Dear all,
This problem came up initially while debugging a function, but it
seems to be a more general problem of R. I hope I'm wrong, but I can't
find another explanation. Let me illustrate with the raster package.
For an object "RasterLayer" (which inherits from Raster), there is a
method xyValues defined with the signature
(object="RasterLayer",xy="matrix"). There is also a method with
signature (object="Raster",xy="vector"). The only thing this method
does, is change xy into a matrix and then pass on to the next method
using callGeneric again. Arguments are passed.
Now this all works smoothly, as long as you stay in the global environment :
require(raster)
a <- raster()
a[] <- 1:ncell(a)
origin <- c(-80,50)
eff.dist <- 100000
unlist(xyValues(a,xy=origin,buffer=eff.dist))
[1] 14140 14141 14500 14501
Now let's make a very basic test function :
test <- function(x,orig.point){
eff.distance <- 100000
p <- unlist(xyValues(x,xy=orig.point,buffer=eff.distance))
return(p)
}
This gives the following result :
> test(a,origin)
Error in .local(object, xy, ...) : object 'eff.distance' not found
huh? Apparently, eff.distance got lost somewhere in the parsetree (am
I saying this correctly?)
The funny thing is when we change origin to a matrix :
> origin <- matrix(origin,ncol=2)
> unlist(xyValues(a,xy=origin,buffer=eff.dist))
[1] 14140 14141 14500 14501
> test(a,origin)
[1] 14140 14141 14500 14501
It all works again! So something goes wrong with passing the arguments
from one method to another using callGeneric. Is this a bug in R or am
I missing something obvious?
The relevant code from the raster package :
setMethod("xyValues", signature(object='Raster', xy='vector'),
function(object, xy, ...) {
if (length(xy) == 2) {
callGeneric(object, matrix(xy, ncol=2), ...)
} else {
stop('xy coordinates should be a two-column matrix or
data.frame,
or a vector of two numbers.')
}
} )
setMethod("xyValues", signature(object='RasterLayer', xy='matrix'),
function(object, xy, method='simple', buffer=NULL, fun=NULL,
na.rm=TRUE) {
if (dim(xy)[2] != 2) {
stop('xy has wrong dimensions; it should have 2
columns' )
}
if (! is.null(buffer)) {
return( .xyvBuf(object, xy, buffer, fun, na.rm=na.rm) )
}
if (method=='bilinear') {
return(.bilinearValue(object, xy))
} else if (method=='simple') {
cells <- cellFromXY(object, xy)
return(.readCells(object, cells))
} else {
stop('invalid method argument. Should be simple or
bilinear.')
}
}
)
--
Joris Meys
Statistical consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
tel : +32 9 264 59 87
joris.m...@ugent.be
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
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