Start creating packages to share your code

class: title-slide, left, bottom, inverse
background-image: url("images/calm.jpeg")
background-position: right
background-size: cover

# Start creating packages to share your code

## Believe it or not, you already know how

### Jesús Vélez Santiago

[<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;fill:#ffffff;" xmlns="http://www.w3.org/2000/svg">  <path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path></svg> @jvelezmagic](https://twitter.com/jvelezmagic)  
[<svg viewBox="0 0 496 512" style="height:1em;position:relative;display:inline-block;top:.1em;fill:#ffffff;" xmlns="http://www.w3.org/2000/svg">  <path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg> @jvelezmagic](https://github.com/jvelezmagic)  
[<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;fill:#ffffff;" xmlns="http://www.w3.org/2000/svg">  <path d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"></path></svg> jvelezmagic.com](https://jvelezmagic.com/)  
[<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;fill:#ffffff;" xmlns="http://www.w3.org/2000/svg">  <path d="M416 48c0-8.84-7.16-16-16-16h-64c-8.84 0-16 7.16-16 16v48h96V48zM63.91 159.99C61.4 253.84 3.46 274.22 0 404v44c0 17.67 14.33 32 32 32h96c17.67 0 32-14.33 32-32V288h32V128H95.84c-17.63 0-31.45 14.37-31.93 31.99zm384.18 0c-.48-17.62-14.3-31.99-31.93-31.99H320v160h32v160c0 17.67 14.33 32 32 32h96c17.67 0 32-14.33 32-32v-44c-3.46-129.78-61.4-150.16-63.91-244.01zM176 32h-64c-8.84 0-16 7.16-16 16v48h96V48c0-8.84-7.16-16-16-16zm48 256h64V128h-64v160z"></path></svg> Slides code](https://github.com/jvelezmagic/talks/tree/main/start_creating_packages_to_share_your_code)
]

---

## Do you recognize the following pattern?

---

.pull-left[
```
├── data/
├── reports/
├── scripts/
  └── good-stuff-here.R
└── your.awesome.analysis.Rproj
```
]

---

.pull-left[
```
├── data/
├── reports/
*├── R/
  └── good-stuff-here.R
└── your.awesome.analysis.Rproj
```
]

---

.pull-left[
```
*├── data/
├── reports/
├── R/
  └── good-stuff-here.R
└── your.awesome.analysis.Rproj
```
]

---

.pull-left[
```
├── data/
*├── vignettes/
├── R/
  └── good-stuff-here.R
└── your.awesome.analysis.Rproj
```
]

.pull-right[
### Minor changes! 😋
- Instead of `scripts` use `R`.
- `data` can remain unchanged!
- Now `reports` are called `vignettes`.
]

---

.pull-left[
```
├── data/ 
├── vignettes/ 
├── R/
  └── good-stuff-here.R
*├── man/
*├── tests/
*├── DESCRIPTION
*├── NAMESPACE
└── your.awesome.analysis.Rproj
```
]

.pull-right[
### Minor changes! 😋
- Instead of `scripts` use `R`.
- `data` can remain unchanged!
- Now `reports` are called `vignettes`.

### New changes, but not from other world! 🤯

- `man`: Represents the full package's documentation!
- `tests`: Automated code to test package functionality.
- `DESCRIPTION`: This is where all the meta-data about your package goes!
- `NAMESPACE`: Indicates what need to be exposed to users of your package.
]

---

.pull-left[
```
├── data/ 
├── vignettes/ 
├── R/
  └── good-stuff-here.R
├── man/
├── tests/
├── DESCRIPTION
├── NAMESPACE
*└── your.awesome.package.Rproj
```

You will probably want to change the name of your project! ✨
]

.pull-right[
### Minor changes! 😋
- Instead of `scripts` use `R`.
- `data` can remain unchanged!
- Now `reports` are called `vignettes`.

### New changes, but not from other world! 🤯

---

.pull-left[
```
├── data/ 
├── vignettes/ 
├── R/
  └── good-stuff-here.R
├── man/
├── tests/
├── DESCRIPTION
├── NAMESPACE
└── your.awesome.package.Rproj
```

You will probably want to change the name of your project! ✨

![](https://media.giphy.com/media/1ym5LJ17vp77BL8X5O/giphy.gif)
]

.pull-right[
### Minor changes! 😋
- Instead of `scripts` use `R`.
- `data` can remain unchanged!
- Now `reports` are called `vignettes`.

