Basic Markov model in R

library("msm")
result4$user_cumcnt <- as.integer(result4$user_cumcnt)
result4$user_cnt <- as.integer(result4$user_cnt)
basic <- data.frame(result4[result4$user_cnt<=60, c(1,5,15,18)])

raw <- statetable.msm(category, userid, data = basic)
write.csv(raw, file= "raw_state.csv")

tmp <- melt(raw)
tmp$to <- as.integer(tmp$to)

tmp2<-cbind(1:23,levels(basic$category))
write.csv(tmp, "data.csv")
write.csv(tmp2, "junk.csv")

#add censor state;
tmp1 <- ddply(basic, .(userid), function(x) data.frame(user_cumcnt = max(x$user_cumcnt)+1))
tmp2 <- unique(basic[,c(1,4)])
tmp3 <- merge(tmp1,tmp2, by = "userid")
tmp4 <- data.frame(tmp3, rep("End", length(tmp1[,1])))
names(tmp4)[4] <- "category"
tmp5 <- data.frame(rbind(basic, tmp4))
basic <- tmp5[order(tmp5$userid, tmp5$user_cumcnt), ]

raw <- ifelse(raw>0, .09, 0)
diag(raw) <- .8
raw <- cbind(raw, rep(0,23))
raw <- rbind(raw, rep(0,24))
dimnames(raw)[[1]][24] <- "24"
dimnames(raw)[[2]][24] <- "End"
twoway4.q <- raw
twoway4.q <- matrix(rep(1, 24*24), nrow=24)
diag(twoway4.q) <- 0
twoway4.q[,24] <- 1
twoway4.q[24,] <- 0

basic$category <- as.integer(basic$category)

Sys.time()
visits.msm <- msm(category ~ user_cumcnt, subject = userid, data = basic, qmatrix = twoway4.q, death = 24)
Sys.time()