[R-sig-Geo] extracting non-NA values from RasterLayer
Dear list, I am currently dealing with extremely large raster datasets (100s of millions of cells), and am masking out large regions which are of no particular interest for our current project. This produces RasterLayers with a large number of NAs (but still millions of non-NA cells as well). What I'd like to do is extract all non-NA values into a vector for use in various statistical analyses, but I am having trouble finding the most efficient means of doing so. Any pointers? I have tried sampleRandom, which is supposed to only take non-NA cells, but there must be a better/faster way to extract *all* non-NA values that I've just missed. Cheers, Carson -- Dr. Carson J. Q. Farmer Centre for GeoInformatics (CGI) School of Geography and Geosciences Irvine Building, University of St Andrews St Andrews, Fife, KY16 9AL Scotland, UK ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Re: [R-sig-Geo] extracting non-NA values from RasterLayer
Hi Carson, check ?rasterToPoints from raster package. That should do it! Rafi On 25.04.2012, at 12:26, Carson Farmer wrote: Dear list, I am currently dealing with extremely large raster datasets (100s of millions of cells), and am masking out large regions which are of no particular interest for our current project. This produces RasterLayers with a large number of NAs (but still millions of non-NA cells as well). What I'd like to do is extract all non-NA values into a vector for use in various statistical analyses, but I am having trouble finding the most efficient means of doing so. Any pointers? I have tried sampleRandom, which is supposed to only take non-NA cells, but there must be a better/faster way to extract *all* non-NA values that I've just missed. Cheers, Carson -- Dr. Carson J. Q. Farmer Centre for GeoInformatics (CGI) School of Geography and Geosciences Irvine Building, University of St Andrews St Andrews, Fife, KY16 9AL Scotland, UK ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo -- Rafael Wüest Swiss Federal Research Institute WSL Zürcherstrasse 111 8903 Birmensdorf Switzerland +41 44 7392126 rafael.wue...@wsl.ch http://www.wsl.ch/info/mitarbeitende/wueest ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
[R-sig-Geo] averaging home range contours
Hello all
I am trying to run some Monte Carlo simulations on single individuals in R.
So far, I have sampled 100 X and Y coordinates from known positions of an
individual, 100 times. This results in a list of 200. I then convert this
list into a dataframe that is more condusive to eventual functions I want
to run for each sample (kernel.area,kernelUD).
So I had a data frame with 200 columns, and I wanted to perform the
kernel.area function (adehabitatHR), using each successive pair of columns
(which represent a resampling). I ended up writing a loop that allows me to
calculate the kernel.area for each of the simulations, as well as the 95%
volume contour, which is saved as a Spatial Polygon.
I now want to take the average of these 95% volume contours, to get an
average 95% volume contour that I can view in Arc. However, I am unsure how
to do this. Any advice would be greatly appreciated!
I can't replicate my data very well here, so I'll give an example of what
the structure is:
# generate dataframe representing X and Y positions
df - data.frame(x=seq(1:200),y=seq(1:200))
# 100 replications of sampling 100 positions
resamp - replicate(100,df[sample(nrow(df),100),])
# convert to data frame (kernel.area needs an xy dataframe)
dfnew - do.call(rbind, resamp[1:2,])
# xy positions need to be in columns for kernel.area
df2 - t(dfnew)
Ok, here is the for loop I've been using for my actual positions:
#calculate the 50,95% kernel area for each simulation, as well as the 95%
volume contour
for (j in seq(1,ncol(df2)-1,2)) {
kud -kernelUD(SpatialPoints(df2[,j:(j+1)]),kern=bivnorm)
kernAr-kernel.area(kud,percent=c(50,95),unin=c(m),unout=c(km2))
print(kernAr)
name[[j]]-getverticeshr(kud, lev = 95)
}
Again, the next step I wish to take is to average the hundred 95% contours
I have created (ie name[[1]],name[[3]]...). Any suggestions?
