Rstudio tips - Key bindings to program and explore data with R

Rstudio is an editor for the R statistical programming language which can be installed on windows, mac and Linux. See my post explaining R setup under Debian.

Edit code

• TAB auto complete object names
• F1 on a function name shows the help page of that function
• F2 on a function name jumps to the code where that function was created. I found this key so useful that I decided to created this blog post.
• CTRL+W  close a tab
• CTRL+F find and replace text
• CTRL+SHIFT+F find in all files in a directory (like grep), then click on results lines to jump in the files

Explore data

In the environment window, click on a data frame to view it then click on filter to filter the data frame according to various criteria.

Create pdf or html reports

When editing a markdown .Rmd document, the pdf or html report can be generated with CTRL+SHIFT+K.

Create a package

The R packages book by Hadley Wickham explains how to create R packages. Useful short-cuts when working with packages:

• CTRL+SHIFT+B build the package
• CTRL+SHIFT+D generate documentation
• CTRL+SHIFT+T run devtools::test()

The documentation step can be set to run automatically with the package building under build / configure build tools / generate documentation with Roxygen / configure.

Vim mode

Vim mode can be activated under Tools / Global options / Code. Enter command mode with ":" and ask for ":help".  I use primarily the following keys:

• jklhw$ggG navigate text
• iaoA enter edit mode to insert text
• Escape return to navigation mode
• v select text
• ypP copy selected text and paste
• d delete 
• /nN search 

R, packages and Rstudio install on Debian wheezy

See also my previous post on Debian GNU-Linux installation on a Lenovo T400.

R install

I used the Synaptic package manager to add the R repository for Debian from a nearby mirror, under : settings / repositories / other software / add.
Add this APT line:

deb http://cran.univ-paris1.fr/bin/linux/debian/ wheezy-cran3/

There was an error:

W: GPG error: http://cran.univ-paris1.fr wheezy-cran3/ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 06F90DE5381BA480

After looking at several forums, and this stackoverflow question, I installed debian-keyring and added the key with the commands:

gpg --keyserver pgpkeys.mit.edu --recv-key 06F90DE5381BA480
gpg -a --export 06F90DE5381BA480 |sudo apt-key add -

I could then install R version 3 from the synaptic package manager.

Rstudio

I downloaded R-studio and installed it. There was a missing dependency for libjpeg62. I installed that package from Synaptic. Then ran the dpkg command to install rstudio.

dpkg -i rstudio-0.98.507-i386.deb

Tools

Then I installed Git in order to clone my R project from an online repository.

git clone  project_repository_url

Packages

Within Rstudio, I installed a few packages:

install.packages(c("plyr", "reshape2", "ggplot2"))
install.packages(c("xtable", "markdown", "devtools"))

devtools

The devtools packages requires a libcurl dev Debian package. You can install it at the shell prompt:

$ sudo apt-get install libcurl4-gnutls-dev

Back at the R prompt

install.packages("devtools")

Other dependencies might be needed, the RStudio page on devtools recommends installing the Debian package r-base-dev.

dplyr

The dplyr package required the latest version of a Rcpp package. Which was not available on my CRAN mirror. I installed it from source, (based on this message):

install.packages("Rcpp", type = "source")

install.packages("dplyr")

xlsx

The xlsx package installation complained:

configure: error: Cannot compile a simple JNI program. See config.log for details.
Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.

Required the latest version of java 7. (inspired by this post). I installed openjdk-7 from the synaptic package manager. Then ran

update-alternatives --config java  # Choose java 7 as the default

R CMD javareconf

Then

install.packages("xlsx") # worked

RMySQL

MySQL client and server are installed on my system.
While installing RMySQL, I struggled with a configuration error:

  could not find the MySQL installation include and/or library
  directories.  Manually specify the location of the MySQL
  libraries and the header files and re-run R CMD INSTALL.

This post has an answer (thanks!):

sudo apt-get install libdbd-mysql  libmysqlclient-dev

That fixes the issue!
I can connect to the database

library(RMySQL)
mychannel <- br="" dbconnect="" host="localhost" user="paul" ysql="">                       password="***", dbname="dbname")

R packages which are better installed from the Debian package manager

Some packages, such as ‘minqa’, ‘SparseM’ and ‘car’ return an error when one tries to install them from the R prompt. The can only be installed from the Debian package manager, where they have names starting with "r-cran": "r-cran-car", "r-cran-sparsem", "r-cran-minqa".

Ready to work!

Regular Expression

Rstudio REGEX
Wanted to replace # at the end of the line. So that they don't appear in the code navigator. $ indicates the end of a line in a regular expression. 
Replaced #######$ by ####### # .