02DataSetup.Rmd

# Data Setup  {-}

The analyses conducted in this supplement will require loading the following packages:

```{r, warning=FALSE}
## Load required packages
suppressPackageStartupMessages(library(lmtest))
suppressPackageStartupMessages(library(tidyr))
suppressPackageStartupMessages(library(sandwich))
suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(ggstance))
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(jtools))
```

Next, by setting the `filePath` variable to match the [location](https://github.com/ehsanx/IPAW-Per-protocol-Estimator) of the supplied `Pragmatic Trial Data.csv`, we can open the dataset. By printing the first few rows, we can start getting ourselves familiar with the data.

```{r, eval=TRUE, include=FALSE, cache=TRUE}
## Load the dataset
simulated.data <- read.csv("data/Pragmatic Trial Data.csv")
```

```{r, eval = FALSE}
## Load the dataset
simulated.data <- read.csv(paste0(filePath, "data/Pragmatic Trial Data.csv"))
```

```{r, cache=TRUE}
head(simulated.data)
```


We see that this dataset consists of 11 variables, including:

- Z the arm the patient was randomized to
- id the patient id that groups observations from the same individual together
- t0 the time point of the observation
- B the measured baseline covariate
- L1 and L2 the time-varying covariates, with L2lag and cavgL1 derived from these columns
- A whether the patient received the treatment for the time interval prior to this observation
- Y whether the individual experienced the outcome of interest