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r-in-repro-research-dc-leedsrss.Rmd
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---
title: "Putting the <img src='assets/logos/R_logo.svg' height=45px> into Reproducible Research"
subtitle: "Directors Cut"
author: " <br/><strong>Dr Anna Krystalli </strong> <br/> University of Sheffield RSE"
date: "<br><br> 2020/04/21 <br> <small> RSS Leeds / Bradford Local Group Seminar </small>"
output:
xaringan::moon_reader:
css: [default, metropolis, assets/css/footer.css, metropolis-fonts, assets/css/metropolis-ak_dc.css]
lib_dir: libs
nature:
beforeInit: "https://platform.twitter.com/widgets.js"
highlightStyle: github
titleSlideClass: [middle, left]
highlightLines: true
countIncrementalSlides: false
---
layout: true
<div class="my-footer"><span> RSS Leeds / Bradford Local Group Seminar
             
             
@annakrystalli <a href="https://twitter.com/annakrystalli">`r shiny::icon("twitter")` </a>
@annakrystalli <a href="https://github.com/annakrystalli">`r shiny::icon("github-alt")` </a>
</span></div>
```{r setup, include=FALSE}
library(magrittr)
```
---
# `r emo::ji("wave")` Hello
### me: **Dr Anna Krystalli**
- **Research Software Engineer**, _University of Sheffield_
+ twitter **@annakrystalli**
+ github **@annakrystalli**
+ email **a.krystalli[at]sheffield.ac.uk**
- **Editor [rOpenSci](http://onboarding.ropensci.org/)**
- **Co-organiser:** [Sheffield R Users group](https://www.meetup.com/SheffieldR-Sheffield-R-Users-Group/)
<br>
### slides: **bit.ly/r-in-repro-research-dc-leeds**
---
class: inverse, center, middle
# Motivation
---
# Calls for reproducibility
> ### **Reproducibility** has the potential to serve as a **minimum standard for judging scientific claims** when full independent replication of a study is not possible.
<br>
.center[
<img src="assets/repro-spectrum.jpg" width="650px" />
]
.img-attr[Reproducible Research in Computational Science
_ROGER D. PENG, SCIENCE 02 DEC 2011 : 1226-1227_
]
<br>
---
# Is code and data enough?
.center[
]
.img-attr[slide: [_Karthik Ram: rstudio::conf 2019 talk_](https://github.com/karthik/rstudio2019)]
---
# Calls for open science
<img src="assets/pgls.png" width="350px" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4957270/"/>
> ... highlight problems with users jumping straight into software implementations of methods (e.g. in r) that may lack documentation on biases and assumptions that are mentioned in the original papers.
> <small> To help solve these problems, we make a number of suggestions including **providing blog posts** or **videos** to **explain new methods in less technical terms**, **encouraging reproducibility and code sharing**, making **wiki-style pages** summarising the literature on popular methods, more careful consideration and testing of whether a method is appropriate for a given question/data set, **increased collaboration**, and a shift from publishing purely novel methods to **publishing improvements to existing methods** and ways of detecting biases or testing model fit. Many of these points are applicable across methods in ecology and evolution, not just phylogenetic comparative methods.</small>
---
# R for Open Reproducible Research
## A whistle-stop tour of tools, practices and conventions in R for more:
--
- ### **Reproducible**
--
- ### **Robust**
--
- ### **Transparent**
--
- ### **Reusable**
--
- ### **Shareable** research materials
---
class: inverse, center, middle
# Project management
<img src="assets/project.svg" height=200px>
.img-attr.bottom[Icon by [Freepik](https://www.freepik.com/) from [flaticon.com](www.flaticon.com)]
---
# Rstudio Projects
## Use Rstudio projects to keep materials associated with a particular analysis together
<br>
.pull-left[
- **Self contained** and **portable**
- **Working directory set to root** of project on launch
- **Fresh session** everytime the project is launched
See Jenny Bryan's post on [**project oriented workflows**](https://www.tidyverse.org/articles/2017/12/workflow-vs-script/) for more details
]
.pull-right.center[
**File > New Project > New Directory**
<img src="assets/new_project.png" height=200px>
]
---
background-image: url('assets/my_awesome_project.png')
background-size: contain
---
# `r emo::ji("package")` `here`
## Use `r emo::ji("package")` `here` to create robust relative paths
<br>
