warning creating an as.array method in a package
I found a solution to this problem, but don't understand why it was
necessary. In a clean workspace, I get:
> methods(as.array)
[1] as.array.default
> showMethods("as.array")
Function "as.array":
<not a generic function>
So, I just added the generic definition to my package, making with
warnings go away.
as.array <- function(x, ...)
UseMethod("as.array")
as.array.loddsratio <- function (x, log=x$log, ...)
drop(array(coef(x, log = log), dim = dim(x), dimnames=dimnames(x)))
Yet, help(as.array) says:
as.array is a generic function for coercing to arrays. The default
method does so by attaching a dim attribute to it. It also attaches
dimnames if x has names. Is this a documentation error?
> sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.11.1
>
On 12/9/2010 10:05 AM, Michael Friendly wrote:
I posted on this topic to r-help, but never got a sufficient answer, so I'm reposting here. [Env: R 2.11.1, Win Xp, using Eclipse/StatET] In a package I'm working on, I want to create as.matrix() and as.array() methods for a particular kind of object (log odds ratios). These are returned in a loddsratio object as the $coefficients component, a vector, but really reflect an underlying (R-1)x(C-1)xstrata array, whose attributes are contained in other components. These are all properly declared in the NAMESPACE as S3 methods, ... S3method(dim, loddsratio) S3method(dimnames, loddsratio) S3method(print, loddsratio) S3method(vcov, loddsratio) S3method(as.matrix, loddsratio) S3method(as.array, loddsratio) Yet, when I run R CMD check, R CMD build, etc. or even load the package, I get the warning,
> library(vcdExtra)
Loading required package: vcd Loading required package: MASS Loading required package: grid Loading required package: colorspace Loading required package: gnm Warning message: found an S4 version of ?as.array? so it has not been imported correctly
> showMethods("as.array")
Function: as.array (package base) x="ANY" x="Matrix" But as.array does show up as a method for my class:
> methods(class="loddsratio")
[1] as.array.loddsratio* as.data.frame.loddsratio* [3] as.matrix.loddsratio* coef.loddsratio* [5] confint.loddsratio* dim.loddsratio* [7] dimnames.loddsratio* print.loddsratio* [9] vcov.loddsratio* Non-visible functions are asterisked
>
Is there some work-around so I can have an S3 as.array() method in my package and avoid this warning?
Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Street Web: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA