## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 5,
  fig.height = 3,
  fig.align = "center"
)

## ----setup--------------------------------------------------------------------
library(survdt)

## -----------------------------------------------------------------------------
aids_fit <- coxph_indtrunc(Survdt(incu, ltrunc, rtrunc) ~ age_gp, 
                           data = aids)
aids_fit
confint(aids_fit)

## -----------------------------------------------------------------------------
coxph_indtrunc(Survdt(incu, ltrunc, rtrunc) ~ age_gp, 
               data = aids,
               ipw_type = "W-1")

## ----fig.height = 3.5---------------------------------------------------------
plot_coxsurv(aids_fit, 
             newdata = aids[c(1,40), ],
             target = "survival")

plot_coxsurv(aids_fit, 
             newdata = aids[c(1, 40, 200), ], 
             ci = FALSE, 
             target = "cumhaz")

## -----------------------------------------------------------------------------
qind_test <- test_quasiindep_covariates(Survdt(incu, ltrunc, rtrunc) ~ age_gp, 
                                        data = aids)
qind_test

## ----fig.height = 3.5---------------------------------------------------------
plot(qind_test)

## ----error=TRUE, warning=TRUE-------------------------------------------------
try({
positivity_sens_indtrunc(Survdt(incu, ltrunc, rtrunc) ~ age_gp, 
                         data = aids, ipw_type = "W-1",
                         trunc_mass = seq(0, 0.11, by = 0.01))

})

## -----------------------------------------------------------------------------
sens <- positivity_sens_indtrunc(Survdt(incu, ltrunc, rtrunc) ~ age_gp, 
                                 data = aids,
                                 trunc_mass = seq(0, 0.11, by = 0.01))
sens


## -----------------------------------------------------------------------------
plot(sens)
plot(sens, hazratio = TRUE)

## -----------------------------------------------------------------------------
strat_fit <- coxph_indtrunc(Survdt(event_time, ltrunc, rtrunc) ~ x, 
                            data = nonprop_sample, 
                            strata_formula = ~group)
strat_fit
confint(strat_fit)

## ----fig.height=3.5-----------------------------------------------------------
plot_coxsurv(strat_fit, 
             newdata = data.frame(group = c(0, 1), x = c(1, 1)),
             target = "cumhaz")

## -----------------------------------------------------------------------------
split_dat <- time_split(nonprop_sample, 
                        cut = 0.6, 
                        stop_name = "event_time", 
                        start = "start",
                        event = "event",
                        id = "id")

## -----------------------------------------------------------------------------
split_dat$group_tgr06 <- (split_dat$event_time > 0.6) * split_dat$group
tvar_fit <- coxph_indtrunc(Survdt2(start, event_time, event, ltrunc, rtrunc, id) ~ 
                             group_tgr06 + x, 
                           data = split_dat)
tvar_fit
confint(tvar_fit)