.pull-left[
- **Robust paths relative to project root**
+ portable
+ independent of:
- working directory
- source code location
]
.pull-right.center[
<img src="assets/you-are-here.svg" height=150px>
]
```{r}
here::here()
```
```{r}
here::here("data", "summaries.csv")
```
.img-attr.right[Icon by [Freepik](https://www.freepik.com/) from [flaticon.com](www.flaticon.com)]
---
# Dependency management
### Minimal approach
##### include an `install.R` script
```{r eval=FALSE}
install.packages("dplyr")
install.packages("purrr")
```
.pull-left[
### Most robust approach
##### use `r emo::ji("package")` `renv` (previously `packrat`)
- Create and manage a per project library of packages
- intialise during project set up
]
.pull-right[
<img src="assets/packrat_init.png" height=200px>
]
_will revisit later on_
---
# `r emo::ji("package")` `drake`
## Use `r emo::ji("package")` `drake` to orchestrate your workflows
<br>
.pull-left[
<img src="assets/drake_workflow.svg" height=150px>
]
.pull-right.center[
<img src="assets/drake_badge.svg" height=150px>
]
#### make plan
```{r}
plan <- drake::drake_plan(
raw_data = readr::read_csv(here::here("data", "iris.csv")),
data = raw_data %>%
dplyr::mutate(Species = forcats::fct_inorder(Species)),
fit = lm(Sepal.Width ~ Petal.Width + Species, data))
```
---
# Plan
#### view plan
```{r}
plan
```
#### re-execute plan
```{r}
drake::make(plan)
```
---
#### inspect targets
```{r}
drake::readd(fit)
```
---
# visualise workflow
.centre[
```{r fig.height=5, fig.width=12}
drake::vis_drake_graph(drake::drake_config(plan))
```
]
---
class: inverse, center, middle
# Version Control
---
# Version Control
### What is it? `r emo::ji("thinking")`
The **management of changes** to documents, computer programs, large web sites, and other collections of information.
### Git <img src="https://git-scm.com/images/logos/downloads/Git-Logo-2Color.png" height="25px" >
Open source (free to use) **Version control software.**
### GitHub <img src="https://raw.githubusercontent.com/annakrystalli/rrresearch/master/docs/assets/github_logo.jpg" height="25px">
A **website** (https://github.com/) that allows you to **store your Git repositories online** and makes it easy to collaborate with others.
---
# Why use them in research?
.pull-left[
### Exhibit A
<img src="http://smutch.github.io/VersionControlTutorial/_images/vc-xkcd.jpg" width="400px">
.img-attr[Image: xkcd CC BY-NC 2.5 ]
]
.pull-right[
### Exhibit B
<img src="http://www.phdcomics.com/comics/archive/phd101212s.gif" height="400px">
.img-attr[ Image: Jorge Cham www.phdcomics.com]
]
---
# Git, Github & Rstudio
#### Before: git only through the terminal `r emo::ji("cry")`
--
***
## Now: Rstudio + `usethis` `r emo::ji("package")` == `r emo::ji("heart")` `Git` & `GitHub` `r emo::ji("star_struck")`
.center[
]
---
# Configure git & GitHub
### Configure git
**Check your configuration**
```{r, eval=FALSE}
usethis::git_sitrep()
```
**Set your configuration**
Use your github username and and the email you used to sign-up on GitHub
```{r, eval=FALSE}
usethis::use_git_config(
user.name = "Jane",
user.email = "jane@example.org")
```
---
# Configure GitHub authentication
### Get GITHUB Personal Authorisation Token
```{r, eval=F}
usethis::browse_github_pat()
```
<img src="assets/browse_github.png" height="300px">
---
### Store in `.Renviron` file
```{r, eval=F}
usethis::edit_r_environ()
```
<img src="assets/GITHUB_PAT.png" height="400px">
---
# Initialise git
### Initialise **Rstudio project** with Git by **just checking a box!**
It's now **a repository**
<img src="assets/project_git.png" height="200px">
Forgot to? use `usethis::use_git()`
---
# Git panel
## Integrated graphical user interface
<br>
.center[
<img src="assets/git_tab.png" height="300px">
]
---
# Git Rstudio workflow
.pull-left[
#### view file status
<img src="assets/git_view.png" height="150px">
#### stage files
<img src="assets/git_add.png" height="150px">
]
.pull-right[
#### commit changes
<img src="assets/git_commit.png" width="600px">
]
---
# Share on GitHub
#### Create repo
```{r, eval=FALSE}
usethis::use_github(protocol = "https")
```
<img src="assets/my_awesome_repo.png" width="500px">
#### Push further changes
<img src="assets/push_github.png" height="50px">
---
# Anatomy of a GitHub Repo
- **`README`**. Explain what your project is, and how to use it.
