[R-sig-ME] corSymm, nlme issue

[Douglas Bates]

On Wed, Aug 19, 2009 at 1:29 PM, Afshartous,
David<DAfshartous at med.miami.edu> wrote:

> All,

> In the course of investigating yesterday's post by Fabian Mollet ([R-sig-ME]
> weighting nlme and multivariate outcomes), I've noticed an issue with
> corSymm. I am getting the error message below even for identical commands
> used from Pinheiro & Bates (p.235).  Perhaps there was a discussion on this
> previously but I didn't see anything in the archives.

This is an issue of long standing in the nlme package.  In S and
S-PLUS we could define a generic function "initialize".  In R that
name is overridden in the methods package and redefining it would
break a lot of code (possibly not now that there are namespaces but we
didn't have namespaces at the time that nlme was ported to R).  For R
the name was changed to Initialize

>> sessionInfo()
> R version 2.9.1 (2009-06-26)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>> library("nlme")
>> cs1Symm = corSymm(value = c(.2, .1, -.1, 0, .2, 0), form = ~ 1 | Subject)
>> cs1Symm = initialize(cs1Symm, data = Orthodont)
> Error in getClass(Class) :
>  c("\"corSymm\" is not a defined class", "\"corStruct\" is not a defined
> class")
> In addition: Warning message:
> In if (!is.na(match(Class, .BasicClasses))) return(newBasic(Class,  :
>  the condition has length > 1 and only the first element will be used
>
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