I've been trying to carry out model selection on a glmmtmb() object and subsetting the "best" models.
dredge() works as expected (but throws some convergence issues).
get.models() runs without errors or warnings but does not subset the suite of models produced by dredge(), rather returns all of the fitted models
After some digging i found this only occurs when there is one or more convergence issue in the models fit by dredge() (see minimum viable below).
Can anyone suggest either:
- a fix/work around to this issue
or
- whether this is actually a bug or some way to force users to ensure their full suite of models fits (I cant think of a reason for this but possibly just my ignorance!)
Many thanks!
Chris
Data available here
library(MuMIn)
library(glmmTMB)
############################################
### full model which fails to subset after dredge
full_mod_min <- glmmTMB(number_of_species ~
scale(Distance) +
scale(Bucket) +
played_cricket +
(1|Group_name),
data=mod_data,
family="nbinom2",
control=glmmTMBControl(optimizer=optim,
optArgs=list(method="BFGS")),
na.action = na.fail)
##then dredge across the full model. Convergence warnings for some models
dredged_models_min <- dredge(full_mod_min)
## 8 models fit by dredge
nrow(dredged_models_min)
## try subsetting, should return 3 but returns 8
length(get.models(dredged_models_min, subset = delta < 2))
############################################
### full model which can subset after dredge
## only difference between the two models is we replace
## `played_cricket` with `sex`
working_mod_min <- glmmTMB(number_of_species ~
scale(Distance) +
scale(Bucket) +
sex +
(1|Group_name),
data=mod_data,
family="nbinom2",
control=glmmTMBControl(optimizer=optim,
optArgs=list(method="BFGS")),
na.action = na.fail)
##then dredge across the full model
working_dredge <- dredge(working_mod_min)
## 8 models fit by dregde, 3 within delta 2 AIC
nrow(working_dredge)
## try subsetting - works, returns 3
length(get.models(working_dredge, subset = delta < 2))
Tried various error structures/types of predictor variable but only consistency is the failure to converge