Dear List, This may be related to this email thread initiated by Ben Bolker last month: https://stat.ethz.ch/pipermail/r-devel/2011-July/061630.html
In answering this Question on StackOverflow http://stackoverflow.com/q/7195628/429846 I noticed that `methods()` was not listing some S3 methods for `plot()` provided by the mgcv package. At the time I wanted to check the development version of R as I recalled Uwe mentioning that `plot.function` was listed by `methods()` there but not in R2.13.x. I have now compiled the development version on two Fedora installations and certain plot methods are still not being listed. Details of the exact revision of R Devel are shown at the end of this email. As an example, consider: > require(mgcv) Loading required package: mgcv This is mgcv 1.7-6. For overview type 'help("mgcv-package")'. > methods("plot") [1] plot.acf* plot.ACF* plot.augPred* [4] plot.compareFits* plot.data.frame* plot.decomposed.ts* [7] plot.default plot.dendrogram* plot.density [10] plot.ecdf plot.factor* plot.formula* [13] plot.function plot.gam plot.gls* [16] plot.hclust* plot.histogram* plot.HoltWinters* [19] plot.intervals.lmList* plot.isoreg* plot.lm [22] plot.lme* plot.lmList* plot.medpolish* [25] plot.mlm plot.nffGroupedData* plot.nfnGroupedData* [28] plot.nls* plot.nmGroupedData* plot.pdMat* [31] plot.ppr* plot.prcomp* plot.princomp* [34] plot.profile.nls* plot.ranef.lme* plot.ranef.lmList* [37] plot.shingle* plot.simulate.lme* plot.spec [40] plot.stepfun plot.stl* plot.table* [43] plot.trellis* plot.ts plot.tskernel* [46] plot.TukeyHSD plot.Variogram* Non-visible functions are asterisked > pmeth <- methods("plot") > grep("plot.mgcv.smooth", pmeth) integer(0) > getS3method("plot", "mgcv.smooth") Error in getS3method("plot", "mgcv.smooth") : S3 method 'plot.mgcv.smooth' not found > pfun <- getAnywhere("plot.mgcv.smooth") > str(pfun) List of 5 $ name : chr "plot.mgcv.smooth" $ objs :List of 1 ..$ :function (x, P = NULL, data = NULL, label = "", se1.mult = 1, se2.mult = 2, partial.resids = FALSE, rug = TRUE, se = TRUE, scale = -1, n = 100, n2 = 40, pers = FALSE, theta = 30, phi = 30, jit = FALSE, xlab = NULL, ylab = NULL, main = NULL, ylim = NULL, xlim = NULL, too.far = 0.1, shade = FALSE, shade.col = "gray80", shift = 0, trans = I, by.resids = FALSE, scheme = NULL, ...) $ where : chr "namespace:mgcv" $ visible: logi FALSE $ dups : logi FALSE - attr(*, "class")= chr "getAnywhere" Both `methods()` and `getS3method()` don't list/find this method, but the function exists in the mgcv name space and this method will be used via R's S3 dispatch system in `plot.gam()`. Shouldn't this method be returned by either `methods()` or `getS3method()`? TIA, Gavin > sessionInfo() R Under development (unstable) (2011-08-26 r56801) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 loaded via a namespace (and not attached): [1] grid_2.14.0 lattice_0.19-33 Matrix_0.9996875-3 nlme_3.1-102 [5] tools_2.14.0 -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
