shift=TRUE not working for confint.gam() about gratia HOT 5 OPEN

This issue is not present when I revert to gratia version 0.8.1

from gratia.

Hi,

I have also encountered this issue. I maintain a package that has a dependency on gratia (https://github.com/McGranahanLab/TcellExTRECT) besides the changing of the column names of confint.gam in 0.9.0 I am now getting different results compared to previous version. I have tested this and it is due to this issue of shift = TRUE not being functional within confint.gam from 0.9.0.

The code for confint.gam in gratia 0.8.2 included the following:

out[["est"]] <- ilink(out[["est"]] + const)
out[["lower"]] <- ilink(out[["lower"]] + const)
out[["upper"]] <- ilink(out[["upper"]] + const)

In gratia 0.9.0 this has changed to:

 out <- mutate(out, across(all_of(c(".estimate", ".lower_ci",
        ".upper_ci")), .fns = ilink))

With no reference to the const value and no shift in values even when shift = TRUE. This could be easily fixed if you just replaced the above with something similar to the old version:

out[[".estimate"]] <- ilink(out[[".estimate"]] + const)
out[[".lower_ci"]] <- ilink(out[[".lower_ci"]] + const)
out[[".upper_ci"]] <- ilink(out[[".upper_ci"]] + const)

from gratia.

Yeah, sorry @TIMAVID and @rbentham; I messed that up. And sorry @TIMAVID for not getting to this sooner, even to acknowledge it (it's been a very busy month at work).

The problem is not in the lines of code you mention @rbentham but here

As far as I can tell, the mutate() call is doing what it is supposed to do, namely transform the using either the inverse link function, a user-supplied function, or the identity function, depending on what's passed to transform. I'm testing a fix now.

@rbentham Is this causing you problems with a package on CRAN? If so I can expedite a patch release to CRAN.

from gratia.