---
title: "Introduction to SEQuential"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introduction to SEQuential}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

## Setting up your Analysis

The flow of the SEQuential R package never changes, nor are there planned changes to this flow in the future.

### Step 1 - Defining your options

In your R script, you will always start by defining your options object, through the `SEQopts` helper. There are many defaults which allow you to target exactly how you would like to change your analysis. Through this wiki there are specific pages dedicated to each causal contrast and the parameters which affect them, but for simplicity let's start with an intention-to-treat analysis with 20 bootstrap samples.

```{r setup, eval=FALSE}
library(SEQTaRget)

options <- SEQopts(km.curves = TRUE, #asks the function to return survival and risk estimates
                   bootstrap = TRUE, #asks the model to preform bootstrapping
                   bootstrap.nboot = 10) #asks the model for 10 bootstrap samples
```

In general, options will be in the form `{option}.{parameter}` - here you may notice that we use `bootstrap.nboot` indicating that this parameter affects the `bootstrap`

### Step 2 - Running the Primary Function

The next step is running the primary R function, `SEQuential`. Here you will give your options, data, and data-level information. We provide some small simulated datasets to test on.

```{r running, eval=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 = "ITT", options = options)
```

`SEQuential` is a rather chunky algorithm and will take some time to run, especially when bootstrapping. We provide some print statements to help track where the function is processing at any given point in time.

### Step 3 - Recovering your results

`SEQuential` produces a lot of internal diagnostics, models, and dataframes out of its main function in an S4 class. We provide a few different methods to handle obtaining your results.

```{r outcome, eval=FALSE}
outcome(model)     # Returns a list of only the outcome models 
km_curve(model)    # Prints the survival curve
```