After looking at this with Roger Koenker off-list, the problem can be replicated running R CMD check tryout on:
http://reclus.nhh.no/R/Devel/tryout_0.1-1.tar.gz With a NAMESPACE file in tryout, the S4 dispatch breaks down for det(), without a NAMESPACE file, it runs without error (on R-devel with SparseM 0.52 for me). Roger pointed me to http://tolstoy.newcastle.edu.au/R/devel/04a/0042.html which looks similar, but was said to be resolved. A practical but too invasive correction is to change the SparseM code to: setGeneric("Det", function(x, ...) standardGeneric("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, ...) [EMAIL PROTECTED]) rather than original below, the alternative is to drop NAMESPACE in spdep, which is not desirable either. Roger On Fri, 19 Nov 2004, Roger Bivand wrote: > On Thu, 18 Nov 2004, roger koenker wrote: > > > 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, ...) [EMAIL PROTECTED]) > > > > 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. > > As I read the SparseM code, it is following the specification, and if > there was something wrong, the simple example 1) would not have worked > either. But it does, so something changes in the context of where a > function like det() and chol() is called from, here through optimize(), > that sends it to the wrong place based on assuming that the class is > unknown. > > I'll try to make an example that doesn't depend on spdep, just on SparseM > and optimize(). > > This is frustrating, because with Ord's trick of using matrices similar to > symmetric, the SparseM route will be very useful for most situations, > even though it requires strictly symmetric matrices. So your provision of > det() for "matrix.csr" is very useful, once we sort out this strange > behaviour. > > Roger > > > > > I hope that this might expose some fly in the soup. > > > > > > url: www.econ.uiuc.edu/~roger Roger Koenker > > email [EMAIL PROTECTED] 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 <- ([EMAIL PROTECTED])^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: [EMAIL PROTECTED] > > > > > > > > > > > > -- 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: [EMAIL PROTECTED] ______________________________________________ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
