Using objects within functions in formulas
On Jan 9, 2013, at 8:53 AM, Aidan MacNamara wrote:
Dear all,
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
Generally regression functions in R will be expecting to get one
'data' argument and build formulas using column names from that object.
test1 <- function(x2, y2, w2) {
w3 <- cbind(w2, x2, x2)
print(str(w3))
form = as.formula(paste("y2 ~ x2 +" ,paste("(1|", names(w2), ")",
collapse=" + ", sep="")))
m1 = glmer(form, data=w3); print(summary(m1))
return(m1)
}
model1 = test1(x2=x1, y2=y1, w2=w1)
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
David Winsemius, MD Alameda, CA, USA