Message-ID: <693264c8-669b-494e-8f1e-720e7f3224dc@gmail.com>
Date: 2024-12-23T17:29:19Z
From: Duncan Murdoch
Subject: [R-pkg-devel] Getting summary.glm to use Matrix::chol2inv
In-Reply-To: <CAKakjMezD_N0+UwgV62=OV1b1duVJbAjBNy=1tb7ipXQGRK_rQ@mail.gmail.com>
I think the only way to do this is to write your own summary.* method
for your objects. You should modify their class (e.g. to `c("glm2",
"glm")` so that your new summary method `summary.glm2` is called instead
of `summary.glm`.
Changing the search path wouldn't work. Search order from within a
package looks at locals, then imports, then the base package (where
chol2inv would be found), then the search list.
The source for the standard summary.glm function is available, e.g.
here:
https://github.com/wch/r-source/blob/cfda9838f261b1c77c5ac6a5b0deed88021a2156/src/library/stats/R/glm.R#L687-L773
. You can copy that into your package, then modify it to work with
Matrix. You should list "The R Core Team" as a copyright holder on that
file if you do this so you're not violating the R license.
Duncan Murdoch
On 2024-12-22 4:26 p.m., Mark Donoghoe wrote:
> Hi,
>
> I am trying to implement a new method for glm2 which allows the use of
> the Matrix package to work with large data.
>
> I have added Matrix to Suggests, and when the new method is requested,
> the following check is performed:
>
> if (!requireNamespace("Matrix", quietly = TRUE)) {
> stop("Package \"Matrix\" must be installed to use method =
> \"glm.fit2.Matrix\".",
> call. = FALSE)
> }
>
> This works fine. However, I would like the user to be able to use
> summary.glm on the fitted object x, and it effectively calls
> chol2inv(x$qr$qr[1:p,1:p]), which fails if x$qr$qr is not a (small m)
> matrix:
>
> Error in chol2inv(Qr$qr[p1, p1, drop = FALSE]) :
> 'a' must be a numeric matrix
>
> I can return the matrix version of x$qr$qr, but this can be quite
> large and ideally I would like to return the Matrix version, and have
> summary.glm automatically call the Matrix version of chol2inv.
>
> I imagine this would require changing the search path, which I
> understand is not recommended, but I am not even sure how to go about
> it, or if there is another solution that wouldn't require a custom
> version of summary.glm. I also tried attachNamespace in a similar code
> block when glm.fit2.Matrix is called, but that did not work.
>
> Thanks in advance for any suggestions.
>
> Mark
>
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