### New changes, but not from other world! 🤯

---
layout: false
class: center, inverse, middle

## "But wait... Should I manually do this every time?"

### You're right! You don't! 🎉🎉🎉

![](https://media.giphy.com/media/o75ajIFH0QnQC3nCeD/giphy.gif)
---

## [`usethis`](https://usethis.r-lib.org/) the blessing behind it all! 😇

```r
usethis::create_package("your.awesome.package")
```

```r
#> ✓ Creating 'your.awesome.project/'
#> ✓ Setting active project to '/private/var/folders/bt/17212s6j0xxfjty0f77xmfq00000gn/T/awesome.project'
#> ✓ Creating 'R/'
#> ✓ Writing 'DESCRIPTION'
#> Package: your.awesome.project
#> Title: What the Package Does (One Line, Title Case)
#> Version: 0.0.0.9000
#> Authors@R (parsed):
#>     * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
#> Description: What the package does (one paragraph).
#> License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
#>     license
#> Encoding: UTF-8
#> LazyData: true
#> Roxygen: list(markdown = TRUE)
#> RoxygenNote: 7.1.1
#> ✓ Writing 'NAMESPACE'
#> ✓ Setting active project to '<no active project>'
```
]
.panel[
.panel-name[Tidyverse-like]

`usethis::create_tidy_package()` creates a new package, immediately applies
as many of the tidyverse conventions as possible, issues a few reminders,
and activates the new package. 🤗

```r
usethis::create_tidy_package("your.awesome.package")
```

What is actually running?
- `usethis::use_testthat()`
- `usethis::use_mit_license(copyright_holder)`
- `usethis::use_tidy_description()`
- `usethis::use_readme_rmd(open = FALSE)`
- `usethis::use_lifecycle_badge("experimental")`
- `usethis::use_cran_badge()`
- `usethis::use_cran_comments(open = FALSE)`
- `usethis::use_tidy_release_test_env()`
- `usethis::use_tidy_github()`

]
.panel[
.panel-name[Bioconductor]

If you want to develop packages for Bioconductor, you must take an eye
to [`biocthis`](https://lcolladotor.github.io/biocthis/)
package developed by [@lcolladotor](https://twitter.com/lcolladotor).

Since the Bioconductor standards are strongly linked with Tidyverse,
I suggest you first create a tidy package and follow the
[@lcolladotor](https://twitter.com/lcolladotor) instructions.
In this way, you must be covered by both parties.
I assure you that this will make your development more fast and optimal. 💜

```r
usethis::create_tidy_package("your.awesome.package")
```

```r
biocthis::use_bioc_pkg_templates()
```

```r
#> ✔ Creating 'dev/'
#> ✔ Adding '^dev$' to '.Rbuildignore'
#> ✔ Writing 'dev/01_create_pkg.R'
#> ✔ Writing 'dev/02_git_github_setup.R'
#> ✔ Writing 'dev/03_core_files.R'
#> ✔ Writing 'dev/04_update.R'
```
]
]

---

class: title-slide, left, top, inverse
background-image: url(images/postcard.jpeg)
background-size: 100%

## "And what about the code? Should I rewrite all my code? 😅👉👈"

### Dont't worry, you're almost there!  😋

#### In fact, you've been doing it all this time,  
#### but you hadn't realized it! 🎉

> ### "One often meets his destiny on the road he takes to avoid it."
>
> #### [Oogway](https://en.wikipedia.org/wiki/Kung_Fu_Panda)

]

---

## Transforming your code!

---

iris %>% 
  group_by(Species) %>% 
  summarise(
    mean_sepal_length = mean(Sepal.Length),
    mean_sepal_Width = mean(Sepal.Width)
  )
```
]

---

*summarise_iris <- function() {
  iris %>% 
    group_by(Species) %>% 
    summarise(
      mean_sepal_length = mean(Sepal.Length), #<<
      mean_sepal_Width = mean(Sepal.Width)
    )
*}
```
]

.pull-right[
### Steps! 😋
1. Create a new `R` file with `usethis::use_r("good-stuff-here")`.
2. Wrap your code inside a `function`.
]

---

summarise_iris <- function() {
  iris %>% 
*    dplyr::group_by(Species) %>%
*    dplyr::summarise(
      mean_sepal_length = mean(Sepal.Length), #<<
      mean_sepal_Width = mean(Sepal.Width)
    )
}
```
]

---

*summarise_data <- function(.data, ..., vars) {
*  .data %>% 
*    dplyr::group_by(...) %>% 
    dplyr::summarise(
*      dplyr::across({{ vars }}, mean)
    )
*}
```
]

---

summarise_data <- function(.data, ..., vars) {
  .data %>% 
    dplyr::group_by(...) %>% 
    dplyr::summarise(
      dplyr::across({{ vars }}, mean)
    )
}
```

