Working with the RStudio IDE

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Foreword

• Output options: the ‘tango’ syntax and the ‘readable’ theme.
• Snippets and results.

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Help: Alt+Shift+K or Tools/Keyboard Shortcuts Help.

Orientation

Commands

• Ctrl+Up; command history.
• Tab; completion for all.
• Ctrl+L; clear the console.
• Tools/Global Options… set up RStudio.
• view(dataframe); open a spreadsheet, show in new window, sort the
  rows, search, filter the rows.

df <- data.frame(colA = c(1, 2), colB = c(3, 6))
df

##   colA colB
## 1    1    3
## 2    2    6

View(df) # in a new window

IDE panes

• Environment pane; load, save, remove objects, read a dataset,
  import dataset.
• History pane; idem, clear all or one item at the time, copy the
  command in the console pane, reload a command with Shift+Enter and
  run it.
• File pane; working directories, files, add a new folder, rename
• getwd(); get working directory.
• setwd(); set working directory.
• Plot pane; save (extension, size, resolution).
• Package pane; update.
• Help pane; pages.
• Viewer pane; more than plots!

Programming

Scripting

• Ctrl+Shift+M; %>%.
• Alt+-; <-.
• Ctrl+Shift+C; add/delete a # for commenting.

%>% 

<- 

# comment

Code

• Ctrl+Alt+I; new chunk.

• Convert into a function.

1. Type code,
2. Highlight it,
3. Code/Extract Function to create a function:

This:

rnorm(10, 0, 1)

Becomes:

rnorm <- function() {
  rnorm(10, 0, 1)
}

• Ctrl+Alt+click; multiple cursors for typing!
• Switch between Default, Vim and Emacs modes with
  Tools/Global Options/Code/Keybindings.
• Shift+Alt+G; go to line.
• Ctrl+F: find/replace in the current document.
• Alt+O, Alt+Shift+O; fold/unfold the code.
• Ctrl+P; jump between symbols like (), {}, [].
• Ctrl+Shift+Enter; run and source the code.
• Ctrl+Enter; run and source the code.
• Ctrl+Shift+F10; restart, refresh the R session.

Error handling

RStudio traces back the error origin.

Toggle the show/hide traceback in the console when there is an error or
rerun with the bug, watch the right pane for traceback.

Investigate, highlight the next line of code, click in the traceback
window, click the dropdown menu in the Global Environment (upper-right).
Stop, continue in the debugger mode, press C, press Q.

Add/remove breakpoints, where the line numbers are.

• debugonce; automatically call the debugger when the function is
  called, but only once.
• debug, undebug; automatically call the debugger when the
  function is called.

Add options(error=browser) or options(error=NULL) at the beginning
of the script; R automatically open the debugger mode.

• N; next line.
• step-into icon.
• Shift+F4; step into.
• Shift+F6; execute the remainder of the bug.

Project

• Create a project with a folder and all the files (Global
  Environment, History, etc.): New Directory, Existing Directory,
  Version Control… Empty Project, R Package (project), Shiny
  Web Application.
• Create a Git repository with the new project

Commands

• Ctrl+Shift+F; find in files.
• Ctrl+F9, F10; go backwards/forwards.

Packrat

Packrat is a dependency management system for R. Use one version of a
package for one project, another version of a package for another
project. Associate a project with its own set of packages.

• Packrat.
• Activate Packrat when creating a project or
  Tools/Project Options/Packrat.
• The library is virtually separate from R library.
• Perfect for collaborating with GitHub

Packages

Introduction to R packages

Anything that can be automated, should be automated. Do as little as
possible by hand. Do as much as possible with functions.

Process:

• Writing R functions.
• Documenting functions.
• Writing tests.
• Checking compatibility.
• Building the package for sharing and using.

See the book: R Packages.

Create a new R package

Create a new directory with new files, folders, and meta-information.

To update or not to update

RStudio generates the NAMESPACE content for you automatically.

See the book: R Packages.

Import & load source files

Move existing functions from an existing project into the new package.
The function are moves to a new folder in the project.

Test created functions all in once with the Load All command in the
Build Tab.

Simulations:

• Ctrl+Shift+L
• Ctrl+Shift+F10; restart a R session.

Packages documentation

Create a help page (.Rd file). Written in HTML.

Use the roxigen package to document.

Tools/Project Optons/Build Tools/Generate documentation. Generate the
doc, add comments.

First, create a doc skeleton above the function:

• Ctrl+Alt+Shift+R

#' Title
#'
#' @param x 
#'
#' @return
#' @export
#'
#' @examples
cEnter <- function(x) {
  x - mean(x)
}

Fill in the blanks.

Package documentation (2)

Title of the help page. Text on how to use.

The 4 tags (@) help organizing the doc: @export (tells R that this
function should be made available to people who load your package. ),
@params, @return, and @examples. There are many more advanced
tags.

Highlight a section and test it, run it.