+ `usethis::use_readme_md()`
+ `usethis::use_readme_rmd()`
- **`LICENSE`**. Without a licence, the contents of the repository are technically closed.
+ Examples licence [MIT](https://tldrlegal.com/license/mit-license): `usethis::use_mit_license(name = "Anna Krystalli")`
+ `?licenses`: details of functions available to generate licenses
+ [https://choosealicense.com/](https://choosealicense.com/) help on choosing a licence.
- **`CONTRIBUTING.md`** - guidelines for contributors.
+ `usethis::use_tidy_contributing()` provides a realtively strict but instructive template
- **`CODE_OF_CONDUCT.md`** set the tone for discourse between contributors.
+ `use_code_of_conduct()`
---
# GitHub issues
### use GitHub issues to plan, record and discuss tasks.
.pull-left[
#### issues
<img src="assets/github_issues.png" width="600px">
]
.pull-right[
#### projects
<img src="assets/github_projects.png" width="600px">
]
---
class: inverse, center, middle
# Literate programming with Rmarkdown
---
# Literate programming
Programming paradigm first introduced by **Donald E. Knuth**.
> ### Treat program as literature to be understandable to human beings
> <br>
> - focus on the logic and flow of human thought and understanding
> - single document to integrate data analysis (executable code) with textual documentation, **linking data, code, and text**
---
# Literate programming in R
### Rmarkdown (`.Rmd`) integrates:
- a **documentantion** language (`.md`)
- a **programming** language (`R`)
- functionality to **"knit" them together** through `r emo::ji("package")` `knitr`
<br>
### features
- `r emo::ji("white_check_mark")` provides a framework for writing narratives around code and data
- `r emo::ji("white_check_mark")` Code re-run in a clean environment every time the document is "knit"
---
background-image: url('assets/1728_TURI_Book sprint_25 pandoc_rmd_040619.jpg')
background-size: contain
# Rmarkdown outputs
.img-attr[This image was created by Scriberia for The Turing Way community and is used under a CC-BY licence.]
---
# Rmarkdown to html
#### **File > New File > RMarkdown... > Document**
.pull-left[
]
.pull-right.top[
<img src="assets/report_knit.png" width = 435px>
]
---
# Applications in research
### Rmd documents can be useful for a number of research related [long form documentation](http://r-pkgs.had.co.nz/vignettes.html) materials:
.pull-left[
<br>
- Documentation of code & data (eg `r emo::ji("package")` [DataMaid](https://github.com/ekstroem/dataMaid))
- Electronic Notebooks
- Supplementary materials
- Reports
- Papers
]
.pull-right[
]
---
# Rmd Vs Word
#### Spell check in Rstudio! <img src="assets/spell_check.png" height=40px>
## `r emo::ji("package")` [redoc](https://github.com/noamross/redoc) <small>**HOT OFF THE PRESS**</small>
**Enables a two-way R Markdown-Microsoft Word workflow**. It generates Word documents that can be de-rendered back into R Markdown, **retaining edits on the Word document**, including tracked changes.
