I am trying to use the MSM R-package to estimate a continuous-time hidden Markov model. I do not know why my code does not show the estimates and confidence intervals for the transition intensities and the hidden Markov model parameters when I print the msm object.
I am attaching the data file and the code I am using. I am brand new to HMM. Any help are sincerely appreciated!
Data: https://drive.google.com/file/d/1qirk7fpCmFvQ6seI3iXKJl-M9ppd50vr/view?usp=sharing
library (tidyLPA)
library (dplyr)
three.q<-rbind(0.3,0.2,0.1),c(0.25,0.5,0.25),c(0.1,0.5,0.25))
hmodel1<-list(hmmNorm(mean = 0.5, sd=0.5),hmmNorm(mean = 20.8, sd=25.1),hmmNorm(mean = 304.9, sd=203.3))
msm<-msm(Y~Day, subject=ID,data=HMMDatav0,qmatrix=three.q,hmodel =hmodel1,
hcovariates = list (~X, ~X, ~X), method="CG",
fixedpars=TRUE, control=list(fnscale=4000))
msm
sojourn.msm(msm,ci="bootstrap",cl=0.95, B=1000)