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

## ----warning=FALSE, message=FALSE---------------------------------------------
library(admiral)
library(admiralonco)
library(pharmaverseadam)
library(dplyr)
library(lubridate)

## -----------------------------------------------------------------------------
data("adsl")
data("adrs_onco")
adrs <- adrs_onco

## ----echo=FALSE---------------------------------------------------------------
knitr::kable(list_tte_source_objects(package = "admiralonco"))

## ----eval=FALSE---------------------------------------------------------------
# adsl_death_event <- event_source(
#   dataset_name = "adsl",
#   date = DTHDT,
#   set_values_to = exprs(
#     EVNTDESC = "STUDY DEATH",
#     SRCDOM = "ADSL",
#     SRCVAR = "DTHDT"
#   )
# )

## -----------------------------------------------------------------------------
adsl <- adsl %>%
  derive_vars_merged(
    dataset_add = adrs,
    filter_add = PARAMCD == "RSP" & AVALC == "Y" & ANL01FL == "Y",
    by_vars = get_admiral_option("subject_keys"),
    new_vars = exprs(TEMP_RESPDT = ADT)
  )

## -----------------------------------------------------------------------------
adtte <- derive_param_tte(
  dataset_adsl = adsl,
  start_date = RANDDT,
  event_conditions = list(death_event),
  censor_conditions = list(lastalive_censor, rand_censor),
  source_datasets = list(adsl = adsl, adrs = adrs),
  set_values_to = exprs(PARAMCD = "OS", PARAM = "Overall Survival")
) %>%
  derive_param_tte(
    dataset_adsl = adsl,
    start_date = RANDDT,
    event_conditions = list(pd_event, death_event),
    censor_conditions = list(lasta_censor, rand_censor),
    source_datasets = list(adsl = adsl, adrs = adrs),
    set_values_to = exprs(PARAMCD = "PFS", PARAM = "Progression Free Survival")
  ) %>%
  derive_param_tte(
    dataset_adsl = filter(adsl, !is.na(TEMP_RESPDT)),
    start_date = TEMP_RESPDT,
    event_conditions = list(pd_event, death_event),
    censor_conditions = list(lasta_censor),
    source_datasets = list(adsl = adsl, adrs = adrs),
    set_values_to = exprs(PARAMCD = "RSD", PARAM = "Duration of Response")
  )

## ----echo=FALSE---------------------------------------------------------------
dataset_vignette(
  adtte,
  display_vars = exprs(USUBJID, PARAMCD, PARAM, STARTDT, ADT, CNSR)
)

## ----eval=FALSE---------------------------------------------------------------
# pd_nact_event <- event_source(
#   dataset_name = "adsl",
#   filter = PDDT < NACTDT | is.na(NACTDT),
#   date = PDDT,
#   set_values_to = exprs(
#     EVNTDESC = "Disease Progression prior to NACT",
#     SRCDOM = "ADSL",
#     SRCVAR = "PDDT"
#   )
# )
# 
# death_nact_event <- event_source(
#   dataset_name = "adsl",
#   filter = DTHDT < NACTDT | is.na(NACTDT),
#   date = DTHDT,
#   set_values_to = exprs(
#     EVNTDESC = "Death prior to NACT",
#     SRCDOM = "ADSL",
#     SRCVAR = "DTHDT"
#   )
# )
# 
# lasta_nact_censor <- censor_source(
#   dataset_name = "adsl",
#   date = LASTANDT,
#   set_values_to = exprs(
#     EVNTDESC = "Last Tumor Assessment prior to NACT",
#     CNSDTDSC = "Last Tumor Assessment prior to NACT",
#     SRCDOM = "ADSL",
#     SRCVAR = "LASTANDT"
#   )
# )
# 
# adtte <- derive_param_tte(
#   dataset_adsl = adsl,
#   start_date = RANDDT,
#   event_conditions = list(pd_nact_event, death_nact_event),
#   censor_conditions = list(lasta_nact_censor, rand_censor),
#   source_datasets = list(adsl = adsl),
#   set_values_to = exprs(PARAMCD = "PFSNACT", PARAM = "Progression Free Survival prior to NACT")
# )

## ----eval=TRUE----------------------------------------------------------------
adtte <- adtte %>%
  derive_vars_duration(
    new_var = AVAL,
    start_date = STARTDT,
    end_date = ADT
  )

## ----echo=FALSE---------------------------------------------------------------
dataset_vignette(
  adtte
)

## ----eval=FALSE---------------------------------------------------------------
# adtte_months <- adtte %>%
#   derive_vars_duration(
#     new_var = AVAL,
#     start_date = STARTDT,
#     end_date = ADT,
#     out_unit = "months"
#   )

## ----eval=TRUE----------------------------------------------------------------
adtte <- adtte %>%
  derive_var_obs_number(
    by_vars = get_admiral_option("subject_keys"),
    order = exprs(PARAMCD),
    check_type = "error"
  )

## ----echo=FALSE---------------------------------------------------------------
dataset_vignette(adtte)

## ----eval=TRUE----------------------------------------------------------------
adtte <- adtte %>%
  derive_vars_merged(
    dataset_add = adsl,
    new_vars = exprs(ARMCD, ARM, ACTARMCD, ACTARM, AGE, SEX),
    by_vars = get_admiral_option("subject_keys")
  )

## ----echo=FALSE---------------------------------------------------------------
dataset_vignette(
  adtte,
  display_vars = exprs(USUBJID, PARAMCD, CNSR, AVAL, ARMCD, AGE, SEX)
)