[GRASS-stats] help coding an anova using raster data

[Dylan Beaudette]

On Friday 21 November 2008, Sam Veloz wrote:
> When I tried this:
> test.aov <- aov(response ~ ., data=SGDF)
> It only gives the next variable in the resulting ANOVA table.
>
> The other option you gave:
> test.aov <- aov(response ~ rep1 + rep2 + rep3 + rep4 + rep5, data=SGDF)
>
> doesn't work because it treats each "rep" as a factor, I would like each
> of these rasters to be a repetition. In other words I would have an n of
>   5. Does this make sense?
> Thanks,
> Sam

In that case you need to 'stack' your data into long format. check the mailing 
list for ideas. Functions of interest:

stack()
reshape()

and the 'reshape' package

Cheers,

Dylan


> Roger Bivand wrote:
> > On Thu, 20 Nov 2008, Sam Veloz wrote:
> >> I would like to run an anova on a set of raster variables imported
> >> from GRASS into R but am confused about how R handles the raster data.
> >> So if I have a model with a treatment with 2 levels, each raster is a
> >> binary file with cells coded for each level of the treatment. I have 1
> >> response raster layer that corresponds spatially with the treatment
> >> layers. So let's say I have 5 rasters representing a different rep of
> >> the treatment how would I code this in R? I started out trying this:
> >>
> >> treatment<-readRAST6(c("rep1","rep2","rep3","rep4","rep5"),cat=TRUE)
> >> response<-readRAST6("response",cat=FALSE)
> >> test.aov<-aov(response~treatment)
> >
> > The objects returned by readRAST6 are SpatialGridDataFrames. I think
> > that you may find that:
> >
> > SGDF <- readRAST6(c("rep1", "rep2", "rep3", "rep4", "rep5", "response"),
> >   cat=c(TRUE, TRUE, TRUE, TRUE, TRUE, FALSE))
> > test.aov <- aov(response ~ ., data=SGDF)
> >
> > does the trick (the . inserts the remaining variables) - or safer:
> >
> > test.aov <- aov(response ~ rep1 + rep2 + rep3 + rep4 + rep5, data=SGDF)
> >
> > Untried.
> >
> > By the way, do you need aov(), or would anova(lm()) do the same? I guess
> > the richer setting needs facilities in aov() that aren't visible here.
> >
> > Hope this helps,
> >
> > Roger
> >
> >> but I don't think this is right. Is it possible to do what I am
> >> trying? My data is actually a bit more complicated than this but if I
> >> can clear this up than I think I can do the rest on my own.
> >> Thanks for your help,
> >> Sam



-- 
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341