From Manuscript to R Package

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Maya Gans

Slides: [bit.ly/manuscriptrpackage](http://bit.ly/manuscriptrpackage)

---

# You Already

- structure your project
- write R code 
- declare dependencies
- test your code
- document your code
- clean your data
- write reports
- share your code

<div style="text-align:right;color:#D55E00FF;font-family:'Cedarville Cursive';font-size:2em;position:absolute;bottom:100px;right:100px;">
So let's do it as a package!
</div>
---

.overview[
<div class="f1 bg-white-o90 pa6 shadow-3 h-75">
<h1>
<em>You already<br>structure your project</em>
</h1>
</div>
]

---

```
├── data/
├── reports/
├── scripts/
└── analysis.Rproj
```

---

```
├── data/
├── reports/
*├── R/
└── analysis.Rproj
```

---

```
*├── data/
├── reports/
├── R/
└── analysis.Rproj
```

---

```
├── data/ 
*├── vignettes/
├── R/
└── analysis.Rproj
```

---

```
├── data/ 
├── vignettes/ 
├── R/
*├── man/
*├── tests/
*├── DESCRIPTION
*├── NAMESPACE
└── analysis.Rproj
```

---

```
├── data/ 
├── vignettes/ 
├── R/
├── man/ 
├── tests/ 
*├── DESCRIPTION
├── NAMESPACE
└── analysis.Rproj
```

---

.smaller-code[
```
Package: manuscriptrpackage
Title: What the Package Does (One Line, Title Case)
Version: 0.0.0.9000
Authors@R: 
    person(given = "Maya",
           family = "Gans",
           role = c("aut", "cre"),
           email = "jaffe.maya@gmail.com")
Description: What the package does (one paragraph).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
```
]

---

![](img/svg/create_project.svg)

---

.overview[
<div class="f1 bg-white-o90 pa6 shadow-3 h-75">
<h1>
<em>You already<br>write R code</em>
</h1>
</div>
]

---

![](img/svg/write_code.svg)

---

![](img/svg/use_r.svg)

---

![](img/svg/write_functions.svg)

---

![](img/svg/load_all.svg)

---

.overview[
<div class="f1 bg-white-o90 pa6 shadow-3 h-75">
<h1>
<em>You already<br>declare your dependencies</em>
</h1>
</div>
]

---

![](img/svg/write_library.svg)

---

![](img/svg/use_package.svg)

---

![](img/svg/use_package_code.svg)

---

---

---

![](img/svg/use_package_install.svg)

---

.overview[
<div class="f1 bg-white-o90 pa6 shadow-3 h-75">
<h1>
<em>You already<br>test your code</em>
</h1>
</div>
]

---

![](img/svg/fiddle.svg)

---

![](img/svg/use_test.svg)

---

.overview[
<div class="f1 bg-white-o90 pa6 shadow-3 h-75">
<h1>
<em>You already<br>document your code</em>
</h1>
</div>
]

---

![](img/svg/comment.svg)

---

![](img/svg/use_roxygen_rmd.svg)

---

```
#' Plot mean sepal length by species
#'
#' @param size the size of the points
#'
#' @return a ggplot
#' @export
#'
#' @examples
#'
#' plot_iris()
#'
plot_iris <- function(size = 2) {
  iris %>%
    dplyr::group_by(Species) %>%
    dplyr::summarize(mean_sepal_length = mean(Sepal.Length)) %>%
    ggplot2::ggplot(ggplot2::aes(mean_sepal_length, Species)) +
    ggplot2::geom_point(size = 2)
}
```

---

![](img/svg/document.svg)

---

.overview[
<div class="f1 bg-white-o90 pa6 shadow-3 h-75">
<h1>
<em>You already<br>clean your data</em>
</h1>
</div>
]

---

![](img/svg/use_data_raw.svg)

---

![](img/svg/use_data.svg)

---

.overview[
<div class="f1 bg-white-o90 pa6 shadow-3 h-75">
<h1>
<em>You already<br>write reports</em>
</h1>
</div>
]

---

![](img/svg/use_vignette.svg)

---

![](img/svg/use_inst.svg)

---

![](img/svg/use_toplevel.svg)

---

.overview[
<div class="f1 bg-white-o90 pa6 shadow-3 h-75">
<h1>
<em>You already<br>share your code</em>
</h1>
</div>
]

---

![](img/svg/install.svg)

---

---