[Rd] methods() not listing some S3 plot methods...?

From: Gavin Simpson <gavin.simpson_at_ucl.ac.uk>
Date: Fri, 26 Aug 2011 12:44:25 +0100


ink1">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. 430qlink2"></a><a name="0430qlink2">ame="0430qlink2">>name="0430qlink2">a> name="0430qlink2"></a><a name="0430qlink2">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 link3"></a><a name="0430qlink3">ame="0430qlink3">>name="0430qlink3">a> name="0430qlink3"></a><a name="0430qlink3">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

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

-- 
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 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
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Received on Fri 26 Aug 2011 - 11:49:39 GMT

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