[R-sig-Geo] Error when predicting a randomForest model to a raster

[Robert J. Hijmans]

Dave,

The example works if you do

rf.mod <- randomForest(color.frame[, c('red','green','blue')],response)

instead of

rf.mod <- randomForest(color.frame,response)

color.frame has 4 variables, one with column name "NA". Given that you
use names(color.frame) <- c('red','green','blue')  it seems that this
is not intentional

Robert




On Tue, Jan 13, 2015 at 5:48 PM, Gregovich, Dave P (DFG)
<dave.gregovich at alaska.gov> wrote:
> Hello,
> Thanks kindly aforehand for any help you can lend. I am trying to perform a simple classification of coarse vegetation types. I am getting an error when trying to predict a randomForest model to a raster:
> #Error in if (any(is.na(x))) stop("missing values in newdata") :
> #  argument is not interpretable as logical
>
> Here is some reproducible code if anyone happens to have the time to give it a shot:
> _________________________________________________________________
> library(raster)
> library(randomForest)
>
> #create random color band rasters and fill with values
> a<-b<-d<-raster(nrows=10,ncols=10)
> a[]<-sample(0:255,ncell(a))
> b[]<-sample(0:255,ncell(a))
> d[]<-sample(0:255,ncell(a))
> rgb.rast<-stack(a,b,d)
> names(rgb.rast)<-c('red','green','blue')
>
>
> #create mock random forest covariate data
> color.offsets<-c(0,20,40)
> color.means<-c(40,80,120,160)
>
> color.mat<-sapply(1:length(color.means),function(x){
>                                                 sapply(1:length(color.offsets),function(y){
>                                                                 round(rnorm(30,color.means[x]+color.offsets[y],sd=1))
>                                                 })
>                                 })
> color.frame<-as.data.frame(color.mat)
> names(color.frame)<-c('red','green','blue')
>
>
> #create mock response data
> response<-as.factor(rep(1:3,each=30))
>
> #run random forest model
> rf.mod<-randomForest(color.frame,response)
>
> #attempt prediction
> rf.predict<-predict(rf.mod,rgb.rast)
> #error message---
> #Error in if (any(is.na(x))) stop("missing values in newdata") :
> #  argument is not interpretable as logical
> _____________________________________________
>> sessionInfo()
> R version 3.0.3 (2014-03-06)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                           LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] randomForest_4.6-10 rgdal_0.9-1         raster_2.2-31       sp_1.0-15
>
> loaded via a namespace (and not attached):
> [1] grid_3.0.3      lattice_0.20-27 tools_3.0.3
>
>
> Thanks a ton folks for any help you can lend!
> __________________________________
> Dave Gregovich
> Research Analyst
> Alaska Department of Fish and Game
> Wildlife Conservation Division
> Douglas, AK 99821
> (907) 465-4291
> dave.gregovich at alaska.gov
> __________________________________
>
>
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>
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