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

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

## -----------------------------------------------------------------------------
# dt2ts <- prepare_data(data = reccolon2ts,
#                       u = "timer",
#                       s_out = "timesr",
#                       events = "status",
#                       ds = 30, du = 30)

## -----------------------------------------------------------------------------
# mod1 <- fit2ts(data2ts = dt2ts,
#                Bbases_spec = list(bdeg = 3,
#                                   nseg_s = 20,
#                                   min_s = 0,
#                                   max_s = 2730,
#                                   nseg_u = 20,
#                                   min_u = 0,
#                                   max_u = 2300),
#                lrho = c(2, 0),
#                pord = 2,
#                optim_method = "ucminf",
#                optim_criterion = "aic")

## -----------------------------------------------------------------------------
# mod2 <- fit2ts(data2ts = dt2ts,
#                Bbases_spec = list(bdeg = 3,
#                                   nseg_s = 20,
#                                   min_s = 0,
#                                   max_s = 2730,
#                                   nseg_u = 20,
#                                   min_u = 0,
#                                   max_u = 2300),
#                lrho = c(2, 0),
#                pord = 2,
#                optim_method = "ucminf",
#                optim_criterion = "bic")
# 

## -----------------------------------------------------------------------------
# mod3 <- fit2ts(data2ts = dt2ts,
#                Bbases_spec = list(bdeg = 3,
#                                   nseg_s = 20,
#                                   min_s = 0,
#                                   max_s = 2730,
#                                   nseg_u = 20,
#                                   min_u = 0,
#                                   max_u = 2300),
#                optim_method = "grid_search",
#                optim_criterion = "aic",
#                lrho = list(seq(-1, 3, by = .2),
#                            seq(-1, 3, by = .2)),
#                par_gridsearch = list(
#                  plot_aic = TRUE,
#                  plot_bic = TRUE,
#                  mark_optimal = TRUE,
#                  plot_contour = TRUE
#                ))

## -----------------------------------------------------------------------------
# mod_LMM <- fit2ts(data2ts = dt2ts,
#                   Bbases_spec = list(bdeg = 3,
#                                      nseg_s = 20,
#                                      min_s = 0,
#                                      max_s = 2730,
#                                      nseg_u = 20,
#                                      min_u = 0,
#                                      max_u = 2300),
#                   pord = 2,
#                   optim_method = "LMMsolver",
#                   optim_criterion = "aic")

## -----------------------------------------------------------------------------
# dt2ts_cov <- prepare_data(data = reccolon2ts,
#                           u = "timer",
#                           s_out = "timesr",
#                           events = "status",
#                           ds = 30,
#                           individual = TRUE,
#                           covs = c("rx", "sex", "adhere", "obstruct", "node4"))

## -----------------------------------------------------------------------------
# mod_cov <- fit2ts(data2ts = dt2ts_cov,
#                   Bbases_spec = list(bdeg = 3,
#                                      nseg_s = 20,
#                                      min_s = 0,
#                                      max_s = 2730,
#                                      nseg_u = 20,
#                                      min_u = 0,
#                                      max_u = 2300),
#                   pord = 2,
#                   optim_method = "ucminf",
#                   optim_criterion = "aic")

## -----------------------------------------------------------------------------
# dt2tsLex <- prepare_data(data = reccolon2ts,
#                          t_in = "timer",
#                          t_out = "timedc",
#                          s_out = "timesr",
#                          events = "status",
#                          ds = 30, dt = 30)
# fields::image.plot(dt2tsLex$bins$midt,
#                    dt2tsLex$bins$mids,
#                    dt2tsLex$bindata$R,
#                    main = "Exposure",
#                    xlab = "time since randomization",
#                    ylab = "time since recurrence",
#                    col = c("white", rev(viridis::plasma(20))))
# abline(a=0,b=1)
# box()