---
# Publish to the web for free!
- **RPubs**: Publish rendered rmarkdown documents on the web with the click of a button <http://rpubs.com/>
- **GitHub**: Host your site through [`gh-pages`](https://pages.github.com/) on GitHub. Enable in GitHub repo `r emo::ji("gear")`**Settings**
.center[
<img src="assets/gh-pages.png" height=400px>
]
---
class: inverse, center, middle
# Rmarkdown extensions
Many great packages and applications build on rmarkdown.
All this makes it [incredibly versatile](https://rmarkdown.rstudio.com/gallery.html).
---
# [bookdown](https://bookdown.org/yihui/bookdown/)
#### Create and mantain online books
Authoring with R Markdown. Offers:
- cross-references,
- citations,
- HTML widgets and Shiny apps,
- tables of content and section numbering
The publication can be exported to HTML, PDF, and e-books (e.g. EPUB)
### Examples
- [rOpenSci Software Review policies](https://ropensci.github.io/dev_guide/)
- [Geocomputation in R](https://geocompr.robinlovelace.net/)
### [Thesisdown](https://github.com/ismayc/thesisdown)
An updated R Markdown thesis template using the bookdown package
---
# [pkgdown](http://pkgdown.r-lib.org/articles/pkgdown.html)
#### For buidling package documentation
Produce **function references** from `.Rd` files and **demonstrate function use** through long form documentation (vignettes).
---
# [workflowr](https://jdblischak.github.io/workflowr/) pkg
#### Build analyses websites and organise your project
Makes it easier for researchers to organize projects and share results. Includes **checks to ensure rendered versions correspond to up to date versions of code**.
.pull-left[
]
.pull-right[
]
---
# [blogdown](https://bookdown.org/yihui/blogdown/)
## For creating and mantaining blogs through R.
Check out <https://awesome-blogdown.com/>, **a curated list of awesome #rstats blogs in blogdown** for inspiration!
[](https://masalmon.eu/)
---
# presentations
## A number of existing frameworks
### [xaringan](https://github.com/yihui/xaringan) `r emo::ji("package")` Presentation Ninja 幻灯忍者 · 写轮眼
.center[
[<img src='assets/xaringan.png' height=350px>](https://slides.yihui.name/xaringan/#1)
]
---
class: inverse, center, middle
# Managing code
---
# Managing analysis code
## Separate function definition and application
.pull-left[
<br>
- When a project is new and shiny, an **analysis script usually contains many lines of directly executated code.**
- As it matures, **reusable chunks get pulled into their own functions**.
- The actual analysis scripts then become relatively short, and **functions defined in separate R scripts.** ]
.pull-right[
]
---
# R Package Structure
## Used to share functionality with the R community
- Useful **conventions**
- Useful **software development tools**
- Easy **publishing** through GitHub
<br>
.center[
<img src="assets/package_friends.png" height=250px>
]
---
# Build panel
## Integrated graphical user interface
<br>
.center[
<img src="assets/build_panel.png" height="300px">
]
---
# R Package conventions:
- **metadata**: in the **`DESCRIPTION` file**
- **functions** in **`.R` scripts** in the **`R/` folder**
- **tests** in the **`tests/` folder**
- **Documentation:**
- _functions_ using **Roxygen notation**
- _workflows_ using **`.Rmd` documents** in the **`vignettes/`** folder
---
# `DESCRIPTION` file
#### Package metadata
```
Package: gaitr
Type: Package
Title: Functions to support BMC gait analysis
Description: Helpers to analyse processed gait data.
Version: 0.0.9000
Authors@R:
c(person(given = "Anna",
family = "Krystalli",
role = c("aut", "cre"),
email = "annakrystalli@googlemail.com"),
person(given = "Lorenza",
family = "Angelini",
role = "aut",
email = "l.angelini@sheffield.ac.uk"))
License: MIT + file LICENSE
```
---
# citation
```{r}
citation("gaitr")
```
---
# Dependency management
It’s the job of the `DESCRIPTION` file to **list the packages that your code depends on**.