```r
test_that("multiplication works", {
*  expect_equal(2 * 2, 4)
})
```
]

---

summarise_data <- function(.data, ..., vars) {
  .data %>% 
    dplyr::group_by(...) %>% 
    dplyr::summarise(
      dplyr::across({{ vars }}, mean)
    )
}
```

```r
test_that("multiplication works", {
  expect_equal(2 * 2, 4)
})
```
![](https://media.giphy.com/media/5Ivz8uxHriaAw/giphy.gif)
]

.pull-right[
### Steps! 😋
1. Create a new `R` file with `usethis::use_r("good-stuff-here")`.
2. Wrap your code inside a `function`.
3. Declare your dependencies with `usethis::use_package("dplyr")`. Then, use
  `package::function()` notation.
4. If possible and convenient for you, try to `generalize` the function.
5. Write a test with `usethis::use_test("good-stuff-here")`
6. Load your package and repeat the cycle. 👀
````r
devtools::load_all() # Cmd/Ctrl + Shift + L
devtools::test() # Cmd/Ctrl + Shit + T
devtools::build() # Cmd/Ctrl + Shit + B
devtools::document()
```
]

---

> ## "When writing code, you're always collaborating with future-you; and past-you doesn't respond to emails."

![](https://media.giphy.com/media/2rKDe8JpAEatWVamEe/giphy.gif)

---
layout: true

background-image: url(images/flower2.jpeg)
background-position: left
background-size: 25% 100%

---

.right-column[
.panelset[
.panel[
.panel-name[Project structure]
### Before
```
├── data/
├── reports/
├── scripts/
  └── good-stuff-here.R
└── your.awesome.analysis.Rproj
```
### After
```
├── data/ 
├── vignettes/ 
├── R/
  └── good-stuff-here.R
├── man/
├── tests/
├── DESCRIPTION
├── NAMESPACE
└── your.awesome.package.Rproj
```
]
.panel[
.panel-name[R code 1]
### Before
```r
library(dplyr)

iris %>% 
  group_by(Species) %>% 
  summarise(
    mean_sepal_length = mean(Sepal.Length),
    mean_sepal_Width = mean(Sepal.Width)
  )
```
### After
```r
summarise_data <- function(.data, ..., vars) {
  .data %>% 
    dplyr::group_by(...) %>% 
    dplyr::summarise(
      dplyr::across({{ vars }}, mean)
    )
}
```
]
.panel[
.panel-name[R code 2]
### Beyond `R code 1`
Document your code using `roxygen2` and `markdown`.
```r
#' Grouped mean
#'
#' Calculate the mean per group across multiple varibles.
#' 
#' @param .data A tibble.
#' @param ... Variables to group.
#' @param vars Variables to summarise.
#' @export
summarise_data <- function(.data, ..., vars) {
  .data %>% 
    dplyr::group_by(...) %>% 
    dplyr::summarise(
      dplyr::across({{ vars }}, mean)
    )
}
```
]
.panel[
.panel-name[Unit tests]
Create a new test file
```r
usethis::use_test("good-stuff-here")
```
Write a new test
```r
test_that("multiplication works", {
  expect_equal(2 * 2, 4)
})
```
Run `testthat` test in your package
```r
devtools::test()
```
```r
ℹ Loading testing
ℹ Testing testing
✓ |  OK F W S | Context
✓ |   1       | good-stuff-here

══ Results ═════════════════════════════════════════════════
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
```
]
.panel[
.panel-name[DESCRIPTION]
```r
*Package: your.awesome.project
*Title: What the Package Does (One Line, Title Case)
*Version: 0.0.0.9000
Authors@R: 
    person(given = "First",
           family = "Last",
           role = c("aut", "cre"),
           email = "first.last@example.com",
           comment = c(ORCID = "YOUR-ORCID-ID"))
*Description: What the package does (one paragraph).
License: MIT + file LICENSE
Suggests: 
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
*Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
*Imports:
*    dplyr
```

## Nice, that's a huge progress! 😋

]
]
]

---
layout: false
class: title-slide, center, middle, inverse
background-image: url("images/postcard2.jpeg")

## "Yesterday is history. Tomorrow is a mystery. But today is a gift, that is why it's called the present."
## Oogway

![](https://media.giphy.com/media/HqFTzrX983uJq/giphy.gif)

---

.pull-left[
### Sincere thanks 
to my advisors in this year of research:
- Julio Saez-Rodríguez
- Ricardo Ramírez
- Christian Holland
]

.pull-right[
.right[
<img style="border-radius: 50%;" src="https://github.com/jvelezmagic.png" width="150px"/>

# Thank you!

### Find me at...