This is great Sandra. Now I am curious to see final ecological relationships you are searching for! D
2014-09-30 3:24 GMT+02:00 Sandra MacFadyen <[email protected]>: > Dear Vaclav, > > > > I did a quick manual test to see if the results were correct for a few 5x5 > windows and yes, everything appears 100%: > > > > # Example data from one 5x5 window > > test1 = c(572,617,661,638,616, > > 662,617,593,638,616, > > 662,639,572,661,616, > > 662,662,639,662,616, > > 594,572,594,639,593) > > > > # Calculate info needed for diversity indices > > freq1 = as.data.frame(table(test1)) # Calculate frequency table > > S = length(unique(test1)) # Total number of species (S) > > N = length(test1) # Total number of individuals (N) > > ln.S = log(S) #Natural log of species (ln S) > > ln.N = log(N) # Natural log of individuals (ln N) > > Pi = freq1$Freq/N # Proportion of individuals that belong to each species > > Pi2 = (Pi ^ 2) > > ln.pi = log(Pi) > > pi.ln.pi = Pi * ln.pi > > pi.ln.pi2 = (ln.pi^2)*Pi > > > > # Calculate different diversity indices > > (M = (S-1)/ln.N) # Margalef's index (M) > > (i.Di = 1/sum(Pi2)) # Simpson's index [Inverse] (i.Di) > > (i.Dc = 1 - (sum(Pi2))) # Simpson's index [Complement] (i.Dc) * This one > calculated with r.diversity > > (H = sum(pi.ln.pi)*-1) # Shannon-Wiener index (H') > > (J = H/ln.S) # Pielou's index (J) > > > > Thanks again > > > > Cheers > > Sandra > > > > *From:* Vaclav Petras [mailto:[email protected] <[email protected]>] > > *Sent:* 18 September 2014 02:46 AM > *To:* Sandra MacFadyen > *Cc:* Markus Neteler; GRASS user list; Duccio Rocchini; Luca Delucchi > *Subject:* Re: [GRASS-user] Solved: execGRASS("r.diversity") Done. No > rasters created (Large rasters) > > > > > > > > On Wed, Sep 17, 2014 at 7:40 PM, Sandra MacFadyen <[email protected]> > wrote: > > Dear Markus, > > Excellent! Thanks to everyone for their help. > 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. > Amazing :) > > > execGRASS("r.diversity",flags="overwrite", parameters=list(input="flow", > prefix="flow_div", alpha=0.5, size=3)) > > r.li.simpson complete. Raster map <flow_div_simpson_size_3.0> created. > > r.li.shannon complete. Raster map <flow_div_shannon_size_3.0> created. > > r.li.pielou complete. Raster map <flow_div_pielou_size_3.0> created. > > r.li.renyi complete. Raster map <flow_div_renyi_size_3.0_alpha_0.5> > > created. > > Done. > > Thanks again and keep well. > > 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? > > > > Vaclav > > > Cheers > Sandra > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On Behalf > Of Markus Neteler > Sent: 06 September 2014 05:15 AM > To: Sandra MacFadyen > Cc: GRASS user list; Duccio Rocchini; Luca Delucchi > Subject: Re: [GRASS-user] execGRASS("r.diversity") Done. No rasters > created (Large rasters) > > Dear Sandra, > > On Fri, Jun 20, 2014 at 7:49 AM, Markus Neteler <[email protected]> wrote: > > On Sat, Jun 14, 2014 at 9:21 AM, Sandra MacFadyen <[email protected]> > wrote: > >> I am using r.diversity (GRASS GIS 7.0.0svn build 60785 win32) through > >> R (R version 3.0.2 win32) on Windows 7 64bit. > ... > >> However, when running the same code on a larger image (cells=6746328) > >> from my own location, although it reports Done, no rasters are > >> created. If I subset the image > >> (cells=1632830) and run it again its works (see # sub2Kruger # code and > results below). > >> So I'm guessing it is a memory issue? > ... > > ... it consumes a lot of memory... will check on a bigger machine, > > perhaps a memory leak. > > The assumption turned out to be right and I think we got it today! > > Vaclav Petras checked it and discovered an "unfortunate" memory allocation > which he fixed in r.li.* in revision > http://trac.osgeo.org/grass/changeset/61812 ("r.li: fix memory handling > (memory leak in avl_to_array function))". > > Now r.li has become very fast, on my laptop: > > GRASS 7.1.svn (nc_spm_08_grass7):~ > g.region -p rast=lsat5_1987_10 > res=10 -a ... > rows: 1355 > cols: 1503 > cells: 2036565 > > GRASS 7.1.svn (nc_spm_08_grass7):~ > time -p r.li.simpson --o > input=lsat5_1987_10@landsat conf=conf_diversity_5.0 > output=lsat5_1987_div__simpson_size_5.0 > r.li.simpson complete. Raster map <lsat5_1987_div__simpson_size_5.0> > created. > --> 29.32 seconds > > or with a simulated higher resolution: > > GRASS 7.1.svn (nc_spm_08_grass7):~ > g.region -p rast=lsat5_1987_10 > res=5 -aprojection: 99 (Lambert Conformal Conic) ... > rows: 2708 > cols: 3005 > cells: 8137540 > > GRASS 7.1.svn (nc_spm_08_grass7):~ > time -p r.li.simpson --o > input=lsat5_1987_10@landsat conf=conf_diversity_5.0 > output=lsat5_1987_div__simpson_size_5.0 > r.li.simpson complete. Raster map <lsat5_1987_div__simpson_size_5.0> > created. > --> 227.37 seconds (used to be > 2 hours) > > So, to grab this improvement for Windows, grab the version from here: > http://wingrass.fsv.cvut.cz/grass71/ > > (or via OSGeo4W installer). Be sure that the revision is at least > r61812 which is indicated in the file name. > > Please let us know if all works to avoid that the change has any negative > impact. > Tests here did not show any changes in the output except for the speed > improvement and solved memory leak. > > Subsequently also r.diversity should behave now. > > I'll backport it to GRASS 7.0 release branch after some testing. > > Markus > > _______________________________________________ > grass-user mailing list > [email protected] > http://lists.osgeo.org/mailman/listinfo/grass-user > > > -- Duccio Rocchini, PhD http://gis.cri.fmach.it/rocchini/ Fondazione Edmund Mach Research and Innovation Centre Department of Biodiversity and Molecular Ecology GIS and Remote Sensing Unit Via Mach 1, 38010 San Michele all'Adige (TN) - Italy Phone +39 0461 615 570 [email protected] [email protected] skype: duccio.rocchini Google Scholar Profile: scholar.google.it/citations?hl=it&user=OJtw7agAAAAJ
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