```
Imports:
dplyr,
purrr,
here,
broom,
tibble,
magrittr,
janitor,
ggplot2
Suggests:
knitr,
rmarkdown
```
#### add dependency
```{r, eval=FALSE}
usethis::use_package("forcats", type = "Imports")
```
---
# Functions in `R/`
### example function script
Create a new function `.R` file in the `R/` folder
```{r, eval=FALSE}
usethis::use_r("add")
```
```
R
└── add.R
0 directories, 1 files
```
---
# Document functions with `Roxygen`
- Create help files on build (autogenerated `.Rd` files in `man/`)
- Specify which functions are exported (autogenerated `NAMESPACE`)
```{r}
#' Add together two numbers.
#'
#' @param x A number.
#' @param y A number.
#' @return The sum of x and y.
#' @examples
#' add(1, 1)
#' add(10, 1)
add <- function(x, y) {
x + y
}
```
---
# [tests](http://r-pkgs.had.co.nz/tests.html)
## Tests provide confidence in what the code is doing.
.center[
]
---
# Example test
```{r, eval=FALSE}
usethis::use_test("add")
```
Creates a `tests/` folder with the following files
```
tests
├── testthat
│ ├── test-add.R
└── testthat.R
```
##### test-add.R
```{r, eval=FALSE}
context("test-add")
test_that("add works", {
expect_equal(add(2, 2), 4)
})
```
---
# Continuous Integration w/ Travis
## A cloud testing framework for automating your tests
.pull-left[
- Monitor the effect of changes to the code
- Safe onboarding of contributions
### Start with a `.travis.yml` file
```{r, eval=FALSE}
usethis::use_travis()
```
]
.pull-right.center[
<br>
<br>
.center[<img src="assets/travis.png" height=300px>]
]
---
# `.travis.yml`
#### Resulting `.travis.yml` file template
```
language: R
sudo: false
cache: packages
```
#### instructions to enable TRAVIS CI
```
✔ Writing '.travis.yml'
✔ Adding '^\\.travis\\.yml$' to '.Rbuildignore'
● Turn on travis for your repo at https://travis-ci.org/profile/annakrystalli
● Copy and paste the following lines into '/Users/Anna/Documents/workflows/talks/README.md':
<!-- badges: start -->
[](https://travis-ci.org/annakrystalli/talks)
<!-- badges: end -->
```
### Update: GitHub Actions
You can now run Continuous Integration on GitHub! See Jim Hester's rstudio conf 2020 talk on [Azure Pipelines and GitHub Actions](https://resources.rstudio.com/rstudio-conf-2020/azure-pipelines-and-github-actions-jim-hester)
---
class: inverse, center, middle
# Research compendia
---
# A Research compendium
### The paper is the advertisement
> “an article about computational result is advertising, not scholarship. The **actual scholarship is the full software environment, code and data, that produced the result.**”
*John Claerbout paraphrased in [Buckheit and Donoho (1995)](https://statweb.stanford.edu/~wavelab/Wavelab_850/wavelab.pdf)*
### The concept of a Research Compendium
>“
...We introduce the **concept of a compendium**
as both a **container for the different elements**
that make up the document and its computations (i.e. text, code, data, ...), and as a **means for distributing, managing and updating the
collection**."
[_Gentleman and Temple Lang, 2004_](https://biostats.bepress.com/bioconductor/paper2/)
---
# Research compendia in R
.pull-left[
]
.pull-right[
]
.img-attr[slides: [_Karthik Ram: rstudio::conf 2019 talk_](https://github.com/karthik/rstudio2019)]
<br>
**Ben Marwick, Carl Boettiger & Lincoln Mullen (2018)** [_Packaging Data Analytical Work Reproducibly Using R (and Friends)_](https://peerj.com/preprints/3192/)
---
# Example compendium
.pull-left[
**Paper**:
##### Boettiger, C. (2018) *From noise to knowledge: how randomness generates novel phenomena and reveals information*. <https://doi.org/10.1111/ele.13085>
<img src="assets/Boettiger-2018.png" heigth="250px" width="400px">
]
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