Tools for Open Science: Reproducible Data Analysis and Paper Writing in R

ICIS 2018 Pre-Conference Workshop

Time: 8:30AM - 4:30PM

Place: Commonwealth AB (2nd floor)

Instructors

Michael C. Frank, Stanford University

Jessica Kosie U. Oregon

Elika Bergelson, Duke

Melissa Kline, MIT

Pre-workshop Setup

This workshop will be hands-on throughout! That means you need to install some software:

• This link goes to a tutorial program (Swirl) which begins by walking you through the process of downloading R and RStudio. If you have never interacted with a terminal/command line before, you might find it helpful to go through just the first few lessons of the 'Basics of R Programming' series, as well. If you have difficulty getting these installed on your laptop, we'll be on hand right before the workshop for troubleshooting!

• Make an account on the Open Science Framework.

Schedule (subject to change)

8:00 - 8:30 - Installation troubleshooting (Melissa)

8:30 - 8:45 - Getting Started (Mike)

8:45 - 11:00 - Introducing R and the Tidyverse (Jessica and Mike)

11:00 - 12:00 - Lunch Break (on your own)

12:00 - 1:15 - Reproducible Reports in RMarkdown (Mike)

1:15 - 2:30 - Intro to GGPlot (Elika) https://docs.google.com/presentation/d/1nzqs7sKOr4LWIJC6y15PLWA93zrY6jlF3xqA68frQ9A/edit#slide=id.g3a3b804d26_0_12

2:30 - 2:45 - Mid-afternoon break

2:45 - 4:00 - Sharing and managing data using the Open Science Framework (Melissa)

4:00 - 4:30 - Open Science Panel and Q&A

How to use this repository

To download a copy of this repository (containing all the files above), click the green button at the top right that says "Clone or Download" and choose "Download Zip" to download a copy to your laptop. We recommend waiting to do this until the workshop itself so you have the most up-to-date versions of everything!

Troubleshooting tidyverse installs

If tidyverse doesn't install, try these things:

• Check if you have the most recent version of R (at time of writing, 3.5). If not, get it from CRAN (google "R CRAN download"), restart, try again.
• See if tidyverse is trying to "build from source." If it is, try saying "no" to this question and see if that works.
• If that doesn't work and you have to install from source, errors may come from not having the appropriate compiler installed on your system. For a mac, this is XCode, which you will need to install from the app store.
• If all else fails, try installing an earlier version of tidyverse, e.g. via the package devtools. Try install.packages("devtools") then devtools::install_version("tidyverse", version = "1.0.0", repos = "http://cran.us.r-project.org"). if that works, you will still find that library("tidyverse") won't work, but you can do the libraries one at a time to get the ones that do, e.g. library(readr) library(tidyr) library(dplyr)

Troubleshooting knit and Rmd

An overview of R and non-western characters (Cyrillic, Chinese, etc.)

If you have non-Latin characters in your path (eg your username), the button that says knit won't work for you. Instead, type the following in the console (not in your .Rmd document):

knit("mydocument.Rmd", encoding = "utf-8")

You may find that you have this trouble in other contexts - things are getting better, but in general (for other programming languages too, not just R) if you see messages saying that a program cannot find a file or that a path doesn't exist, it may be this problem happening again!