Charles C. Berry wrote:
> On Tue, 22 Apr 2008, Gad Abraham wrote:
>
>> Charles C. Berry wrote:
>>> On Sat, 19 Apr 2008, Gad Abraham wrote:
>>>
>>>> Charles C. Berry wrote:
>>>>> On Fri, 18 Apr 2008, Gad Abraham wrote:
>>>>>
>>>>>> Frank E Harrell Jr wrote:
>>>>>>> Gad Abraham wrote:
>>>>>>>> Hi,
>>>>>>>>>>> Design isn't strictly an R base package, but maybe
>>>>> someone can > > > explain
>>>>>>>> the following.
>>>>>>>>>>> When lrm is called within a function, it can't find the
>>>>> dataset dd:
>>>>>>>>>>>> library(Design)
>>>>>>>>> age <- rnorm(30, 50, 10)
>>>>>>>>> cholesterol <- rnorm(30, 200, 25)
>>>>>>>>> ch <- cut2(cholesterol, g=5, levels.mean=TRUE)
>>>>>>>>> fit <- function(ch, age)
>>>>>>>> + {
>>>>>>>> + d <- data.frame(ch, age)
>>>>>>>> + dd <- datadist(d)
>>>>>>>> + options(datadist="dd")
>>>>>>>> + lrm(ch ~ age, data=d, x=TRUE, y=TRUE)
>>>>>>>> + }
>>>>>>>>> fit(ch, age)
>>>>>>>> Error in Design(eval(m, sys.parent())) :
>>>>>>>> dataset dd not found for options(datadist=)
>>>>>>>>>>> It works outside a function:
>>>>>>>>> d <- data.frame(ch, age)
>>>>>>>>> dd <- datadist(d)
>>>>>>>>> options(datadist="dd")
>>>>>>>>> l <- lrm(ch ~ age, data=d, x=TRUE, y=TRUE)
>>>>>>>>>>>>>> Thanks,
>>>>>>>> Gad
>>>>>>>>> My guess is that you'll need to put dd in the global
>>>>> environment, not > > in
>>>>>>> fit's environment. At any rate it is inefficient to call
>>>>> datadist > > every
>>>>>>> time. Why not call it once for the whole data frame containing
>>>>> all > > the
>>>>>>> predictors, at the top of the program?
>>>>>>> This is just sample code, in practice the datadist will be
>>>>> different for
>>>>>> each invocation of the function.
>>>>>>> I think it boils down to this behaviour, which I don't
>>>>> understand ---
>>>>>> although ls can see x in the parent of f2, eval cannot:
>>>>>
>>>>>
>>>>> That is because (from ?eval):
>>>>>
>>>>> "Objects to be evaluated can be of types call or expression or name
>>>>> (when
>>>>> the name is looked up in the current scope and its binding is
>>>>> evaluated)..."
>>>>>
>>>>> And 'x' is of type name (aka 'symbol').
>>>>>
>>>>> So eval never gets around to looking in 'p', because it never
>>>>> succeeded in
>>>>> looking up 'x' and evaluating its binding in the current scope.
>>>>>
>>>>> What you probably want is
>>>>>
>>>>> b <- evalq( x, envir=p)
>>>>>
>>>>
>>>> Thanks, that solves the problem with this sample code, but not with
>>>> the Design::lrm function, because there are several more layers of
>>>> evaluation there.
>>>>
>>>> I can get around that with the ugly hack of setting a global NULL
>>>> datadist and assigning to it with "<<-" within the fit function every
>>>> time, so it's always visible to Design. But it's still an ugly hack :)
>>>
>>> Well, the ultimate problem is here
>>>
>>> <from Design>
>>> XDATADIST <- .Options$datadist
>>> if (length(XDATADIST)) {
>>> if (!exists(XDATADIST))
>>> stop(paste("dataset", XDATADIST, "not found for
>>> options(datadist=)"))
>>> ...
>>>
>>> exists() mandates that there be an object as.name(XDATADIST) in the
>>> search() list. And a further eval(as.name(XDATADIST)) also requires
>>> this.
>>>
>>> Another way to do make your function work is to use this in it:
>>>
>>> on.exit( detach("design.options") )
>>> attach(list(), name= "design.options" )
>>> d <- data.frame(ch, age)
>>> assign('dd', datadist(d), pos='design.options')
>>>
>>> Admittedly still a hack, but it keeps your function from messing around
>>> with .GlobalEnv, and unless you are willing to rewrite lrm and Design,
>>> this is what you are stuck with.
>>
>>
>> I've changed the original example to:
>>
>> library(Design)
>> attach(list(), name="design.options")
>> on.exit(detach("design.options"))
>> age <- rnorm(30, 50, 10)
>> cholesterol <- rnorm(30, 200, 25)
>> ch <- cut2(cholesterol, g=5, levels.mean=TRUE)
>>
>> fit <- function(ch, age) [
>> d <- data.frame(ch, age)
>> assign('dd', datadist(d), pos='design.options')
>> options(datadist="dd")
>> lrm(ch ~ age, data=d, x=TRUE, y=TRUE)
>> }
>>
>> fit(ch, age)
>>
>>
>> This works when I paste it into the R console, but not when I source()
>> the script:
>>
>>
>> > library(Design)
>> Loading required package: Hmisc
>> ...
>> > attach(list(), name="design.options")
>> > on.exit(detach("design.options"))
>> > age <- rnorm(30, 50, 10)
>> > cholesterol <- rnorm(30, 200, 25)
>> > ch <- cut2(cholesterol, g=5, levels.mean=TRUE)
>> > fit <- function(ch, age)
>> + {
>> + d <- data.frame(ch, age)
>> + assign('dd', datadist(d), pos='design.options')
>> + options(datadist="dd")
>> + lrm .... [TRUNCATED]
>> > fit(ch, age)
>> Error in as.environment(pos) :
>> no item called "design.options" on the search list
>>
>> Or is that asking for too much? ;)
>
> Well, I did say to use that bit of code IN your function.
>
That nuance was lost on me. Thanks!
--
Gad Abraham
Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: [EMAIL PROTECTED]
web: http://www.csse.unimelb.edu.au/~gabraham
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