'Re: [R-sig-Geo] how to export results of predict.randomForest'

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List:       r-sig-geo
Subject:    Re: [R-sig-Geo] how to export results of predict.randomForest
From:       zack holden <zack_holden () hotmail ! com>
Date:       2008-12-28 23:49:12
Message-ID: BAY125-W48EFC26962D5F1506E108987E90 () phx ! gbl
[Download RAW message or body]

Hi Ann,
I've created prediction surfaces from random forest models and can try to help you. 

I don't know Rgdal well enough to guide you through your current approach. What you \
could do is create ascii grids for each of your raster/image bands, then call to \
those grids to create your prediction surface.   
Check out package = yaImpute and the AsciiGridPredict function within. I can send you \
some code to make this work if you'd like to try it. Just ask. Feel free to email off \
list, you can post the solution if it works.  
Cheers,

Zack

> From: r-sig-geo-request@stat.math.ethz.ch
> Subject: R-sig-Geo Digest, Vol 64, Issue 25
> To: r-sig-geo@stat.math.ethz.ch
> Date: Sat, 27 Dec 2008 12:00:02 +0100
> 
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> Today's Topics:
> 
> 1. Re: adding a background shape to ssplot (Edzer Pebesma)
> 2. Re: how to export results of predict.randomForest (Edzer Pebesma)
> 3. Re: adding a background shape to ssplot (Hengl, T.)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 26 Dec 2008 12:20:44 +0100
> From: Edzer Pebesma
> Subject: Re: [R-sig-Geo] adding a background shape to ssplot
> To: Jon Loehrke
> Cc: r-sig-geo@stat.math.ethz.ch
> Message-ID: 
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Jon Loehrke wrote:
> > Greetings and Happy Holidays!
> > 
> > 
> > 
> ...
> > #However I can seem to pass the polygon colors argument through spplot
> > spplot(nc1, c("f","g"), col.regions=brewer.pal(10, "Set3"),
> > scales=list(draw = TRUE),
> > panel=function(...) {
> > panel.mapper()
> > sp.polygons(nc1)
> > }
> > )
> > 
> > 
> A better panel function would be this:
> 
> spplot(nc1, c("f","g"), # col.regions=brewer.pal(10, "Set3"),
> scales=list(draw = TRUE),
> panel=function(...) {
> panel.mapper()
> panel.polygonsplot(...)
> }
> )
> 
> 
> see
> 
> getMethod("spplot", "SpatialPolygonsDataFrame")
> 
> to find out how the appropriate spplot method does it.
> 
> I am worried, however, about the absence of the last 5 colors and factor
> levels f-j.
> --
> Edzer
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Fri, 26 Dec 2008 12:26:29 +0100
> From: Edzer Pebesma
> Subject: Re: [R-sig-Geo] how to export results of predict.randomForest
> To: Anne Axel
> Cc: r-sig-geo@stat.math.ethz.ch
> Message-ID: 
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> I might have missed something obvious, but did you try something like
> 
> bands$randomForest = output
> spplot(bands, "randomForest")
> 
> ?
> --
> Edzer
> 
> 
> Anne Axel schrieb:
> > Hi Robert and list,
> > 
> > Thanks so much for the Christmas message! I tried your great
> > suggestion and I got the following error:
> > 
> > > spgrid <- SpatialGridDataFrame(bands, output)
> > Error in rbind(grid@cellcentre.offset, grid@cellcentre.offset +
> > (grid@cells.dim - :
> > no slot of name "cellcentre.offset" for this object of class
> > "SpatialGridDataFrame"
> > 
> > So, I examined the structure of both files (see below). In addition,
> > there are no NAs in "imgtabla" or "bands", but there are NAs in the
> > rf.prediction ("output").
> > 
> > I tried to writeGDAL(bands, "test2.tif") and this worked without any
> > errors. Could it have something to do with the fact that my output is
> > of class factor?
> > 
> > Again, thanks Robert, for setting me on the right path. Any other
> > suggestions out there to clear this last hurdle?
> > 
> > Best,
> > Anne Axel
> > 
> > > str(bands)
> > Formal class 'SpatialGridDataFrame' [package "sp"] with 6 slots
> > ..@ data :'data.frame': 163982 obs. of 55 variables:
> > .. ..$ band1 : num [1:163982] 0 0 0 0 0 0 0 0 0 0 ...
> > .. ..
> > ..@ grid :Formal class 'GridTopology' [package "sp"] with 3 slots
> > .. .. ..@ cellcentre.offset: Named num [1:2] 0.5 0.5
> > .. .. .. ..- attr(*, "names")= chr [1:2] "x" "y"
> > .. .. ..@ cellsize : num [1:2] 1 1
> > .. .. ..@ cells.dim : int [1:2] 442 371
> > ..@ grid.index : int(0)
> > ..@ coords : num [1:2, 1:2] 0.5 441.5 0.5 370.5