Melanie
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Melanie Shapiera
MSc candidate
Memorial University of Newfoundland
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[R-sig-Geo] Overlaying maps
Dear all, I am a botanist and I need some assistance for overlaying maps under R. I have an altimetric file for Madagascar in .gri. This file come from http://www.diva-gis.org/gdata (and the original data seem to have been edited by CGIAR STRM). I realize a plot of this file and Iâm overlaying an Arview file (bioclimate 5) in .shp (polygon) but I donât know his specific features. Finally Iâm overlaying my sheet herbarium geographical localities points. My final map donât have any problems in a global points of view (figure 1). Problems come when 1) I would a more detailed part of this final map or 2) I wish to modify the size of the final plot (figure 2). For the detailed plot : the files are not correctly superposed and numerous pixels of the .gri file are outside of the limits of the polygons of the .shp file. For the modified size of the final plot : the .gri file not change his conformation but the .shp file and the distance between my sheet herbarium geographical localities points are proportionally modified with the draw of the plot. Is it a problem with the geographical projections ? Who know how to do have a good overlaying between .gri file and .shp file for the removal of my problems ? As an advance, thank you for your responses, Cyrille MAS My code is : # display the bioclimate 5 file library(maptools) SHP=E:/Bioclimate 5/bc5.shp bc5 plot(bc5,xlim=c(44,50),ylim=c(-26,-12),cex.axis=0.6,cex.names=0.6,axis.lty=0,xlab=Longitude, ylab=Latitude,axes=TRUE,border=black,col=white) # display the altimetric file require(raster) alt str(alt) plot(alt,cex.axis=0.6,cex.names=0.6,axis.lty=0,xlab=Longitude (en °E),ylab=Latitude (en °S),axes=TRUE) # overlaying the bioclimate 5 file upon the altimetric file plot(bc5,add=TRUE) # apply of my sheet herbarium geographical localities data library(dismo) data [[alternative HTML version deleted]] ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Re: [R-sig-Geo] Overlaying maps
Hi Cyrille, This can be something linked to the projection of your files. All geographical data have a projection, and, for a correct overlaying, the projection should be informed to the software (ArcView, ArcGIS, R, etc), and will be better if all the data have the same projection. Can you inform us the projection of your files? On Wed, Apr 25, 2012 at 11:05 AM, mas.cyrille2 mas.cyril...@wanadoo.fr wrote: Dear all, I am a botanist and I need some assistance for overlaying maps under R. I have an altimetric file for Madagascar in .gri. This file come from http://www.diva-gis.org/gdata (and the original data seem to have been edited by CGIAR STRM). I realize a plot of this file and I’m overlaying an Arview file (bioclimate 5) in .shp (polygon) but I don’t know his specific features. Finally I’m overlaying my sheet herbarium geographical localities points. My final map don’t have any problems in a global points of view (figure 1). Problems come when 1) I would a more detailed part of this final map or 2) I wish to modify the size of the final plot (figure 2). For the detailed plot : the files are not correctly superposed and numerous pixels of the .gri file are outside of the limits of the polygons of the .shp file. For the modified size of the final plot : the .gri file not change his conformation but the .shp file and the distance between my sheet herbarium geographical localities points are proportionally modified with the draw of the plot. Is it a problem with the geographical projections ? Who know how to do have a good overlaying between .gri file and .shp file for the removal of my problems ? As an advance, thank you for your responses, Cyrille MAS My code is : # display the bioclimate 5 file library(maptools) SHP=E:/Bioclimate 5/bc5.shp bc5 plot(bc5,xlim=c(44,50),ylim=c(-26,-12),cex.axis=0.6,cex.names=0.6,axis.lty=0,xlab=Longitude, ylab=Latitude,axes=TRUE,border=black,col=white) # display the altimetric file require(raster) alt str(alt) plot(alt,cex.axis=0.6,cex.names=0.6,axis.lty=0,xlab=Longitude (en °E),ylab=Latitude (en °S),axes=TRUE) # overlaying the bioclimate 5 file upon the altimetric file plot(bc5,add=TRUE) # apply of my sheet herbarium geographical localities data library(dismo) data [[alternative HTML version deleted]] ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo -- Atenciosamente, Raphael Saldanha saldanha.plan...@gmail.com ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Re: [R-sig-Geo] earth Package question for running a loop
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Re: [R-sig-Geo] semi-transparent mapping - overlapping areas
Dear Roger and Roman, Thanks for answering, with your kind help I compiled the maps I wanted. Best wishes, Juta From: Roger Bivand [roger.biv...@nhh.no] Sent: 25 April 2012 11:34 To: Roman Luštrik Cc: Juta Kawalerowicz; r-sig-geo [r-sig-geo@r-project.org] Subject: Re: [R-sig-Geo] semi-transparent mapping - overlapping areas On Wed, 25 Apr 2012, Roman Luštrik wrote: You could use the alpha argument to set transparency to each color. The overlaying colors should have a mixture of both. For example, see the bottom two images (http://had.co.nz/ggplot2/geom_histogram.html) of how alpha mixing works. Lattice graphics also have an alpha argument. Right. In base graphics: library(maptools) set.seed(1) xx - readShapeSpatial(system.file(shapes/sids.shp, package=maptools)[1], proj4string=CRS(+proj=longlat)) xx$reds - 1 is.na(xx$reds) - sample(1:100, 50) xx$blues - 1 is.na(xx$blues) - sample(1:100, 50) plot(xx, col=grey80, border=transparent) plot(xx, col=ifelse(is.na(xx$reds), transparent, red), border=transparent, add=TRUE) plot(xx, col=ifelse(is.na(xx$blues), transparent, rgb(red=0, green=0, blue=1, alpha=0.5)), border=transparent, add=TRUE) with rather too brutal red/blue colours. Roger Cheers, Roman On Wed, Apr 25, 2012 at 12:13 PM, Juta Kawalerowicz juta.kawalerow...@stx.ox.ac.uk wrote: Hi, Does anyone know how to create mapping of attribute A and attribute B so that the overlapping areas are not colour A or B but the mixture of the two (the semi-transparent effect). In case that does not sound clear, I am looking for this kind of effect http://tinyurl.com/cko7c4b created by Divid McCandless (probably not using R?) If anyone knows a function/package which could allows to do something like this, I would be very gretful for suggestions. Cheers, Juta [[alternative HTML version deleted]] ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo -- Roger Bivand Department of Economics, NHH Norwegian School of Economics, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: roger.biv...@nhh.no ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
