Software Carpentry Workshop - R

Institute of Agriculture and Animal Science, Tribhuvan University

Online

August 18-19, 2020

9:00am - 5:00pm (NPT)

Instructors: Elnaz AmanzadehJajin, Nick Wong, Sourav Singh, Aditya Bandla

Helpers: Kishor Dahal, Subodh Khanal, Roshan Subedi, Rajesh Poudel

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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: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: August 18-19, 2020. 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 dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email kishor.dahal@iaas.tu.edu.np , nick.wong@monash.edu , subodh.khanal@pakc.tu.edu.np , roshan.subedi@lac.tu.edu.np , rajesh.poudel@iaas.tu.edu.np or elibio449@gmail.com for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

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.

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1

Before Pre-workshop survey
09:00 Analysing Patient Data, Creating Functions in R
10:30 Morning break
11:00 Analyzing Multiple Datasets, Making Choices in R
12:00 Lunch break
13:00 Command-Line Programs, Best Practices for Writing R Code
14:30 Afternoon break
15:00 Reading and Writing CSV Files, Understanding Factors
16:00 Data Types and Structures
16:40 Wrap up
17:00 END

Day 2

09:00 R for Reproducible Scientific Analysis, R and R Studio
10:30 Morning break
11:00 Data Structures, Data Frames and Subsetting Data
12:00 Lunch break
13:00 Creating plots with ggplot2
14:30 Afternoon break
15:00 Vectorisation and Functions
16:00 dplyr and plyr
16:30 Wrap-up
16:15 Post-workshop Survey
17:00 END

Syllabus

Programming in R

  • Working with Vectors and Data Frames
  • Reading and Plotting Data
  • Creating and Using Functions
  • Loops and Conditionals
  • Using R from the Command Line
  • Reference...

R for Reproducible Scientific Analysis

  • R and RStudio
  • Producing reports with knitr
  • Creating Publication-Quality Graphics with ggplot2
  • Functions and Vectorisation
  • Tidyverse, plyr, dplr
  • Reference...

Setup

To participate in a Software Carpentry workshop, you will need access to the software 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.

Install the videoconferencing client

We will be using Microsoft Teams for this workshop, while you could use the web version, we would encourage you to download and install the client. Download Microsoft Teams

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

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

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.