> > .. ..- attr(*, "dimnames")=List of 2
> > .. .. ..$ : NULL
> > .. .. ..$ : chr [1:2] "x" "y"
> > ..@ bbox : num [1:2, 1:2] 0 0 442 371
> > .. ..- attr(*, "dimnames")=List of 2
> > .. .. ..$ : chr [1:2] "x" "y"
> > .. .. ..$ : chr [1:2] "min" "max"
> > ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slots
> > .. .. ..@ projargs: chr " +proj=utm +zone=38 +south +a=6378137
> > +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0"
> > 
> > > str(output)
> > Factor w/ 4 levels "dry","gallery",..: 3 3 3 3 3 3 3 3 3 3 ...
> > 
> > 
> > > class(bands)
> > [1] "SpatialGridDataFrame"
> > attr(,"package")
> > [1] "sp"
> > 
> > 
> > > class(output)
> > [1] "factor"
> > 
> > > summary(output)
> > dry gallery notforest spiny NA's
> > 33009 5878 103772 21315 8
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > At 12/24/2008 09:02 PM, you wrote:
> > > Hi Anne,
> > > 
> > > The first argument of writeGDAL is "an object of class
> > > SpatialGridDataFrame-class or SpatialPixelsDataFrame-class"
> > > So you need to create a new SpatialGridDataFrame with the spatial
> > > properties of "multibands3.img" and with the RandomForest predictions
> > > ("output"). Note that there are some additional complications when
> > > there are NAs in your predictors (i.e. in "imgtabla"), but if there
> > > are none, I think that something like this might work:
> > > 
> > > spgrid <- SpatialGridDataFrame(bands, output)
> > > writeGDAL(spgrid, "rf_results.tif")
> > > 
> > > Robert
> > > 
> > > On Thu, Dec 25, 2008 at 4:58 AM, Anne Axel
> > > wrote:
> > > Hi List,
> > > 
> > > I am requesting help with exporting results from the
> > > predict.randomForest function. This is my first attempt at working
> > > with spatial data in R--I was able to import the data and run the
> > > randomForest model, but I cannot figure out how to export the data
> > > for use in ArcGIS or ENVI.
> > > 
> > > I've pasted below the code I used for randomForest and exporting of
> > > results. If anyone has suggestions, I would be eternally grateful!
> > > Thanks, and Happy Holidays.
> > > 
> > > Anne Axel
> > > 
> > > 
> > > Department of Fisheries and Wildlife
> > > Michigan State University
> > > 20 Natural Resources Building
> > > East Lansing, MI 48824 USA
> > > 517-930-2248
> > > axelanne@msu.edu
> > > 
> > > 
> > > ####Read in *img file with 55 bands
> > > bands=readGDAL("multibands3.img")
> > > imgtabla <- as(bands, "data.frame")
> > > 
> > > ######Read in training data and run randomForest
> > > data=read.csv("bandnumsOutput_cond2.csv", header=TRUE)
> > > data2=data[,1:58]
> > > data.rf=randomForest(COVERTYPE~ ., data=data2, mtry=16, importance =
> > > TRUE, do.trace=100)
> > > print(data.rf)
> > > output=predict(data.rf, imgtabla)
> > > 
> > > #### I've tried numerous ways of exporting the data, but I don't seem
> > > to have the data in a format that's acceptable to the functions. In
> > > addition, I've tried to coerce data into other formats, but nothing
> > > has worked. Any suggestions?
> > > 
> > > 
> > > > writeGDAL(bands, output, drivername = "GTiff", type = "Float32",
> > > mvFlag = NA, options=NULL)
> > > Error in .local(.Object, ...) :
> > > STRING_ELT() can only be applied to a 'character vector', not a
> > > 'integer'
> > > In addition: Warning messages:
> > > 1: In if (nchar(fname) == 0) stop("empty file name") :
> > > the condition has length> 1 and only the first element will be used
> > > 2: In if (nchar(filename) == 0) stop("empty file name") :
> > > the condition has length> 1 and only the first element will be used
> > > 
> > > > writeGDAL(output, bands, drivername = "GTiff", type = "Float32",
> > > mvFlag = NA, options=NULL)
> > > Error in nchar(fname) : cannot coerce type S4 to character vector
> > > 
> > > > write.ENVI(output)
> > > Error in dim(X) = c(nRow, nCol, nBand) : length-0 dimension vector is
> > > invalid
> > > 
> > > > write.ascii.grid(output, "output", header = NULL, write.header = TRUE)
> > > Error: is.matrix(data) is not TRUE
> > > 
> > > 
> > > 
> > > 
> > > 
> > > Anne C. Axel
> > > Department of Fisheries and Wildlife
> > > Michigan State University
> > > 20 Natural Resources Building
> > > East Lansing, MI 48824 USA
> > > 517-930-2248
> > > axelanne@msu.edu
> > > 
> > > _______________________________________________
> > > R-sig-Geo mailing list