Package documentation (3)

Build Tab/build the package.

• Ctrl+Shift+D

Compile all. Load all. Open the help page with ?function.

Learn the roxigen workflow to ease the work.

Test your package

With the testthat (and devtools) package.

Install both packages. Run devtools::use_testthat() and a now
directory with subdir appears in the package. This is where we save
tests.

Test your package (2)

Ready. Write tests. Open a new R script and save it to the tests
directory. Create a context function. Add test_that functions with
arguments.

context("cEnter")

test_that("cEnter handles integers", {
  expect_equal(cEnter(1:3), -1:1)
  expect_equal(cEnter(-(1:3)), 1:-1)
})

context("scale")

test_that("scale handles integers", {
  expect_equal(scale(1:3), 1:3)
  expect_equal(scale(-(1:3)), -(1:3))
})

context("standardize")

test_that("standardize handles integers", {
  expect_equal(standardize(1:3), -1:1)
  expect_equal(standardize(-(1:3)), 1:-1)
})

Test your package (3)

Run the tests.

• Ctrl+Shift+T

Get a summary (pass or not pass). Test and retest the package.

See the book: R Packages.

Time to test your package

Run the test with Build Tab/Test package.

Check your package

Upload the package to GitHub. Recreate the package structure in the
repo. Download and install the package with install_github() from the
devtools package. Test the package on GitHub to complete the tests.
Type R CMD check in the terminal. Or Build Tab/Check icon.

• Ctrl+Shift+E

Build your package

A package is a tarball or package bundle.

Build Tab/Build & Reload. Install and load the package.

• Ctrl+Shift+B

Build and reload will overwrite the existing package. Run
devtools::dev_mode() creates a separate library for development.
Running the command again cancels it.

Two formats: source package or binary package (more compresses and
optimized).

See the book: R Packages.

Wrap-up

Get the cheat sheet

Version Control

Introduction to Git

Use Git to work in team. Even on R scripts, reports and packages.

Install Git.

In RStudio, Tools/Global Options/Git/SVN + Tools/Project Options/Select
VCS, restart RStudio. RStudio has now a Git pane and a Git icon.

Stage & commit

The Git Tab is a directory. The real life (local) version of the
project. The official version of the project as recorded with Git.

The two versions are different. View the differences. When you commit,
you add thing from the real to the official version.

Green highlighting indicates something you’ve added to the official
version, while red highlighting indicates lines you have removed.

.gitignore

Inside the project, ther is a .gignore file. Add file that are excluded
from the offcial version. The file can be accessed from the Git pane.

Git icons

Add, (cancel), commit, (cancel). The icons will changed.

Commit history

History viewer: each commitment. HEAD commit and parent commit. Master
branch or another.

Undo commited changes: checkout

Checkout command. Go back to a previous commit. The commit stays in the
history (not deleted).

Run it in the shell: Tools/shell.

git checkout sha# nameofthefile and Git will reverse the commit. The
file is in the stage area as before the commit.

Undo uncommited changes

The file is in the stage area, ready to commit. Cancel the addition.

In the Change window, click on the Revert button.

Or, click on Discard chunk.

Or, Ctrl+Z to undo.

Then, Save the file.

Introduction to GitHub

Centralize, host, track issues, track metrics.

Install a R package From GitHub with install_github from the the
devtools packages.

Pull & Push

Local and GitHub

Wrap-up

Go to help.github.com

Go to stackoverflow.com

Reporting

Tools for reporting

R Markdown and Shiny (over the web).

Introduction to R Markdown

Text and code.

Web link: <http://www>

R Markdown in RStudio

Report (HTML, PDF, Word) or presentation(slide).

Create a template. Load in new templates. The rticles package has
templates for academic journals.

The outline (name the chunks).

Help/Markdown Quick Reference

Add a code chunk wih Ctrl+Alt+I

Rendering R Markdown

Knit or preview. For pdf, need $\LaTeX$ (install).

Adding runtime: shiny generates a Shiny report. Launch the interactive
app.

Publish reports online.

Compile notebook

File/Compile Notebook for R script. The script becomes a report (Word,
PDF, HTML).

RStudio’s $\LaTeX$ editor

Install $\LaTeX$.

Open a .tex file in RStudio. RStudio has limited options to edit $\LaTeX$;
enough to write and compile.

The preview window is linked to the source window. If we click on a
character in the source window, press Ctrl+click: the corresponding
character is highlighted in the preview window. Vice-versa.

Tools/Global options/Sweave to change the $\LaTeX$ options.

Shiny

The server is online.

shiny.rstudio.com

When we create a Shiny app, we create two files: ui.R and server.R

Run App (the app) or Ctrl+Shift+Enter

Publish Shiny apps

Need an account and the shinyapps package.

devtools::install_github("rstudio/shinyapps")

Deploy the local app online. Unique URL. Monitor usage, view logs,
archive or delete the app. Max 5 apps at a time for free. Paid account.