## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)

## -----------------------------------------------------------------------------
# library(TwoTimeScales)

## -----------------------------------------------------------------------------
# plot(mod)

## ----original, fig = TRUE, dependson="load-mod", fig.width=6, fig.align='center', fig.height=9----
# par(mfrow = c(2,1),
#     font.main = 1)
# plot(mod,
#      plot_options = list(
#        rectangular_grid = TRUE,               # for grid of rectangles
#        original = TRUE,                       # for plot in (t,s)-plane
#        main = "Original plane - rectangular grid",
#        xlab = "Time since randomization",
#        ylab = "Time since recurrence"
#      ))
# plot(mod,
#      plot_options = list(
#        rectangular_grid = F,                # for grid of parallelograms
#        original = TRUE,                        # for plot in (t,s)-plane
#        main = "Original plane - grid of parallelograms",
#        xlab = "Time since randomization",
#        ylab = "Time since recurrence"
#      ))
# par(mfrow = c(1,1))

## -----------------------------------------------------------------------------
# plot(mod,
#      plot_grid = list(c(umin = 0, umax = 2300, du = 10),
#                       c(smin = 0, smax = 2730, du = 10)),
#      plot_options = list(n_shades = 100,
#                          main = "Denser plotting grid",
#                          xlab = "Time at recurrence",
#                          ylab = "Time since recurrence"))

## -----------------------------------------------------------------------------
# par(mfrow = c(2,1),
#     font.main = 1)
# plot(mod,
#      plot_options = list(
#        loghazard = TRUE,
#        main = "Log-hazard (u,s)",
#        xlab = "Time at recurrence",
#        ylab = "Time since recurrence"
#      ))
# plot(mod,
#      plot_options = list(
#        original = TRUE,
#        loghazard = TRUE,
#        main = "Log-hazard (t,s)",
#        xlab = "Time since randomization",
#        ylab = "Time since recurrence"
#      ))
# par(mfrow = c(1,1))

## -----------------------------------------------------------------------------
# par(mfrow = c(2,1),
#     font.main = 1)
# plot(mod,
#      plot_options = list(
#        log10hazard = TRUE,
#        main = "Log10-hazard (u,s)",
#        xlab = "Time at recurrence",
#        ylab = "Time since recurrence"
#      ))
# plot(mod,
#      plot_options = list(
#        original = TRUE,
#        log10hazard = TRUE,
#        main = "Log10-hazard (t,s)",
#        xlab = "Time since randomization",
#        ylab = "Time since recurrence"
#      ))
# par(mfrow = c(1,1))

## -----------------------------------------------------------------------------
# par(mfrow = c(2,1),
#     font.main = 1)
# plot(mod,
#      plot_options = list(cut_extrapolated = TRUE,
#                          tmax = 3214,
#                          main = "Cut extrapolated hazard",
#                          xlab = "Time at recurrence",
#                          ylab = "Time since recurrence"))
# 
# plot(mod,
#      plot_options = list(cut_extrapolated = TRUE,
#                          tmax = 3214,
#                          original = TRUE,
#                          main = "Cut extrapolated hazard",
#                          xlab = "Time since randomization",
#                          ylab = "Time since recurrence"))

## -----------------------------------------------------------------------------
# mycol <- function(nshades){
#   colorspace::sequential_hcl(n = nshades, "Blues 3")
# }
# plot(mod,
#      plot_options = list(col_palette = mycol,
#                          main = "New colors",
#                          xlab = "Time at recurrence",
#                          ylab = "Time since recurrence",
#                          contour_col = "pink",
#                          contour_nlev = 20))

## -----------------------------------------------------------------------------
# plot(mod,
#      which_plot = "SE",
#      plot_options = list(main = "Standard Errors of the hazard",
#                          xlab = "Time at recurrence",
#                          ylab = "Time since recurrence"))
# 
# plot(mod,
#      which_plot = "SE",
#      plot_options = list(
#        loghazard = TRUE,
#        main = "Standard Errors of the log-hazard",
#        xlab = "Time at recurrence",
#        ylab = "Time since recurrence"))
# 
# plot(mod,
#      which_plot = "SE",
#      plot_options = list(
#        log10hazard = TRUE,
#        main = "Standard Errors of the log10-hazard",
#        xlab = "Time at recurrence",
#        ylab = "Time since recurrence"))

## -----------------------------------------------------------------------------
# plot(mod,
#      which_plot = "slices",
#      where_slices = c(30, 60, 90, 180, 365, 1000, 2000),
#      direction = "u",
#      plot_options = list(main = "Slices of the hazard",
#                          xlab = "Time since recurrence",
#                          ylab = "Hazard"))
# legend("topright",
#        legend = c(30, 60, 90, 180, 365, 1000, 2000),
#        lty = 1,
#        col = grDevices::gray.colors(7))

## ----slices-s, fig = TRUE, chache = TRUE, dependson="load-mod", fig.width=6, fig.align='center', fig.height=4.5----
# plot(mod,
#      which_plot = "slices",
#      where_slices = c(30, 60, 90, 180, 365, 1000, 2000),
#      direction = "s",
#      plot_options = list(main = "Slices of the hazard",
#                          xlab = "Time since randomization",
#                          ylab = "Hazard"))
# legend("topright",
#        legend = c(30, 60, 90, 180, 365, 1000, 2000),
#        lty = 1,
#        col = grDevices::gray.colors(7))

## -----------------------------------------------------------------------------
# mycol2 <- function(nshades){
#   colorspace::sequential_hcl(n = nshades, "PurpOr")
# }
# plot(mod,
#      which_plot = "survival",
#      plot_options = list(col_palette = mycol2,
#                          main = "Survival function",
#                          xlab = "Time at recurrence",
#                          ylab = "Time since recurrence",
#                         contour_nlev = 20))
# 
# plot(mod,
#      which_plot = "survival",
#      where_slices = c(30, 60, 90, 180, 365, 1000, 2000),
#      direction = "u",
#      plot_options = list(
#                          surv_slices = TRUE,
#                          main = "Slices of the survival function",
#                          xlab = "Time since randomization",
#                          ylab = "Survival"))
# legend(x = 3000, y = .9,
#        xpd = TRUE,
#        inset = c(-0.3,0),
#        legend = c(30, 60, 90, 180, 365, 1000, 2000),
#        lty = 1,
#        lwd = 2,
#        bty = "n",
#        title = "Time of\n recurrence",
#        col = grDevices::gray.colors(7))
# 

## -----------------------------------------------------------------------------
# mycol3 <- function(nshades){
#   colorspace::sequential_hcl(n = nshades, "BluGrn")
# }
# plot(mod,
#      which_plot = "cumhaz",
#      plot_options = list(col_palette = mycol3,
#                          main = "Cumulative hazard",
#                          xlab = "Time at recurrence",
#                          ylab = "Time since recurrence",
#                          contour_nlev = 20))
# 
# plot(mod,
#      which_plot = "cumhaz",
#      where_slices = c(30, 60, 90, 180, 365, 1000, 2000),
#      direction = "u",
#      plot_options = list(
#                          cumhaz_slices = TRUE,
#                          main = "Slices of the cumulative hazard",
#                          xlab = "Time since randomization",
#                          ylab = "Cumulative hazard"))
# legend(x = 3000, y = 3.5,
#        xpd = TRUE,
#        inset = c(-0.3,0),
#        legend = c(30, 60, 90, 180, 365, 1000, 2000),
#        lty = 1,
#        lwd = 2,
#        bty = "n",
#        title = "Time of\n recurrence",
#        col = grDevices::gray.colors(7))