S3 and S4 clash
Dear Prof. Ripley:
Thanks for your help. I very much appreciate your great
generosity in both your substantive contributions to the code and
documentation for R and in responding to so many questions, helping to
make R what it is today.
In the real application that led to the toy example below, I had
defined
AIC.factanal <- function(object, ..., k=c(2, "BIC")){ ... }
1. If I understand your suggestion, I'd be better NOT defining an
"AIC.factanal" but instead define only "logLik.factanal" and let methods
dispatch go through "AIC.default" to "logLik.factanal". Is this correct?
2. Is it inappropriate to supply other optional values for an
argument in a generic function like this?
3. If it is OK to specify options for "k" like this, how would
you suggest I do it? Use the S4 standard?
Thanks again.
Spencer Graves
Prof Brian Ripley wrote:
I'd say that was pretty clearly a bug in stats4 (which as I recall was needed to get around the scoping awkwardnesses of S4). But could you not write a logLik method for your class? E.g.
logLik.bar <- function(object, ...) structure(pi, class="logLik", df=1) AIC(bar.tmp)
[1] -4.283185
library(stats4) AIC(bar.tmp)
[1] -4.283185 On Thu, 6 Dec 2007, Spencer Graves wrote:
Hello:
How can I work around the conflict between the S3 and S4
illustrated in the example below? I'm developing a package that
requires a function in 'stats4', but when 'stats4' is attached, it
breaks my AIC function. I could give my AIC function another name so it
no longer uses the generic dispatch, but I wonder if there is another
way.
Thanks,
Spencer Graves
################################
bar.tmp <- structure(1, class = "bar")
AIC.bar <- function(object, ..., k=2) {
3
}
AIC(bar.tmp)
[1] 3
library(stats4) AIC(bar.tmp)
Error in UseMethod("logLik") : no applicable method for "logLik"
detach("package:stats4")
AIC(bar.tmp)
[1] 3
objects()
[1] "AIC.bar" "bar.tmp"
sessionInfo()
R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;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] stats4_2.6.1
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