Re: [Rd] long-standing documentation bug in ?anova.lme
Silence on this so far? Trying here one more time, otherwise I'll submit it as a bug report ... cheers Ben Bolker On 2019-01-17 12:32 p.m., Ben Bolker wrote: > tl;dr anova.lme() claims to provide sums of squares, but it doesn't. And > some names are misspelled in ?lme. I can submit all this stuff as a bug > report if that's preferred. > > ?anova.lme says: > > When only one fitted model object is present, a data frame with > the sums of squares, numerator degrees of freedom, denominator > degrees of freedom, F-values, and P-values > > The output of > > fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age > anova(fm1) > > gives columns > > numDF denDF F-value p-value > > -- i.e. the sums of squares aren't there! (For fairly good reasons; lme > doesn't actually compute them internally, and it might not always be > straightforward to compute them, for more complex models. They would > mostly be useful for comparison with simpler, method-of-moments based > approaches like aov()). Federico Calboli pointed this out on r-help in > 2004: https://stat.ethz.ch/pipermail/r-help/2004-May/051444.html > > > Two more points: > > * the last sentence of the Description might need one fewer comma > [after "statistic"] or one more [after "p-value"]. > * in ?lme, Littell's name is misspelled at least twice and Reinsel's > at least once. > > Is there a publicly accessible SVN server for recommended packages (in > general) and nlme (in particular) anywhere? > > cheers > Ben Bolker > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Request: make `var` a generic
Hi all,
I am running into problems using `summary.lm` as calling `var` on a `units`
object does not retain the `units` attribute.
The units package addresses this issue for `mean` by implementing
`mean.units`:
units:::mean.units
function (x, ...)
{
.as.units(NextMethod(), units(x))
}
This is, however, not possible for `var` (as it's not a generic), which
breaks `summary.lm`:
```
library(units)
#> udunits system database from C:/R/Library/3.5/units/share/udunits
iris$Sepal.Length <- set_units(iris$Sepal.Length, "cm")
summary(lm(Sepal.Length ~ Sepal.Width,
data = iris))
#> Error in Ops.units(mean(f)^2, var(f)): both operands of the expression
should be "units" objects
```
Created on 2019-01-21 by the [reprex package](https://reprex.tidyverse.org)
(v0.2.1.9000)
Apologies if `stats` package emails shouldn't go here.
Cheers,
Kenny
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Re: [Rd] Request: make `var` a generic
Hi Kenny,
yes, there's only so much you can do with S3 methods penetrating other
packages' code; Iñaki discusses this in the blog about the r-quantities
project found at:
https://www.r-spatial.org/r/2018/08/31/quantities-final.html#fitting-linear-models-with-quantities
I'm not sure whether making "var" a generic would not shift the problem
to the next function not being generic, you could experiment with that.
On 1/20/19 6:39 PM, Kenny Bell wrote:
> Hi all,
>
> I am running into problems using `summary.lm` as calling `var` on a `units`
> object does not retain the `units` attribute.
>
> The units package addresses this issue for `mean` by implementing
> `mean.units`:
>
> units:::mean.units
> function (x, ...)
> {
> .as.units(NextMethod(), units(x))
> }
>
> This is, however, not possible for `var` (as it's not a generic), which
> breaks `summary.lm`:
>
> ```
> library(units)
> #> udunits system database from C:/R/Library/3.5/units/share/udunits
> iris$Sepal.Length <- set_units(iris$Sepal.Length, "cm")
>
> summary(lm(Sepal.Length ~ Sepal.Width,
>data = iris))
> #> Error in Ops.units(mean(f)^2, var(f)): both operands of the expression
> should be "units" objects
> ```
>
> Created on 2019-01-21 by the [reprex package](https://reprex.tidyverse.org)
> (v0.2.1.9000)
>
> Apologies if `stats` package emails shouldn't go here.
>
> Cheers,
> Kenny
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
Edzer Pebesma
Institute for Geoinformatics
Heisenbergstrasse 2, 48151 Muenster, Germany
Phone: +49 251 8333081
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