fitTMB {glmmTMB} | R Documentation |
Optimize TMB models and package results, modularly
Description
These functions (called internally by glmmTMB
) perform
the actual model optimization, after all of the appropriate structures
have been set up (fitTMB
), and finalize the model after
optimization (finalizeTMB
). It can be useful to run glmmTMB
with
doFit=FALSE
, adjust the components as required, and then
finish the fitting process with fitTMB
(however, it is the
user's responsibility to make sure that any modifications
create an internally consistent final fitted object).
Usage
fitTMB(TMBStruc, doOptim = TRUE)
finalizeTMB(TMBStruc, obj, fit, h = NULL, data.tmb.old = NULL)
Arguments
TMBStruc |
a list containing lots of stuff ... |
doOptim |
logical; do optimization? If FALSE, return TMB object |
obj |
object created by |
fit |
a fitted object returned from |
h |
Hessian matrix for fit, if computed in previous step |
data.tmb.old |
stored TMB data, if computed in previous step |
Examples
## regular (non-modular) model fit
m0 <- glmmTMB(count ~ mined + (1|site),
family=poisson, data=Salamanders)
## construct model structures
m1 <- update(m0, doFit=FALSE)
names(m0)
m2 <- fitTMB(m1, doOptim = FALSE)
## could modify the components of m1$env$data at this point ...
## rebuild TMB structure (*may* be necessary)
m2 <- with(m2$env,
TMB::MakeADFun(data,
parameters,
map = map,
random = random,
silent = silent,
DLL = "glmmTMB"))
m3 <- with(m2, nlminb(par, objective = fn, gr = gr))
m4 <- finalizeTMB(m1, m2, m3)