> > > R-sig-Geo@stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> > > 
> > 
> > " Know your own bone. Gnaw at it, bury it, unearth it, and gnaw it
> > still."
> > -Henry David Thoreau
> > 
> > "Outside of a dog, a book is a man's best friend. Inside of a dog,
> > it's too dark to read."
> > - Groucho Marx
> > 
> > Anne C. Axel
> > Department of Fisheries and Wildlife
> > Michigan State University
> > 20 Natural Resources Building
> > East Lansing, MI 48824 USA
> > 517-930-2248
> > axelanne@msu.edu
> > 
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Fri, 26 Dec 2008 15:01:27 +0100
> From: "Hengl, T."
> Subject: Re: [R-sig-Geo] adding a background shape to ssplot
> To: "Jon Loehrke" ,
> Message-ID: 
> Content-Type: text/plain
> 
> 
> take a look also at some examples from the book by Reimann et al. (2008). They \
> actually load a jpg map (showing coast-line/borders) as a background plot (method \
> "plotbg" in package "StatDA"): 
> 6.4 Spatial Trends
> http://www.statistik.tuwien.ac.at/StatDA/R-scripts/page138.html
> 
> 8.9 Data Subsets in Maps
> http://www.statistik.tuwien.ac.at/StatDA/R-scripts/page157.html
> 
> 
> HTH
> 
> Tom Hengl
> http://spatial-analyst.net
> 
> ________________________________
> 
> From: r-sig-geo-bounces@stat.math.ethz.ch on behalf of Jon Loehrke
> Sent: sri 12/24/2008 7:01
> To: r-sig-geo@stat.math.ethz.ch
> Subject: [R-sig-Geo] adding a background shape to ssplot
> 
> 
> 
> Greetings and Happy Holidays!
> 
> I am an ~experienced R user but new to spatially oriented packages. I
> have been trying to add a 'background' shape to a ssplot. My example
> is to add a background state map to the sids data.
> 
> My 2 questions, 1) What am I missing with the spplot - lattice
> interaction[this seems like it should be simple]?, and 2) is there a
> better way to add the 'background' map if the object is a
> SpatialPolygonsDataFrame?
> 
> #Examples mostly from http://r-spatial.sourceforge.net/gallery/
> #Library's required for example
> library(sp)
> library(grid)
> library(lattice)
> library(maps)
> library(RColorBrewer)
> library(maptools)
> 
> #First a Basic plot and an added map
> 
> nc1 <- readShapePoly(system.file("shapes/sids.shp", package="maptools")
> [1], proj4string=CRS("+proj=longlat +datum=NAD27"))
> 
> names(nc1)
> rrt <- nc1$SID74/nc1$BIR74
> brks <- quantile(rrt, seq(0,1,1/7))
> cols <- grey((length(brks):2)/length(brks))
> dens <- (2:length(brks))*3
> plot(nc1, col=cols[findInterval(rrt, brks, all.inside=TRUE)])
> 
> # add US State map
> map('state', add=TRUE, xlim=par('usr')[1:2], ylim=par('usr')[3:4])
> 
> 
> #This works fine, but I have issues when using spplot.
> 
> example
> nc1$f = factor(sample(1:5,100,replace=T),labels=letters[1:5])
> nc1$g = factor(sample(1:5,100,replace=T),labels=letters[6:10])
> 
> spplot(nc1, c("f","g"), col.regions=brewer.pal(10, "Set3"),
> scales=list(draw = TRUE))
> 
> 
> # create a custom panel to add a map polygon to lattice plot
> 
> panel.mapper <- function(...){
> library(maps)
> mp<-map('state', fill=TRUE, plot=FALSE)
> lpolygon(mp$x, mp$y, col='gray', ...)
> }
> 
> #The panel mapper appears to work
> spplot(nc1, c("f","g"), col.regions=brewer.pal(10, "Set3"),
> scales=list(draw = TRUE), panel=function(...) {
> panel.mapper()
> })
> 
> #However I can seem to pass the polygon colors argument through ssplot
> spplot(nc1, c("f","g"), col.regions=brewer.pal(10, "Set3"),
> scales=list(draw = TRUE),
> panel=function(...) {
> panel.mapper()
> sp.polygons(nc1)
> }
> )
> 
> 
> Thanks for the help and happiest holidays.
> 
> Jon Loehrke
> Graduate Research Assistant
> Department of Fisheries Oceanography
> School for Marine Science and Technology
> University of Massachusetts
> 200 Mill Road, Suite 325
> Fairhaven, MA 02719
> jloehrke@umassd.edu
> > sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-apple-darwin8.11.1
> 
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] grid stats graphics grDevices utils datasets
> methods base
> 
> other attached packages:
> [1] lattice_0.17-17 RColorBrewer_1.0-2 maps_2.0-40
> maptools_0.7-15 foreign_0.8-29 sp_0.9-28
> 
> loaded via a namespace (and not attached):
> [1] tools_2.8.1
> 
> 
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> 
> 
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> 
> 
> ------------------------------
> 
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