With the following code
library(lme4)
data(cbpp)
testprofile <- function(herd,incidence,size,period) {
thedata <- data.frame(herd,incidence,size,period)
gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
data = thedata, family = binomial)
pr4 <- profile(gm1)
}
testprofile(cbpp$incidence,cbpp$incidence,cbpp$size,cbpp$period)
I get the error in profile " Error: 'data' not found, but variables found
in environment of formula: try specifying 'formula' as a formula rather
than a string in the original model"
I have tried with as.formula for the formula. The profile and glmer work
fine when they are called outside the function.
*Ken Beath*
Lecturer
Statistics Department
MACQUARIE UNIVERSITY NSW 2109, Australia
Phone: +61 (0)2 9850 8516
Building E4A, room 526
http://stat.mq.edu.au/our_staff/staff_-_alphabetical/staff/beath,_ken/
CRICOS Provider No 00002J
This message is intended for the addressee named and may...{{dropped:9}}
It works with replacing
thedata <- data.frame(herd,incidence,size,period)
with
thedata <<- data.frame(herd,incidence,size,period)
so it seems that when searching for thedata, glmer searches in the
parent environnement of testprofile() and not in the local
environnement of testprofile().
I guess it has to do with the line
glmod <- eval(mc, parent.frame(1L))
but my knowledge stops here...
Hope that will help as a workaround until developpers find a fix for
that...
On Mon, Sep 15, 2014 at 02:21:37PM +1000, Ken Beath wrote:
? With the following code
?
? library(lme4)
? data(cbpp)
?
? testprofile <- function(herd,incidence,size,period) {
? thedata <- data.frame(herd,incidence,size,period)
? gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
? data = thedata, family = binomial)
? pr4 <- profile(gm1)
? }
?
? testprofile(cbpp$incidence,cbpp$incidence,cbpp$size,cbpp$period)
?
? I get the error in profile " Error: 'data' not found, but variables found
? in environment of formula: try specifying 'formula' as a formula rather
? than a string in the original model"
?
? I have tried with as.formula for the formula. The profile and glmer work
? fine when they are called outside the function.
? --
?
? *Ken Beath*
? Lecturer
? Statistics Department
? MACQUARIE UNIVERSITY NSW 2109, Australia
?
? Phone: +61 (0)2 9850 8516
?
? Building E4A, room 526
? http://stat.mq.edu.au/our_staff/staff_-_alphabetical/staff/beath,_ken/
?
? CRICOS Provider No 00002J
? This message is intended for the addressee named and may...{{dropped:9}}
?
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