_08_grass7):~ > g.region -p rast=lsat5_1987_10 res=10 -a ...<br>rows: 1355<br>cols: 1503<br>cells: 2036565<br><br>GRASS 7.1.svn (nc_spm_08_grass7):~ > time -p r.li.simpson --o input=lsat5_1987_10@landsat conf=conf_diversity_5.0<br>output=lsat5_1987_div__simpson_size_5.0<br>r.li.simpson complete. Raster map <lsat5_1987_div__simpson_size_5.0><br>created.<br>--> 29.32 seconds<br><br>or with a simulated higher resolution:<br><br>GRASS 7.1.svn (nc_spm_08_grass7):~ > g.region -p rast=lsat5_1987_10<br>res=5 -aprojection: 99 (Lambert Conformal Conic) ...<br>rows: 2708<br>cols: 3005<br>cells: 8137540<br><br>GRASS 7.1.svn (nc_spm_08_grass7):~ > time -p r.li.simpson --o input=lsat5_1987_10@landsat conf=conf_diversity_5.0<br>output=lsat5_1987_div__simpson_size_5.0<br>r.li.simpson complete. Raster map <lsat5_1987_div__simpson_size_5.0><br>created.<br>--> 227.37 seconds (used to be > 2 hours)<br><br>So, to grab this improvement for Windows, grab the version from here:<br><a href="http://wingrass.fsv.cvut.cz/grass71/" target="_blank">http://wingrass.fsv.cvut.cz/grass71/</a><br><br>(or via OSGeo4W installer). Be sure that the revision is at least<br>r61812 which is indicated in the file name.<br><br>Please let us know if all works to avoid that the change has any negative impact.<br>Tests here did not show any changes in the output except for the speed improvement and solved memory leak.<br><br>Subsequently also r.diversity should behave now.<br><br>I'll backport it to GRASS 7.0 release branch after some testing.<br><br>Markus<br><br>_______________________________________________<br>grass-user mailing list<br><a href="mailto:grass-user@lists.osgeo.org" target="_blank">grass-user@lists.osgeo.org</a><br><a href="http://lists.osgeo.org/mailman/listinfo/grass-user" target="_blank">http://lists.osgeo.org/mailman/listinfo/grass-user</a><u></u><u></u></p></blockquote></div><p class="MsoNormal"><u></u> <u></u></p></div></div></div></div></div></div></blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr">Duccio Rocchini, PhD<br><br><a href="http://gis.cri.fmach.it/rocchini/" target="_blank">http://gis.cri.fmach.it/rocchini/</a><br><br>Fondazione Edmund Mach<br>Research and Innovation Centre<br>Department of Biodiversity and Molecular Ecology<br>GIS and Remote Sensing Unit<br>Via Mach 1, 38010 San Michele all'Adige (TN) - Italy<br>Phone +39 0461 615 570<br><a href="mailto:ducciorocchini@gmail.com" target="_blank">ducciorocchini@gmail.com</a><br><a href="mailto:duccio.rocchini@fmach.it" target="_blank">duccio.rocchini@fmach.it</a><br>skype: duccio.rocchini<br><span style="font-size:small"><span>Google Scholar Profile: <a href="http://scholar.google.it/citations?hl=it&user=OJtw7agAAAAJ" target="_blank">scholar.google.it/citations?hl=it&user=OJtw7agAAAAJ</a></span></span><br><br> </div>
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