xpf100/course

R programming courses material

Jump to slides, install, settings, packages, sumatra, resources

Find info about the fall 2018 course at Potsdam university here.

slides

Here are the slides I use for R courses in several versions:

• handout (one pdf page per slide)
• presentation (animated with LaTeX \onslide et al.)
• source code (.Rnw, I suggest rightclick - save as)

You can download all datasets or the complete repository at once.
The presentation template is available through berryFunctions::createPres.

install

First install R itself and then Rstudio:

• R itself
  • R on Windows: https://cloud.r-project.org/bin/windows/base/release.htm (update through installr)
  • R on Mac: follow e.g. these instructions: https://www.r-bloggers.com/installing-r-on-os-x
  • R on Linux Ubuntu: See instructions below
• Rstudio on all platforms: https://www.rstudio.com/products/rstudio/download/#Desk

Installing R on Linux Ubuntu so that sudo apt upgrade updates to the latest R version if outdated (idea from Kris Eberwein and Dean Attali):
Open a terminal (CTRL+ALT+T) and paste (CTRL+SHIFT+V) the following lines.
Replace xenial with e.g. trusty if you have another Ubuntu version (check in shell with lsb_release -a ):
18.10 cosmic-cran35, 18.04 bionic-cran35, 16.04 xenial, 14.04 trusty

sudo echo "deb https://cloud.r-project.org/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -
sudo apt-get update
sudo apt-get install r-base r-base-dev

In case you run into GPG problems like the example below, try replacing both gpg lines with the single line (idea source):

sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv E084DAB9

gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com ?: keyserver.ubuntu.com: No route to host gpgkeys: HTTP fetch error 7: couldn't connect: No route to host gpg: no valid OpenPGP data found. gpg: Total number processed: 0 gpg: keyserver communications error: keyserver unreachable gpg: keyserver communications error: public key not found gpg: keyserver receive failed: public key not found

settings

Suggested Rstudio settings (for reproducibility and compatibility):

• Tools - Global Options - General
  • ON: Restore previously open source documents at startup
  • OFF: Restore .Rdata into workspace at startup
  • Save workspace to .RData on exit: NEVER
    Instead use save(object, file="object.Rdata") after long computations.
    You can load them later with load("object.Rdata").
• Tools - Global Options - Code - Display
  • ON: Show margin (Margin column:80) People hate horizontal scrolling!
  • ON: Highlight R function calls
• Tools - Global Options - Code - Saving
  • Line ending conversion: Windows (CR/LF)
  • Default Text Encoding: UTF-8
• Tools - Global Options - Code - Completion - Completion Delay
  • Show completions after characters entered: 2
  • Show completions after keyboard idle (ms): 0
• Tools - Global Options - Sweave
  • Weave Rnw files using: knitr
• Tools - Modify Keyboard Shortcuts
  • remove CTRL+Y from the command "paste last yank" (if you want it to mean "redo" as in other programs)
  • Set Working Directory to Current Document's Directory: CTRL + H

packages

Installing add-on R packages usually is easy from within R (and works without admin rights):

install.packages("ggplot2")

On Linux, some packages with external dependencies (like rJava) can be more difficult. In such cases, you probably just want to open a terminal (CTRL+ALT+T) and paste (CTRL+SHIFT+V) sudo apt-get install r-cran-rjava (all lower-cased). Here's the official information on this topic.

Installing the sf package for spatial data is a bit tricky on Linux because it needs a recent version of gdal. If install.packages("sf") does not work, please try the following:

sudo apt-get install libudunits2-dev
sudo add-apt-repository ppa:ubuntugis/ppa && sudo apt-get update
sudo apt-get install gdal-bin
sudo apt install libgdal-dev libproj-dev

sumatra

I like to use sumatra PDF viewer as the default viewer. It doesn't lock files from editing, hence currently opened files can be changed (by R, e.g.). It comes in Rstudio/bin/sumatra and I like to change some settings:
open Rstudio/bin/sumatra/sumatrapdfrestrict.ini and set SavePreferences = 1
open and close a pdf, so that Rstudio/bin/sumatra/SumatraPDF-settings.txt will be created
now change the following entries:

• DefaultZoom = fit page (probably already the default)
• ShowToc = 0
• DefaultDisplayMode = single page

resources

• R-weekly - weekly newsletter about all things R
• Rbloggers - blog aggregator about R
• Shiny - web application framework for R/Rstudio
• Rmarkdown - document/notebook generation framework for R/Rstudio
• Github guides - Introduction to github

online tutorials

• http://stat545.com/topics.html (excellent tutorial)
• https://www.edx.org/course/introduction-r-programming-microsoft-dat204x-0 (Datacamp, with login, but free)
• http://tryr.codeschool.com/levels/1/challenges/1 (codeschool, interactive, login to save progress)