Joris Meys
2010-Aug-26 13:32 UTC
[R] Passing arguments between S4 methods fails within a function:bug? example with raster package.
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.Meys at Ugent.be
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
Niels Richard Hansen
2010-Aug-26 15:43 UTC
[R] Passing arguments between S4 methods fails within a function:bug? example with raster package.
Joris,
I looked at the problem. Here is a minimal example reproducing
the error
setGeneric("myplus",function(x,y,...)
standardGeneric("myplus"))
setMethod("myplus",c(x="numeric",y="numeric"),
function(x,y,z=0) x+y+z
)
setMethod("myplus",c(x="numeric",y="list"),
function(x,y,...) callGeneric(x,unlist(y),...)
)
myplus(1,1) ## 2; OK
myplus(1,1,1) ## 3; OK
myplus(1,list(1)) ## 2; OK
myplus(1,list(1),z=1) ## 3; OK
a.c1 <- 1
myplus(1,list(1),z=a.c1) ## 3; OK
test <- function(x,y) {
a.c <- 1 ## Problem occurs when using '.' in variable name
myplus(a,y,z=a.c)
}
test(1,list(1)) ## error
test(1,1) ## 3; OK
It looks like a bug. I went through all environments from inside
the call of myplus("numeric","numeric") and a.c is nicely
located
in parent.frame(6) with the value 1. However, when it has a '.' (dot)
in the variable name, the variable is not found. If it has a name
without a '.' (dot) there is no problem:
test <- function(x,y) {
a <- 1
myplus(a,y,z=a)
}
test(1,list(1)) ## 3; OK
- Niels
On 26/08/10 15.32, Joris Meys wrote:> 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.')
> }
> }
> )
>
>
>
--
Niels Richard Hansen Web: www.math.ku.dk/~richard
Associate Professor Email: Niels.R.Hansen at math.ku.dk
Department of Mathematical Sciences nielsrichardhansen at gmail.com
University of Copenhagen Skype: nielsrichardhansen.dk
Universitetsparken 5 Phone: +45 353 20783 (office)
2100 Copenhagen ? +45 2859 0765 (mobile)
Denmark