csstd/time-dependent-comparison.R

library(tidyverse)

csstd      <- new.env()
no_tunnel  <- new.env()
tunnel9    <- new.env()
tunnel98   <- new.env()
phase_type <- new.env()

system.time(source("time-dependent-CSSTD.R",            echo = TRUE, local = csstd))
system.time(source("time-dependent-no-tunnel-states.R", echo = TRUE, local = no_tunnel))
system.time(source("time-dependent-9-tunnel-states.R",  echo = TRUE, local = tunnel9))
system.time(source("time-dependent-98-tunnel-states.R", echo = TRUE, local = tunnel98))
system.time(source("time-dependent-phase-type.R",       echo = TRUE, local = phase_type))

res <- 
  tibble(
    cycle               = csstd$cycles,
    diseased.csstd      = csstd$state_membership[, 2],
    diseased.no_tunnel  = no_tunnel$state_membership[, 2],
    diseased.tunnel9    = tunnel9$summarised_state_membership[, 2],
    diseased.tunnel98   = tunnel98$summarised_state_membership[, 2],
    diseased.phase_type = phase_type$summarised_state_membership[, 2],
    survival.csstd      = 1 - csstd$state_membership[, 3],
    survival.no_tunnel  = 1 - no_tunnel$state_membership[, 3],
    survival.tunnel9    = 1 - tunnel9$summarised_state_membership[, 3],
    survival.tunnel98   = 1 - tunnel98$summarised_state_membership[, 3],
    survival.phase_type = 1 - phase_type$summarised_state_membership[, 3]) %>%
    pivot_longer(cols = -cycle, names_to = c(".value", "method"), names_sep = "\\.") %>%
  left_join(
    tibble(
      method = c("csstd", "no_tunnel", "tunnel9", "tunnel98", "phase_type"),
      description = c("CSSTD", "No tunnel states", "Nine tunnel states", "98 tunnel states", "Phase-type")))

ggplot(res, aes(x = cycle, y = diseased, colour = description, linetype = description)) +
  geom_line() +
  labs(x = "Cycle", y = "Proportion of cohort in Diseased state", colour = NULL, linetype = NULL) +
  theme_bw()
ggsave("time-dependent-diseased.png", width = 15.92, height = 15.92 * 3/4, units = "cm", dpi = 600)

ggplot(res, aes(x = cycle, y = survival, colour = description, linetype = description)) +
  geom_line() +
  labs(x = "Cycle", y = "Proportion of cohort alive", colour = NULL, linetype = NULL) +
  theme_bw()
ggsave("time-dependent-survival.png", width = 15.92, height = 15.92 * 3/4, units = "cm", dpi = 600)