Welcome & get ready for the course

Research Beyond the Lab: Open Science and Research Methods for a Global Engineer

Prof. Elizabeth Tilley and Lars Schöbitz

Feb 22, 2024

This class is being recorded. Access to the recording is restricted to ETH members.

Welcome! 👋

Meet the lecturers

Prof. Elizabeth Tilley

Headshot of Elizabeth Tilley

  • Environmental Engineer 🔨
  • Economist 📈
  • Turkey Lover 🦃
  • Canadian 🇨🇦

Lars Schöbitz

Headshot of Lars Schöbitz

Learning Goals (for the course)

  1. Be able to use a common set of data science tools (R, RStudio IDE, Git, GitHub, tidyverse, Quarto) to illustrate and communicate the results of data analysis projects.

  2. Learn to use the Quarto file format and the RStudio IDE visual editing mode to produce documents with citations, footnotes, cross-references, figures, and tables.

  3. Be able to design a questionnaire to collect information that can be analysed to answer a waste-related research question that is relevant for Zurich.

  4. Understand the main challenges associated with managing different types of waste, and how they differ between Europe and Africa.

Why all of this?

Your turn: About you

Pick an item and take notes for 1 minute:

What does the item you have picked have to do with the reason for you being here?

01:00

In pairs

Take 2 minutes each to share with your partner:

What does the item you have picked have to do with the reason for you being here?

05:00

Course Calendar

module date topic
1 22 February 2024 Welcome & get ready for the course
2 29 February 2024 Data science lifecycle & Exploratory data analysis using visualization
3 07 March 2024 Data transformation with dplyr
4 14 March 2024 Data import & Data organization in spreadsheets
5 21 March 2024 Conditions & Dates & Tables
6 28 March 2024 Data types & Vectors & Pivoting
04 April 2024 Easter Break
7 11 April 2024 Joining tables & Creating and publishing scholarly articles with Quarto and GitHub pages
8 18 April 2024 Waste Research
9 25 April 2024 Research Design
10 02 May 2024 Survey Design
09 May 2024 Auffahrt Break
11 16 May 2024 Pre-test and logistics
23 May 2024 Data collection
12 30 May 2024 Data analysis & report writing
06 June 2024 Project Submission Deadline
13 June 2024 Exam

Course structure

  • My turn: Lecture segments + live coding
  • Our turn: Live coding + follow along
  • Your turn: Exercises in pairs

My turn: Lecture segments + live coding

  • Instructor writes and narrates code out loud
  • Instructor explains concepts and principles that are relevant
  • Code is displayed on screen

Our turn: Live coding + follow along

  • Instructor writes and narrates code out loud
  • Instructor explains concepts and principles that are relevant
  • Code is displayed on screen
  • Learners join by writing and executing the same code

Your turn: Exercises in pairs

  • Two learners work together in pairs
  • One person does the typing (the driver)
  • One person offers comments and suggestions (the navigator)

Getting help

  • (from next week), please use a pink sticky note to indicate that you have a problem. I will try to address your issue if time permits.

  • (from next week), during your turn exercises, please use a yellow sticky note to indicate when you have completed an exercise.

Platforms and Tools

  • Course website
  • R
  • tidyverse R Packages
  • Posit Cloud
  • RStudio IDE
  • Quarto publishing system
  • Zotero reference management
  • Google Workspace (Sheets & Forms)

Course website

rbtl-fs24.github.io/website/

Our turn: Open and bookmark the course webiste

  1. Open a web browser on your laptop.
  2. Navigate to the course website: rbtl-fs24.github.io/website/
  3. Create a bookmarks folder named rbtl-fs24 in your bookmarks toolbar
  4. Add a bookmark of the course website to the folder rbtl-fs24
05:00

Learning Objectives (for this week)

  1. Learners can access the Posit Cloud workspace for the course.
  2. Learners can use the Element chat to introduce themselves.
  3. Learners can open an issue on GitHub and tag the course instructor.
  4. Learners can clone a repository from GitHub and use the GitHub PAT to push a commit from their local repository to GitHub.
  5. Learners can navigate the course website and understand the learning objectives of the course.

Version Control

Version Control with Git and GitHub

A way to share files with others, so they can:

  • download
  • re-use
  • contribute

You can view the history of files, and jump back in time to any point.

Why is it useful?

Git and GitHub

  • Git is a software for version control
  • Created in 2005
  • Popular among programmers collaboratively developing code
  • Tracks changes in a set of files (directory/folder/repository)

  • GitHub is a hosting platform for version control using Git

  • Launched in 2008, aquired by Microsoft in in 2018, Microsoft for US$ 7.5 billion

  • 100 million Users (20.5 in 2022 alone) (October, 2023)

  • Social media for software developers

My turn: A tour of GitHub

Sit back and enjoy!

