nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.
University of New Mexico Health Sciences Center
May 16-17, 2022
8:00 am - 5:00 pm MDT
Instructors: Lori Sloane, Harry Snow, Todd Quinn, Qingqing Li
Helpers: Jon Wheeler
General Information
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: HSLIC Room 428, University of New Mexico, Albuquerque, NM, 87131. Get directions with OpenStreetMap or Google Maps.
When: May 16-17, 2022. Add to your Google Calendar.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).
Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:
- The room is wheelchair / scooter accessible.
- Accessible restrooms are available.
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email LSloane@salud.unm.edu or jwheel01@unm.edu for more information.
Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.
Registration: To register, please complete the form at https://www.nmepscor.org/software-carpentry-r-for-reproducible-scientific-analysis. Registration is capped at 20 people.
Code of Conduct
Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.
Collaborative Notes
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Surveys
Please be sure to complete these surveys before and after the workshop.
Schedule
Day 1
| Before | Pre-workshop survey |
| 08:00 | Setup & Introduction to R and RStudio |
| 09:00 | Project Management with RStudio |
| 09:30 | Seeking Help |
| 10:00 | Morning break |
| 10:15 | Data Structures |
| 12:00 | Lunch break |
| 13:00 | Exploring Data Frames |
| 13:30 | Subsetting Data |
| 14:30 | Afternoon break |
| 14:45 | Control Flow |
| 15:45 | Creating Publication-Quality Graphics with ggplot2 |
| 16:30 | END |
Day 2
| 08:00 | Vectorization |
| 09:00 | Functions Explained |
| 10:30 | Morning break |
| 10:45 | Writing Data |
| 11:00 | Splitting and Combining Data Frames with plyr |
| 12:00 | Lunch break |
| 13:00 | Data Frame Manipulation with dplyr |
| 14:30 | Afternoon break |
| 14:45 | Data Frame Manipulation with tidyr |
| 15:30 | Producing Reports with knitr |
| 16:00 | Wrap-up |
| 16:30 | Post-workshop Survey |
| 16:40 | END |
Setup
To participate in a Software Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
Text Editor
When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.
nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.
Video Tutorial
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
R
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
Video Tutorial
Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.
Video Tutorial
Instructions for R installation on various Linux platforms (debian,
fedora, redhat, and ubuntu) can be found at
<https://cran.r-project.org/bin/linux/>. These will instruct you to
use your package manager (e.g. for Fedora run
sudo dnf install R and for Debian/Ubuntu, add a ppa
repository and then run sudo apt-get install r-base).
Also, please install the
RStudio IDE.
Acknowledgment
This workshop is funded through the National Science Foundation EPSCoR Cooperative Agreement OIA-1757207. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
