[R] Rare behaviour for nlme::reStruct example and question about ?lmeObject

[Iago]

Thank you Martin,


Regarding my question about `terms`, I meant the `terms` component of 
the `lme` output. For example, for

fm1 <- lme(distance ~ age, data = Orthodont)

I can see through str(fm1), the next:

$ terms       :Classes 'terms', 'formula'  language distance ~ age
   .. ..- attr(*, "variables")= language list(distance, age)
   .. ..- attr(*, "factors")= int [1:2, 1] 0 1
   .. .. ..- attr(*, "dimnames")=List of 2
   .. .. .. ..$ : chr [1:2] "distance" "age"
   .. .. .. ..$ : chr "age"
   .. ..- attr(*, "term.labels")= chr "age"
   .. ..- attr(*, "order")= int 1
   .. ..- attr(*, "intercept")= int 1
   .. ..- attr(*, "response")= int 1
   .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
   .. ..- attr(*, "predvars")= language list(distance, age)
   .. ..- attr(*, "dataClasses")= Named chr [1:2] "numeric" "numeric"
   .. .. ..- attr(*, "names")= chr [1:2] "distance" "age"

However, there is no paragraph for this component among those in 
?lmeObject (in the Value section) as there is for fixDF, apVar, call, 
etc.. If not needed, I assume the explanation would be that `terms` does 
not need to be included in a legitimate ´"lme"´ object'.


Kind regards,

Iago

On 17/11/2022 09:16, Martin Maechler wrote:
>>>>>> Andrew Simmons
>>>>>>      on Tue, 15 Nov 2022 18:01:55 -0500 writes:
>     > This seems to be a bug. I tried creating this function in the global
>     > environment:
>
>     > str.pdMat <- function (object, ...)
>     > {
>     >     if (nlme::isInitialized(object)) {
>     >         NextMethod()
>     >     }
>     >     else {
>     >         cat(" Uninitialized positive definite matrix structure of class ",
>     >             class(object)[1], ".\n", sep = "")
>     >     }
>     > }
>
> Thank you, Iago, for the question and Andrew for your proposal.
>
> Yes, I agree that something like the above -- which is derived from the
> print.pdMat method --  should be added to nlme and will do this
> myself.
>
>     > and the code you sent works:
>     >
>     > > library(nlme)
>     > > rs1 <- reStruct(list(Dog = ~day, Side = ~1), data = Pixel)
>     > > rs1
>     > Uninitialized random effects structure
>     > > str(rs1)
>     > List of 2
>     >  $ Side: Uninitialized positive definite matrix structure of class pdLogChol.
>     >  $ Dog : Uninitialized positive definite matrix structure of class pdLogChol.
>     >  - attr(*, "settings")= int [1:5] 0 1 0 4 4
>     >  - attr(*, "class")= chr "reStruct"
>
> In addition, Iago, asked
>
>     > > >     In addition to that I would like to ask if shouldn't be `terms`
>     > > >     documented in `?lmeObject`.
>
> I probably have misunderstood the question completely (?)
>
> I've now searched through ?lmeObject
> which was written under the assumption that the reader has
> already read (parts of) the  ?lme  help page.
>
> Now "terms" only appears in  ?lmeObject in this paragraph
>
>     fixDF: a list with components ‘X’ and ‘terms’ specifying the
>            denominator degrees of freedom for, respectively, t-tests for
>            the individual fixed effects and F-tests for the
>            fixed-effects terms in the models.
>
> and I don't think that there needs to be more explanation.
>
> (??)
>
> Martin
>
>