## ---- SETTINGS-knitr, include=FALSE-------------------------------------------
stopifnot(require(knitr))
opts_chunk$set(
  comment=NA, 
  message = FALSE, 
  warning = FALSE, 
  eval = identical(Sys.getenv("NOT_CRAN"), "true"),
  dev = "png",
  dpi = 150,
  fig.asp = 0.618,
  fig.width = 5,
  out.width = "60%",
  fig.align = "center"
)

## ---- SETTINGS-gg, include=TRUE-----------------------------------------------
library(ggplot2)
library(bayesplot)
theme_set(bayesplot::theme_default())

## ----setup_jm, include=FALSE, message=FALSE-----------------------------------
knitr::opts_chunk$set(fig.width=10, fig.height=4)
library(rstanarm)

## ----traj_figure, echo=FALSE--------------------------------------------------
# Plot observed longitudinal trajectories for log serum bilirubin
ids <- c(25,31:33,36,38:40)
pbcLong_subset <- pbcLong[pbcLong$id %in% ids, ]
pbcLong_subset <- merge(pbcLong_subset, pbcSurv)
pbcLong_subset$Died <- factor(pbcLong_subset$death,
                              labels = c("No", "Yes"))
patient_labels <- paste("Patient", 1:8)
names(patient_labels) <- ids
ggplot() + 
  geom_line(aes(y = logBili, x = year, lty = Died), 
            data = pbcLong_subset) + 
  facet_wrap(~ id, ncol = 4, labeller = labeller(id = patient_labels)) +
  theme_bw() +
  ylab("Log serum bilirubin") +
  xlab("Time (years)")

## ----pbcLong------------------------------------------------------------------
head(pbcLong)

## ----pbcSurv------------------------------------------------------------------
head(pbcSurv)

## ----datasets_help, eval = FALSE----------------------------------------------
#  help("datasets", package = "rstanarm")

## ----univariate_fit, results = "hold", message = FALSE, warning = FALSE-------
library(rstanarm)
mod1 <- stan_jm(formulaLong = logBili ~ sex + trt + year + (year | id), 
                dataLong = pbcLong,
                formulaEvent = survival::Surv(futimeYears, death) ~ sex + trt, 
                dataEvent = pbcSurv,
                time_var = "year",
                chains = 1, refresh = 2000, seed = 12345)

## ----print, echo = FALSE------------------------------------------------------
alpha_mod1 <- as.data.frame(mod1)[["Assoc|Long1|etavalue"]]
alpha_median <- round(median(alpha_mod1), 3)
print(mod1)

## ----summary------------------------------------------------------------------
summary(mod1, probs = c(.025,.975))

## ----VarCorr------------------------------------------------------------------
as.data.frame(VarCorr(mod1))

## ----assoc_etaslope, eval = FALSE---------------------------------------------
#  mod2 <- stan_jm(formulaLong = logBili ~ sex + trt + year + (year | id),
#                  dataLong = pbcLong,
#                  formulaEvent = survival::Surv(futimeYears, death) ~ sex + trt,
#                  dataEvent = pbcSurv,
#                  assoc = c("etavalue", "etaslope"),
#                  time_var = "year",
#                  chains = 1, refresh = 2000, seed = 12345)

## ----fitmodel_mv_ev_ev, warning=FALSE, message=FALSE--------------------------
mod3 <- stan_jm(
    formulaLong = list(
        logBili ~ sex + trt + year + (year | id), 
        albumin ~ sex + trt + year + (year | id)),
    formulaEvent = survival::Surv(futimeYears, death) ~ sex + trt, 
    dataLong = pbcLong, dataEvent = pbcSurv,
    time_var = "year",
    chains = 1, refresh = 2000, seed = 12345)

## ----results_print------------------------------------------------------------
print(mod3)

## ----results_summary----------------------------------------------------------
summary(mod3, pars = "assoc")

## ----plots_872312-------------------------------------------------------------
p1 <- posterior_traj(mod3, m = 1, ids = 6:8)
pp1 <- plot(p1, plot_observed = TRUE)
pp1

## ----plots_555762-------------------------------------------------------------
p2 <- posterior_traj(mod3, m = 2, ids = 6:8)
pp2 <- plot(p2, plot_observed = TRUE)
pp2

## ----plots_65662--------------------------------------------------------------
p3 <- posterior_traj(mod3, m = 1, ids = 6:8, extrapolate = TRUE)
pp3 <- plot(p3, plot_observed = TRUE, vline = TRUE)
pp3

## ----plots_998889-------------------------------------------------------------
p4 <- posterior_traj(mod3, m = 2, ids = 6:8, extrapolate = TRUE)
pp4 <- plot(p4, plot_observed = TRUE, vline = TRUE)
pp4

## ----plots_23812--------------------------------------------------------------
p5 <- posterior_survfit(mod3, ids = 6:8)
pp5 <- plot(p5)
pp5

## ----plots_987321, fig.height=13----------------------------------------------
plot_stack_jm(yplot = list(pp3, pp4), survplot = pp5)

## ----newdata_23188------------------------------------------------------------
ndL <- pbcLong[pbcLong$id == 8, , drop = FALSE]
ndE <- pbcSurv[pbcSurv$id == 8, , drop = FALSE]
ndL$id <- paste0("new_patient")
ndE$id <- paste0("new_patient")

## ----plots_999333-------------------------------------------------------------
p6 <- posterior_traj(mod3, m = 1, 
                     newdataLong = ndL, 
                     newdataEvent = ndE,
                     last_time = "futimeYears")
pp6 <- plot(p6, plot_observed = TRUE, vline = TRUE)
pp6

## ----plots_122223-------------------------------------------------------------
p7 <- posterior_traj(mod3, m = 2, 
                     newdataLong = ndL, 
                     newdataEvent = ndE,
                     last_time = "futimeYears")
pp7 <- plot(p7, plot_observed = TRUE, vline = TRUE)
pp7

## ----plots_65401--------------------------------------------------------------
p8 <- posterior_survfit(mod3,
                        newdataLong = ndL, 
                        newdataEvent = ndE,
                        last_time = "futimeYears")
pp8 <- plot(p8)
pp8

## ----plots_0089231, fig.height=13---------------------------------------------
plot_stack_jm(yplot = list(pp6, pp7), survplot = pp8)

## ----b_pars_23123-------------------------------------------------------------
c(ranef(mod3)[["Long1"]][["id"]][8,], 
  ranef(mod3)[["Long2"]][["id"]][8,])

## ----b_pars_5436765-----------------------------------------------------------
colMeans(attr(p6, "b_new"))

## ----newdata_19213------------------------------------------------------------
ndL <- expand.grid(year = seq(0, 10, 1),
                   sex = c("m", "f"), 
                   trt = 0:1)
ndL$id <- rep(c("male_notrt", "female_notrt",
                "male_trt", "female_trt"), each = 11)
ndL <- ndL[, c(4,1,2,3)]
str(ndL)

## ----plot_traj_218391---------------------------------------------------------
p1 <- posterior_traj(mod3, m = 1, newdataLong = ndL, dynamic = FALSE)
plot(p1) + ggplot2::coord_cartesian(ylim = c(-10,15))

## ----fixef_2132---------------------------------------------------------------
fixef(mod3)$Long1

## ----ranef_5664---------------------------------------------------------------
VarCorr(mod3)

## ----standsurv----------------------------------------------------------------
p1 <- posterior_survfit(mod3, standardise = TRUE, times = 0)
head(p1) # data frame with standardised survival probabilities
plot(p1) # plot the standardised survival curve