[R] Defining S3-methods for S4-objects: cannot coerce type 'S4' to vector of type 'integer'

[Martin Morgan]

Søren Højsgaard wrote:
> In the 'doBy' package there is an esticon() function for calculating linear contrasts for various model types. I have defined an S3-method 'esticon.mer()' for 'mer' objects from the lme4 package. Building the package and invoking the method gives:
> 
>> esticon(fm1, c(1,1))
> Confidence interval ( WALD ) level = 0.95
> Error in as.integer(x) :
>   cannot coerce type 'S4' to vector of type 'integer'
> However, if is source the source code into R then I get what I expected:
>> esticon(fm1, c(1,1))
> Confidence interval ( WALD ) level = 0.95
>   beta0 Estimate Std.Error X2.value DF Pr(>|X^2|) Lower.CI Upper.CI
> 1     0 261.8724  6.786701 1488.888  1          0 248.5707 275.1741
> The problem above arises because esticon.mer() uses the variance-covariance matrix of the fixed effects (vcv below) in a calculation (cm is a matrix):
>   cm %*% vcv %*% t(cm). The result is:
> 
> 1 x 1 Matrix of class "dgeMatrix"
>          [,1]
> [1,] 46.05931
> - and taking diag() of that matrix causes the error above... However, things work fine if I use as.matrix() as is:  diag(as.matrix(cm %*% vcv %*% t(cm))).
> 
> - This tentatively suggests that there is no diag() method for 'dgeMatrix' objects (can hardly be the case!), but why then does my code work when it is sourced into R???
> 
> - Does anyone have an idea about what goes wrong? )

A little bit of a guess, but does doBy have a NAMESPACE? If so, then
perhaps the appropriate methods are not being imported
(iimportFrom(Matrix, diag) ??)

Martin

> - Is there anything 'special' that one must do in connection with defining S3-methods for S4 objects (e.g. in connection with package building)??
> 
> I use R 2.9.2 on windows XP. I am sure that such issues must have come up for others in the past but I've been unable to find questions/answers in the archives. Sorry if the topic has already been covered.
> 
> Regards
> Søren Højsgaard
> 
> 
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Martin Morgan
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