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? ;)
--
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
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
