## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment  = "#>",
  message  = FALSE,
  warning  = FALSE
)
has_survival <- requireNamespace("survival", quietly = TRUE)

## -----------------------------------------------------------------------------
library(mmbcv)

data("msdat3")
dim(msdat3)
length(unique(msdat3$id))
length(unique(msdat3$clus_id))
table(msdat3$event)

## -----------------------------------------------------------------------------
with(msdat3, table(from, to))

## -----------------------------------------------------------------------------
library(survival)

fit <- coxph(
  list(
    Surv(Tstart, Tstop, event) ~ 1,
    state("(s0)"):state("S1") + state("S1"):state("S2") + state("S2"):state("S3") ~
      Z + X,
    state("(s0)"):state("D") + state("S1"):state("D") + state("S2"):state("D") +
      state("S3"):state("D") ~ (Z + X)/common
  ),
  data = msdat3,
  id = id,
  ties = "breslow",
  timefix = FALSE
)

fit

## -----------------------------------------------------------------------------
out <- MMBCV(
  fit, msdat3,
  StartTime = Tstart,
  StopTime  = Tstop,
  ClusterID = clus_id,
  SubjectID = id,
  Event     = event,
  tie       = "breslow",
  details   = FALSE
)

names(out)

## -----------------------------------------------------------------------------
Vlist <- out[c("robust","varMR","varMD","varMDMR","varFG","varFGMR","varKC","varKCMR","varMBN","varMBNMR")]
SE <- sapply(Vlist, function(V) sqrt(diag(V)))
SE

## -----------------------------------------------------------------------------
out_efron <- MMBCV(
  fit, msdat3,
  StartTime = Tstart,
  StopTime  = Tstop,
  ClusterID = clus_id,
  SubjectID = id,
  Event     = event,
  tie       = "efron",
  details   = FALSE
)

sqrt(diag(out_efron$robust))