I've been going through the manual of the R
msm package for multi-state Markov models and have a question regarding how the default intensities are reported. The code below is taken from the documentation:
twoway4.q <- rbind( c(0, 0.25, 0, 0.25), c(0.166, 0, 0.166, 0.166), c(0, 0.25, 0, 0.25), c(0, 0, 0, 0) ) cavsex.msm <- msm::msm( state ~ years, subject=PTNUM, data = msm::cav, qmatrix = twoway4.q, death = 4, covariates = ~ sex)
Now, I've defined
intens1 <- msm::qmatrix.msm(cavsex.msm) intens2 <- msm::qmatrix.msm(cavsex.msm, covariates = list(sex = mean(msm::cav$sex)))
The default value of the
covariates parameter of the
msm::qmatrix.msm function is 'mean'. Indeed,
msm::qmatrix.msm(cavsex.msm, covariates = 'mean') gives the same response as
intens1; 'mean' here is defined as 'denoting the means of the covariates in the data'.
The question: why are
intens2 different? The latter pre-calculates the mean of the sex covariate and passes it to the function, but I would think the responses should be the same.