---
title: "Install your working environment"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Install your working environment}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

Rmonize is an R package developed by Maelstrom Research to address some of the 
methodological and technical challenges in data harmonization and to promote a 
streamlined, reusable, and well documented harmonization workflow. To get 
started with Rmonize, you first need to get set up in R.

## Install R and RStudio

To use Rmonize, you must [install R](https://www.r-project.org/) (version 3.4 or 
higher), and you should have a basic familiarity with using R. While not 
required, we strongly recommend that you [install RStudio](https://posit.co/downloads/), 
an integrated development environment for R that enhances the user experience 
and extends R functionality.

## Install and load Rmonize

Before using Rmonize for the first time, you need to install the package. The 
latest stable version of the package can be installed from CRAN. The package is 
also available on Github. After initial installation, you will only need to 
reinstall Rmonize for updates. After installing Rmonize, load the package to use
it each time you start a new session.

```{r eval=FALSE}
# To install Rmonize from CRAN:
install.packages("Rmonize")

# To install Rmonize from Github:
remotes::install_github(
  repo = "https://github.com/maelstrom-research/Rmonize",
  ref = "main")

# Load the package
library(Rmonize)
```

Rmonize uses two underlying packages, [madshapR](https://cran.r-project.org/package=madshapR) 
and [fabR](https://cran.r-project.org/package=fabR), which include helpful 
functions to work with data and metadata. Installing Rmonize also installs these 
two packages, and Rmonize functions automatically call madshapR and fabR where 
needed. In the vignettes, we will highlight some useful madshapR and fabR 
functions.

You must also have the 'car' package installed, which is used internally by 
Rmonize to recode variables, to avoid errors during processing.

```{r eval=FALSE}
# Install package car from CRAN
install.packages("car")
```

Rmonize and its related packages additionally use underlying packages from 
[tidyverse](https://www.tidyverse.org/), a useful and popular collection of 
R packages for data science, which we will use in the vignettes and suggest 
users also install.

## Get help with Rmonize

You can get package and function documentation in R, and additional help and
documentation are also provided on the website <https://maelstrom-research.github.io/Rmonize-documentation/>

```{r eval=FALSE}
# Get package documentation in R
?Rmonize
help("Rmonize")

# Access the website with a function
Rmonize_website()
```

The package includes illustrative examples of input elements, outputs, and 
reports to demonstrate the structure and content of key elements in the Rmonize 
workflow. These examples are based on a use case with synthetic datasets from 
five studies to be harmonized, and they are also used in the Rmonize help files 
and vignettes.

```{r eval=FALSE}
# See available examples
names(Rmonize_examples)

# Downloadable templates are also available
Rmonize_templates()
```

You can report issues with the package or see known issues on Github at 
<https://github.com/maelstrom-research/Rmonize/issues>.

## Next steps

For a basic example of the harmonization processing workflow, see the vignette 
Simple example of data processing with Rmonize.

For more in-depth exploration of specific steps, see the vignettes and 
documentation:

- [Explore and prepare input datasets and data dictionaries](https://maelstrom-research.github.io/Rmonize-documentation/articles/c-explore-and-prepare-input-datasets-and-data-dictionaries.html)

- [Prepare the Data Processing Elements](https://maelstrom-research.github.io/Rmonize-documentation/dpe/index.html)

- [Process inputs into harmonized outputs](https://maelstrom-research.github.io/Rmonize-documentation/articles/d-process-inputs-and-generate-harmonized-outputs.html)

- [Summarize and secure harmonized outputs](https://maelstrom-research.github.io/Rmonize-documentation/articles/e-summarize-and-secure-harmonized-outputs.html)