Method dispatch S3/S4 through optimize()
I am far from an expert on S4 method dispatch, so at the risk of
embarrassing
myself I will just indicate how the det() function is written in
SparseM now
in the hope that someone else will see the source of the problem:
setGeneric("det")
setMethod("det","matrix",get("det", pos=NULL, mode= "function"))
setMethod("det","matrix.csr", function(x, ...) det(chol(x))^2)
setMethod("det","matrix.csr.chol", function(x, ...) x@det)
The Cholesky function chol in SparseM was recently extended slightly
to compute this determinant as an additional component, so if the
argument is already of the matrix.csr.chol class det() just extracts
this
component, otherwise it tries to do the cholesky, or defaults to the
base function.
I hope that this might expose some fly in the soup.
url: www.econ.uiuc.edu/~roger Roger Koenker
email rkoenker@uiuc.edu Department of Economics
vox: 217-333-4558 University of Illinois
fax: 217-244-6678 Champaign, IL 61820
On Nov 18, 2004, at 3:34 PM, Roger Bivand wrote:
I have been running into difficulties with dispatching on an S4 class
defined in the SparseM package, when the method calls are inside a
function passed as the f= argument to optimize() in functions in the
spdep
package. The S4 methods are typically defined as:
setMethod("det","matrix.csr", function(x, ...) det(chol(x))^2)
that is within setMethod() rather than by name before the setMethod().
When called from within functions passed as the f= argument to
optimize,
the S3 generics for det() and chol() get picked up, not the S4 generics
for the S4 SparseM classes. This looks for instance like (from
example(boston)):
gp2 <- lagsarlm(log(CMEDV) ~ CRIM + ZN + INDUS + CHAS + I(NOX^2) + I(RM^2)
+ + AGE + log(DIS) + log(RAD) + TAX + PTRATIO + B + log(LSTAT),
+ data=boston.c, nb2listw(boston.soi), method="SparseM")
matrix.csr
Error in chol(tmp1) : non-numeric argument to chol
(this is the error message in chol.R in base). tmp1 is of class
"matrix.csr", but is being sent to the S3 class (error in function
sar.lag.mix.f.sM() in R/lag.spsarlm.R).
sar.lag.mix.f.sM <- function(rho, W, e.a, e.b, e.c, n, quiet)
{
SSE <- e.a - 2*rho*e.b + rho*rho*e.c
s2 <- SSE/n
tmp1 <- asMatrixCsrIrW(W, rho)
cat(class(tmp1), "\n")
tmp2 <- chol(tmp1)
# tmp2 <- .cholMatrixCsr(tmp1)
cat(class(tmp2), "\n")
tmp3 <- (tmp2@det)^2
cat(tmp3, "\n")
ret <- (log(tmp3)
- ((n/2)*log(2*pi)) - (n/2)*log(s2) - (1/(2*s2))*SSE)
if (!quiet)
cat("(SparseM) rho:\t", rho, "\tfunction value:\t", ret, "\n")
ret
}
Three further observations:
1) In a simpler case:
library(spdep)
Loading required package: tripack Loading required package: maptools Loading required package: foreign Loading required package: SparseM [1] "SparseM library loaded"
example(similar.listw)
... smlr.l> log(det(asMatrixCsrIrW(asMatrixCsrListw(similar.listw(COL.W)), 0.5))) [1] -1.627660 just works, and the appropriate det() and chol() are found; det() dispatches on class "matrix.csr" and finds the right chol() for that class - this is the same code context as found in the function passed to optimize(); 2) When the R source file containing the lagsarlm() function, and the function sent as f= through optimize is sourced(), the appropriate det() and chol() are found; and 3) When the SparseM R code is modified, and the function defined prior to its setMethod (so visible as a function independently of setMethod) and called by name rather than as a method, everything works, as it should. But this isn't a solution, setMethod() defined methods should dispatch on class irrespective of context, I think. SparseM does not have a namespace, spdep does, but I don't think this is the issue. I'm pretty sure this isn't an issue with SparseM either, because of 1). I've put a copy of the problematic spdep on: http://reclus.nhh.no/R/spdep/spdep_0.2-24.tar.gz should that be of any use, the issue is present in both R-2.0.1 and R-devel (2004-11-16), SparseM is 0.52. I hope that I'm missing something fairly obvious. Roger -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Breiviksveien 40, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93 e-mail: Roger.Bivand@nhh.no