[R] Using objects within functions in formulas
Ben Bolker
bbolker at gmail.com
Wed Jan 9 23:07:12 CET 2013
David Winsemius <dwinsemius <at> comcast.net> writes:
> On Jan 9, 2013, at 8:53 AM, Aidan MacNamara wrote:
> > I'm looking to create a formula within a function to pass to glmer()
> > and I'm having a problem that the following example will illustrate:
> >
> > library(lme4)
> > y1 = rnorm(10)
> > x1 = data.frame(x11=rnorm(10), x12=rnorm(10), x13=rnorm(10))
> > x1 = data.matrix(x1)
> > w1 = data.frame(w11=sample(1:3,10, replace=TRUE), w12=sample(1:3,10,
> > replace=TRUE), w13=sample(1:3,10, replace=TRUE))
> >
> > test1 <- function(x2, y2, w2) {
> >
> > print(str(w2))
> > form = as.formula(paste("y2 ~ x2 +" ,paste("(1|w2$", names(w2), ")",
> > collapse=" + ", sep="")))
> > m1 = glmer(form)
> > return(m1)
> > }
> >
> > model1 = test1(x2=x1, y2=y1, w2=w1)
> >
> > As can be seen from the print statement within the function, the
> > object "w2" is present and is a data frame. However, the following
> > error occurs:
> >
> > Error in is.factor(x) : object 'w2' not found
>
[snip David's solution to try to make gmane happy about the amount
of quoted material]
> > This can be rectified by making 'w2' global - defining it outside the
> > function. I know there are issues with defining formulas and
> > environment but I'm not sure why this problem is specific to 'w2' and
> > not the other objects passed to the function.
> >
> > Any help would be appreciated.
> >
> > Aidan MacNamara
> > EMBL-EBI
I haven't had a chance to look at this, but I will try to get to it.
It would help if you could post it on the "Issues" page of the lme4
github site, https://github.com/lme4/lme4/ . The bottom line is that
dealing appropriately with all the different possible ways to assign
and evaluate variables within formulas is trickier than I would like
it to be. To the best of my knowledge I have solved most of these
problems in the development version of lme4, but another test case
will be useful. As long as there is a reasonable workaround I'm unlikely
to put the effort into fixing the stable version of lme4 (sorry ...)
Follow-ups to r-sig-mixed-models at r-project.org or (preferably)
to the aforementioned "Issues" list.
Ben Bolker
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