---
title: "Intention-To-Treat Analysis"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Intention-To-Treat Analysis}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = identical(Sys.getenv("IN_PKGDOWN"), "true") && identical(Sys.getenv("GITHUB_ACTIONS"), "true")
)
```

Here, we'll go over some examples of using ITT. First we need to load the library before getting in to some sample use cases.

```{r setup}
library(SEQTaRget)
```

## ITT With 5 bootstrap samples

```{r}
options <- SEQopts(# tells SEQuential to create Kaplan-Meier curves
                   km.curves = TRUE,
                   # tells SEQuential to bootstrap
                   bootstrap = TRUE,
                   # tells SEQuential to run bootstraps 5 times
                   bootstrap.nboot = 5)

# use example data
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 = "ITT", 
                          options = options)

km_curve(model, plot.type = "risk")        # retrieve risk plot
risk_data(model)
risk_comparison(model)
```

## ITT with 5 bootstrap samples and losses-to-followup

```{r}
options <- SEQopts(km.curves = TRUE,               
                   bootstrap = TRUE,                
                   bootstrap.nboot = 5,
                   # tells SEQuential to expect LTFU as the censoring column
                   cense = "LTFU",
                   # tells SEQuential to treat this column as the 
                   # censoring eligibility column
                   cense.eligible = "eligible_cense")

# use example data for 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 = "ITT", 
                          options = options)

km_curve(model, plot.type = "risk")
risk_data(model)
risk_comparison(model)
```


## ITT with 5 bootstrap samples and competing events

```{r}
options <- SEQopts(km.curves = TRUE,               
                   bootstrap = TRUE,                
                   bootstrap.nboot = 5,
                   # Using LTFU as our 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 = "ITT", 
                          options = options)

km_curve(model, plot.type = "risk")
risk_data(model)
risk_comparison(model)
```


## ITT hazard ratio with 5 bootstrap samples and competing events
```{r}
options <- SEQopts(# km.curves must be set to FALSE to turn on hazard 
                   # ratio creation
                   km.curves = FALSE,
                   # set hazard to TRUE for hazard ratio creation
                   hazard = TRUE,
                   bootstrap = TRUE,                
                   bootstrap.nboot = 5,     
                   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 = "ITT", 
                          options = options)

# retrieve hazard ratios
hazard_ratio(model)
```

## ITT with 5 bootstrap samples and competing events in subgroups defined by sex
```{r}
options <- SEQopts(km.curves = TRUE,               
                   bootstrap = TRUE,                
                   bootstrap.nboot = 5,     
                   compevent = "LTFU",
                   # define the subgroup
                   subgroup = "sex")

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 = "ITT", 
                          options = options)

km_curve(model, plot.type = "risk")
risk_data(model)
risk_comparison(model)
```
