glmulti not working in for-loop - r

Question

I'm having trouble writing a for loop function where I ask gmulti to find the best model. I have the following example data set:
dput(Data)
structure(list(Studbook.ID = structure(c(16L, 16L, 16L, 16L,
16L, 16L, 16L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L,
17L, 17L, 17L, 17L, 30L, 30L, 30L), .Label = c("230", "298",
"308", "329", "357", "358", "374", "382", "385", "394", "397",
"399", "404", "413", "414", "418", "432", "433", "434", "437",
"439", "444", "446", "455", "458", "460", "473", "475", "476",
"477", "478", "492", "495", "496", "499", "503"), class = "factor"),
Season = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,
2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L), .Label = c("Breeding", "Nonbreeding"), class = "factor"),
Year = c(1999L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L,
2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L,
2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L,
2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L,
2000L, 2000L, 2000L, 2000L, 2000L, 2000L), Age.Class = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L), .Label = c("Adult",
"Sub-Adult"), class = "factor"), Sex = structure(c(1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("Female", "Male"
), class = "factor"), Captive_Wild = structure(c(2L, 2L,
2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("Captive", "Wild"
), class = "factor"), C.SA.F = c(0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L), C.HA.F = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L), W.MW.F = c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L,
0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L
), W.MW.DUR = c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 0L,
1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L),
C.CHEW.F = c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 1L, 0L,
1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L)), .Names =c("Studbook.ID",
"Season", "Year", "Age.Class", "Sex", "Captive_Wild", "C.SA.F",
"C.HA.F", "W.MW.F", "W.MW.DUR", "C.CHEW.F"), row.names = c(NA,
40L), class = "data.frame")
Code for my total loop is:
#lmer wrapper for glmulti function
lmer.glmulti <- function (formula, data, family=binomial, random, ...) {
lmer(paste(deparse(formula), random), data = data,...)
}
#make a dependent variable list for loop
dep_list<-colnames(Bamboo)
dep_list<-dep_list[-c(1:6)]
outglm<-c()
outdesc<-c()
#start loop coding
for (depend in dep_list){
y <-Bamboo[,depend]
#gmluti loop
#glm full model (substitute behavioral variables in place of 'depend')
glmmod<-y~Captive_Wild+Sex+Age.Class+Season
glm.glmulti<-glmulti(glmmod, random="+(1|Studbook.ID)", data=Bamboo, fitfunc = lmer.glmulti, family=binomial, level=2)
#make and print table for final best model
htmlreg(glm.glmulti#objects[[1]], file=paste(depend, ".doc", sep=""), caption = depend, caption.above = TRUE)
}
It's hanging up on the glmulti code where it gives me this error:
Error in model.frame.default(as.formula(paste(y, "~", paste(x, sep = "", :
variable lengths differ (found for 'Captive_Wild')
And traceback looks like:
8 model.frame.default(as.formula(paste(y, "~", paste(x, sep = "",
collapse = "+"), sep = "")), data = data)
7 model.frame(as.formula(paste(y, "~", paste(x, sep = "", collapse = "+"),
sep = "")), data = data)
6 glmulti(y = "y", data = Bamboo, level = 2, fitfunction = lmer.glmulti,
random = "+(1|Studbook.ID)", xr = c("Sex", "Season"), exclude = 1)
5 glmulti(y = "y", data = Bamboo, level = 2, fitfunction = lmer.glmulti,
random = "+(1|Studbook.ID)", xr = c("Sex", "Season"), exclude = 1)
4 eval(expr, envir, enclos)
3 eval(call)
2 glmulti(y ~ Sex + Season, random = "+(1|Studbook.ID)", data = Bamboo,
fitfunc = lmer.glmulti, level = 2)
1 glmulti(y ~ Sex + Season, random = "+(1|Studbook.ID)", data = Bamboo,
fitfunc = lmer.glmulti, level = 2)
I've also tried When I run the variables through by hand one-by-one the glmulti works just fine and when I remove Captive_Wild (which of course I don't want to do) it gives me the same error with Sex and ditto with Season. I've checked all variable lengths and they are the same.
This implies to me that glmulti is having a problem with the for loop somewhere but I'm not sure where. Can anyone suggest fixes? This is my first attempt at for loops so any and all help would be much appreciated!

Answer 1

After a little more fooling around I found two problems in the code:
1) lmer wrapper is old so need to call:
glmer.glmulti <- function (formula, data, family=binomial, random, ...) {
glmer(paste(deparse(formula), random), data = data,...)
}
and 2) using the alternate form of calling glmulti in the for-loop like so:
for (depend in dep_list){
glm.glmulti = glmulti(depend, c("Captive_Wild", "Sex", "Age.Class", "Season"), random="+(1|Studbook.ID)", data=Bamboo, fitfunc=lmer.glmulti, family=binomial, level=2)
#make and print table for final best model
htmlreg(glm.glmulti#objects[[1]], file=paste(depend, ".doc", sep=""), caption = depend, caption.above = TRUE)
}