README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# paprpkgr

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The goal of **paprpkgr** is to generate a skeleton to develop a research 
compendium containing the data, analysis, code, and images to reproduce one 
manuscript. I began working on this package around the same time that the more 
sophisticated [**rrtools**](https://github.com/benmarwick/rrtools) package was being 
developed by Ben Marwick and colleagues. If you are looking to incorporate Docker 
or Travis in your workflows, that package will definitely be more useful to you. 

## Installation

You can install **paprpkgr** from [GitHub](https://github.com) with either of the 
following:

``` r
devtools::install_github("wmoldham/paprpkgr")
renv::install("wmoldham/paprpkgr")
```

## Getting Started

1. Create a new package using `usethis::create_package()`. 
1. Start version control with Git by `usethis::use_git()`.
1. Link version control to GitHub by `usethis::use_github()`.
1. Restart the session when prompted.
1. Run `paprpkgr::new_papr()`. 

## Compendium Development

1. Edit `README.Rmd` and `DESCRIPTION` files with basic information about your
project.
1. Original data goes into the `data-raw` folder.
1. Analyze the raw data and generate cleaned data for analysis using Rmarkdown
files in `analysis/`. Figures from these analyses should be saved in
`analysis/figures/`.
1. The clean data should be saved by `usethis::use_data()` and documented 
appropriately.
1. Draft the manuscript and supplement using the `Rmd` templates installed in 
`manususcript/`. 
1. Build processing pipeline using the `targets` package.

## Research Compendium Resources

Many others have thought much more deeply about the hows and whys of using 
R packages in service of reproducible research efforts. I took my inspiration from
their efforts: 

* Ben Marwick and his [rrtools](https://github.com/benmarwick/rrtools) package
* Francisco Rodriguez-Sanchez and his [template](https://github.com/Pakillo/template) package
* Carl Boettiger and his [template](https://github.com/cboettig/template) package
* Jeff Hollister and his [manuscriptPackage](https://github.com/jhollist/manuscriptPackage)
* Robert Flight: http://rmflight.github.io/posts/2014/07/analyses_as_packages.html
* https://github.com/ropensci/rrrpkg
* https://github.com/Reproducible-Science-Curriculum/rr-init
* http://ropensci.github.io/reproducibility-guide/