[Rd] Problem with contrasts bug fix?

[Murray Efford]

Thanks for your comprehensive explanation. Recent changes exposed errors in my code (and understanding!).
Murray

________________________________________
From: Sebastian Meyer <seb.meyer using fau.de>
Sent: 30 June 2022 20:19
To: Murray Efford
Cc: r-devel using r-project.org
Subject: Re: [Rd] Problem with contrasts bug fix?

For reference: this is about
<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbugs.r-project.org%2Fshow_bug.cgi%3Fid%3D17616&data=05%7C01%7Cmurray.efford%40otago.ac.nz%7Cad75da3bbad346a7d0c108da5a715362%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637921740057400452%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=XOLVFd9sZKQKebLOj%2BiIN%2FmNnvLNSNKdzakHHZXX2O4%3D&reserved=0>.

The problem with your 'contr.none' example is that it is not a proper
contrasts function (and has never been). ?contrasts says

>      Suitable
>      functions have a first argument which is the character vector of
>      levels, a named argument 'contrasts' (always called with
>      'contrasts = TRUE') and optionally a logical argument 'sparse'.

Your example function fails also in R 4.1.3 and 4.2.1:

> contr.none <- function(n) contrasts(factor(1:n), contrasts = FALSE)
> contrasts(CO2$Treatment) <- "contr.none"
> contrasts(CO2$Treatment)

Error in ctrfn(levels(x), contrasts = contrasts) :
   unused argument (contrasts = contrasts)

Even if we fix the missing argument:

> contr.none <- function(n, ...) contrasts(factor(1:n), contrasts = FALSE)
> contrasts(CO2$Treatment) <- "contr.none"
> contrasts(CO2$Treatment)

Error in 1:n : NA/NaN argument
In addition: Warning messages:
1: In 1:n : numerical expression has 2 elements: only the first used
2: In factor(1:n) : NAs introduced by coercion

What *did* work (inconsistently) was :

> contrasts(CO2$Treatment) <- contr.none
> contrasts(CO2$Treatment)

            1
nonchilled 1
chilled    0

It no longer does in R-devel as 'contr.none' is now called with the
factor *levels* (not nlevels) also in this case as documented.

Note that the argument name 'n' in the default contrast functions such
as contr.treatment() is a bit delicate as these support passing either
levels or nlevels.

Hope this helps.
Best regards,

        Sebastian Meyer


Am 30.06.22 um 00:27 schrieb Murray Efford:
> This worked previously but gives an error in R-devel (Windows today), triggering a warning to a package maintainer:
>
> contr.none <- function(n) contrasts(factor(1:n), contrasts = FALSE)
> lm(uptake~Treatment, CO2, contrasts=list(Treatment=contr.none))
>
> Error in 1:n : NA/NaN argument
> In addition: Warning messages:
> 1: In 1:n : numerical expression has 2 elements: only the first used
> 2: In factor(1:n) : NAs introduced by coercion
>
> ______________________________________________
> R-devel using r-project.org mailing list
> https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-devel&data=05%7C01%7Cmurray.efford%40otago.ac.nz%7Cad75da3bbad346a7d0c108da5a715362%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637921740057400452%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vVBIv0EsP%2FmbohM9menUPmhfMl%2BsrLkohHA3JLu5BDc%3D&reserved=0