Is there a way of extracting the functional form of the likelihood function that gets formed by the msm function in R?
How can I extract the likelihood function that gets formed in the example below? I want to try and implement my own version of the quasi-Newton maximisation algorithm to improve my understanding.
library(msm)
# look at transition counts
statetable.msm(state, PTNUM, data = cav)
# define transition intensity matrix
# 1's mean a transition can occur
# 0's mean a transition should not occur
# any number can be placed on the diagonal as R overwrites the diagonals
# prior to maximising
q <- rbind(
c(0, 1, 0, 1),
c(1, 0, 1, 1),
c(0, 1, 0, 1),
c(0, 0, 0, 0)
)
# fit msm to the data
# the fnscale rescales the likelihood to prevent overflow
msm.fit <- msm(state ~ years, PTNUM, data = cav, qmatrix = q, control=list(fnscale=4000))