## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = identical(Sys.getenv("IN_PKGDOWN"), "true") && identical(Sys.getenv("GITHUB_ACTIONS"), "true")
)
data.table::setDTthreads(2)

## ----setup--------------------------------------------------------------------
# library(SEQTaRget)

## ----fig.alt="Risk plot by treatment group."----------------------------------
# options <- SEQopts(# tells SEQuential to create Kaplan-Meier curves
#                    km.curves = TRUE,
#                    # tells SEQuential to weight the outcome model
#                    weighted = TRUE,
#                    # tells SEQuential to build weights from the pre-expanded data
#                    weight.preexpansion = TRUE)
# 
# # use some example data in the package
# data <- SEQdata
# model <- SEQuential(data,
#                     id.col = "ID",
#                     time.col = "time",
#                     eligible.col = "eligible",
#                     treatment.col = "tx_init",
#                     outcome.col = "outcome",
#                     time_varying.cols = c("N", "L", "P"),
#                     fixed.cols = "sex",
#                     method = "censoring",
#                     options = options)
# 
# # retrieve risk plot
# km_curve(model, plot.type = "risk")
# # retrieve survival and risk data
# survival_data <- km_data(model)
# risk_data(model)
# risk_comparison(model)

## ----fig.alt="Risk plot by treatment group."----------------------------------
# options <- SEQopts(km.curves = TRUE,
#                    weighted = TRUE,
#                    # tells SEQuential to build weights from the post-expanded data
#                    weight.preexpansion = FALSE)
# 
# data <- SEQdata
# model <- SEQuential(data,
#                     id.col = "ID",
#                     time.col = "time",
#                     eligible.col = "eligible",
#                     treatment.col = "tx_init",
#                     outcome.col = "outcome",
#                     time_varying.cols = c("N", "L", "P"),
#                     fixed.cols = "sex",
#                     method = "censoring",
#                     options = options)
# 
# km_curve(model, plot.type = "risk")
# risk_data(model)
# risk_comparison(model)

## ----fig.alt="Risk plot by treatment group."----------------------------------
# options <- SEQopts(km.curves = TRUE,
#                    weighted = TRUE,
#                    weight.preexpansion = TRUE,
#                    # tells SEQuential to run a dynamic intervention
#                    excused = TRUE,
#                    # tells SEQuential to use columns excusedOne and
#                    # excusedZero as excused conditions for treatment switches
#                    excused.cols = c("excusedZero", "excusedOne"),
#                    # tells SEQuential to expect treatment levels 0, 1
#                    # (mapping to the same positions as the list in excused.cols)
#                    treat.level = c(0, 1))
# data <- SEQdata
# model <- SEQuential(data,
#                     id.col = "ID",
#                     time.col = "time",
#                     eligible.col = "eligible",
#                     treatment.col = "tx_init",
#                     outcome.col = "outcome",
#                     time_varying.cols = c("N", "L", "P"),
#                     fixed.cols = "sex",
#                     method = "censoring",
#                     options = options)
# 
# km_curve(model, plot.type = "risk")
# risk_data(model)
# risk_comparison(model)

## ----fig.alt="Risk plot by treatment group."----------------------------------
# options <- SEQopts(km.curves = TRUE,
#                    weighted = TRUE,
#                    weight.preexpansion = FALSE,
#                    excused = TRUE,
#                    excused.cols = c("excusedZero", "excusedOne"),
#                    treat.level = c(0, 1),
#                    weight.p99 = TRUE)
# data <- SEQdata
# model <- SEQuential(data,
#                     id.col = "ID",
#                     time.col = "time",
#                     eligible.col = "eligible",
#                     treatment.col = "tx_init",
#                     outcome.col = "outcome",
#                     time_varying.cols = c("N", "L", "P"),
#                     fixed.cols = "sex",
#                     method = "censoring",
#                     options = options)
# 
# km_curve(model, plot.type = "risk")
# risk_data(model)
# risk_comparison(model)

## ----fig.alt="Risk plot by treatment group."----------------------------------
# options <- SEQopts(km.curves = TRUE,
#                    weighted = TRUE,
#                    weight.preexpansion = FALSE,
#                    excused = TRUE,
#                    excused.cols = c("excusedZero", "excusedOne"),
#                    treat.level = c(0, 1),
#                    # add a competing event
#                    compevent = "LTFU")
# 
# data <- SEQdata.LTFU
# model <- SEQuential(data,
#                     id.col = "ID",
#                     time.col = "time",
#                     eligible.col = "eligible",
#                     treatment.col = "tx_init",
#                     outcome.col = "outcome",
#                     time_varying.cols = c("N", "L", "P"),
#                     fixed.cols = "sex",
#                     method = "censoring",
#                     options = options)
# 
# km_curve(model, plot.type = "risk")
# risk_data(model)
# risk_comparison(model)

## -----------------------------------------------------------------------------
# options <- SEQopts(# tell SEQuential to run hazard ratios
#                    hazard = TRUE,
#                    weighted = TRUE,
#                    weight.preexpansion = FALSE,
#                    excused = TRUE,
#                    excused.cols = c("excusedZero", "excusedOne"),
#                    weight.p99 = TRUE)
# 
# data <- SEQdata
# model <- SEQuential(data,
#                     id.col = "ID",
#                     time.col = "time",
#                     eligible.col = "eligible",
#                     treatment.col = "tx_init",
#                     outcome.col = "outcome",
#                     time_varying.cols = c("N", "L", "P"),
#                     fixed.cols = "sex",
#                     method = "censoring",
#                     options = options)
# hazard_ratio(model)