[Rd] stats::getInitial: requires the model to live in the stats namespace or above

[Duncan Murdoch]

On 22/06/2022 12:44 p.m., Bill Dunlap wrote:
> Shouldn't the get()'s in stats:::getInitial.formula be looking in the
> environment of the formula, not the environment of getInitial.formula?

Yes, that definitely looks like the right environment to use.  Ivan, is 
that what you meant by "environment(object)"?

Duncan Murdoch

> 
> --- selfStart.R (revision 82512)
> +++ selfStart.R (working copy)
> @@ -78,13 +79,19 @@
>       switch (length(object),
>               stop("argument 'object' has an impossible length"),
>           {                              # one-sided formula
> -           func <- get(as.character(object[[2L]][[1L]]))
> +            if (!is.call(object[[2L]])) {
> +                stop("Right-hand side of formula is not a call")
> +            }
> +           func <- get(as.character(object[[2L]][[1L]]), mode="function",
> envir=environment(object))
>              getInitial(func, data,
>                         mCall = as.list(match.call(func, call =
> object[[2L]])),
>                          ...)
>           },
>           {                              # two-sided formula
> -           func <- get(as.character(object[[3L]][[1L]]))
> +            if (!is.call(object[[3L]])) {
> +                stop("Right-hand side of formula is not a call")
> +            }
> +           func <- get(as.character(object[[3L]][[1L]]), mode="function",
> envir=environment(object))
>              getInitial(func, data,
>                         mCall = as.list(match.call(func, call =
> object[[3L]])),
>                         LHS = object[[2L]], ...)
> 
> -Bill
> 
> 
> On Wed, Jun 22, 2022 at 8:25 AM Ivan Krylov <krylov.r00t using gmail.com> wrote:
> 
>> Hello R-devel,
>>
>> Here's a corner case I've stumbled upon recently:
>>
>> local({
>>          # Originally this was a package namespace, but a local
>>          # environment also leads to failure
>>          stopifnot(!identical(environment(), globalenv()))
>>
>>          # Make a self-starting model inside this private environment...
>>          SSlinear <- selfStart(
>>                  ~ a * x + b,
>>                  function(mCall, data, LHS, ...) {
>>                          xy <- sortedXyData(mCall[['x']], LHS, data)
>>                          setNames(
>>                                  coef(lm(y ~ x, xy)),
>>                                  mCall[c('b', 'a')]
>>                          )
>>                  },
>>                  c('a', 'b')
>>          )
>>
>>          # ...and try to use it
>>          x <- 1:100
>>          y <- 100 + 5 * x + rnorm(length(x), sd = 10)
>>          nls(y ~ SSlinear(x, a, b))
>>          # error in get('SSlinear'): object not found
>> })
>>
>> As a workaround, I'll just provide the starting values manually,
>> but should this work?
>>
>> As implemented [1], getInitial requires the model object to live in the
>> stats package namespace or any of its parents, which eventually include
>> the global environment and the attached packages, but not the private
>> namespaces of the packages or any other local environments. This
>> results from the fact that getInitial() uses plain get() in order to
>> resolve the symbol for the self-starting model, and get() defaults to
>> the current environment, which leads a chain of stats -> imports:stats
>> -> base -> global environment -> attached packages.
>>
>> It seems easy to suggest get(., envir = environment(object)) as a fix,
>> which would be able to access anything available at the time of
>> creation of the formula. On the other hand, it would break the case
>> when the stats package is not attached to the global environment or the
>> formula environment, which currently works.
>>
>> --
>> Best regards,
>> Ivan
>>
>> [1]
>>
>> https://github.com/r-devel/r-svn/blob/d43497cbc927e632c6f597fa23001c3f31d4cae6/src/library/stats/R/selfStart.R#L81-L87
>>
>> ______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
> 
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