Your turn: Get a GitHub account

  1. Open a web browser on your laptop.
  2. Navigate to the course website: rbtl-fs24.github.io/website/
  3. If you haven’t yet, bookmark the course website
  4. In the left-hand menu, clock on Module 1, then select am-01: GitHub
  5. Follow the instructions
  6. Place a yellow sticky note on your laptop when you have completed the assignment
05:00

Posit Cloud

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Your turn: Log into Posit Cloud with GitHub account

  1. Open a web browser on your laptop.
  2. Navigate to the course website: rbtl-fs24.github.io/website/
  3. If you haven’t yet, bookmark the course website
  4. In the left-hand menu, clock on Module 1, then select am-02: Posit Cloud
  5. Follow the instructions
  6. Place a yellow sticky note on your laptop when you have completed the assignment

GitHub Authorisation

  • If this is your first time logging in to Posit Cloud with your GitHub account, you will be prompted to authorize Posit Cloud to access your GitHub account information.
  • Once you have authorized access, you will be redirected back to the Posit Cloud website and logged in to your account.
05:00

Hello Quarto

Meeting you where you are

I’ll assume you

  • do not have R or git experience

  • have not worked in an IDE before (e.g. RStudio IDE)

  • want to learn about R

  • want to learn about Quarto and publishing

  • want to learn about project management with GitHub

I’ll teach you

  • R

  • Quarto syntax and formats

  • Markdown

  • Git via RStudio GUI

  • GitHub issues, project management, and publishing

What is Quarto?

Quarto …

  • is a new, open-source, scientific, and technical publishing system
  • aims to make the process of creating and collaborating dramatically better
A schematic representing the multi-language input (e.g. Python, R, Observable, Julia) and multi-format output (e.g. PDF, html, Word documents, and more) versatility of Quarto.

Artwork from “Hello, Quarto” keynote by Julia Lowndes and Mine Çetinkaya-Rundel, presented at RStudio Conference 2022. Illustrated by Allison Horst.

My turn: A tour of Quarto



Sit back and enjoy!

Take a break

Please get up and move! Let your emails rest in peace.

15:00

Your turn: md-01-exercises

  1. Open posit.cloud in your browser (use your bookmark).
  2. Open the rbt-fs24 workspace for the course.
  3. Click Start next to md-01-exercises.
  4. In the File Manager in the bottom right window, locate the hello-quarto.qmd file and click on it to open it in the top left window.
  5. Render the document.
  6. Add your name to the author: key in the YAML header
  7. Render the document
  8. Inspect components of the document and make one more update and re-render.
  9. Discuss notes about updates you’ve made with your neighbor. Note any aspects of the document that are not clear after the tour and your first interaction with it.
05:00

From the comfort of your own workspace

A screenshot of a Quarto document rendered inside RStudio

A screenshot of a Quarto document rendered inside JupyterLab

A screenshot of a Quarto document rendered inside VSCode

Quarto formats

One install, “Batteries included”

  • RMarkdown grew into a large ecosystem, with varying syntax.

  • Quarto comes “batteries included” straight out of the box

    • HTML reports and websites
    • PDF reports
    • MS Office (Word, Powerpoint)
    • Presentations (Powerpoint, Beamer, revealjs)
    • Books
  • Any language, exact same approach and syntax

Many Quarto formats

Feature R Markdown Quarto
Basic Formats

html_document

pdf_document

word_document

html

pdf

docx
Beamer beamer_presentation beamer
PowerPoint powerpoint_presentation pptx
HTML Slides

xaringan

ioslides

revealjs

 revealjs
Advanced Layout

tufte

distill

 Quarto Article Layout

Many Quarto formats

Feature R Markdown Quarto
Cross References

html_document2

pdf_document2

word_document2

 Quarto Crossrefs
Websites & Blogs

blogdown

distill

Quarto Websites

Quarto Blogs
Books bookdown Quarto Books
Interactivity Shiny Documents Quarto Interactive Documents
Journal Articles rticles Journal Articles
Dashboards flexdashboard Quarto Dashboards

Take a break

Please get up and move! Let your emails rest in peace.

15:00

Course information

Weekly Structure

Monday
Tuesday Student hours from 14:00 to 16:00 (CET)
Wednesday Assignment submission, latest by 23:59 (CET)
Thursday Lecture from 12:15 to 15:00 (CET)
Friday

Performance assessment

  • End-of-semester exam: 50 points
  • Compulsory continuous performance assessment: 50 points, of which
    • Homework assignments: 20 points (n = 10)
    • Capstone project: 30 points, of which
      • Technical parts of submitted report: 20 points (we will communicate what we expect)
      • Intellectual framing of results: 10 points (we will communicate what we expect)

Grading scheme

Table Table 1 shows the conversion from points to grades. Grades follow the ETHZ’s Grading System. Points are rounded to the nearest grade, for example:

  • 97 points = 5.75
  • 93 points = 5.75
  • 92 points = 5.50
  • 45 points = 4.00
  • 44 points = 3.50
Table 1: Conversion from points to grades.
grade points
6.00 100
5.75 95
5.50 90
5.25 85
5.00 80
4.75 75
4.50 70
4.25 60
4.00 50
3.50 40
3.00 30
2.50 20
2.00 10
1.00 0

End-of semester exam

  • 2-hour final written exam
  • 50 points
  • all material allowed (incl. internet)
  • for the use of AI tools we expect you to add a link to the prompt
  • programming exercises using the R programming language
  • success depends on the effort put into the compulsory continuous performance assessment

Compulsory continuous performance assessment

Homework assignments:

  • 10 assignments
  • assessed as pass/fail
  • 2 points each
  • 20 points in total
  • submitted as rendered Quarto documents on GitHub

Compulsory continuous performance assessment

Capstone Project

  • Data analysis project report with a dataset generated by you
  • Method: Survey or Observational Study using Google Forms and Sheets
  • 1 project per student, submitted as rendered Quarto document on GitHub
  • 30 points in total
    • 20 points for the technical parts of the submitted report
    • 10 points for the intellectual framing of results

Readings

  • Some required for homework assignments
  • Additional readings provided to support learning
  • Not graded

Policies

Class attendance

  • Can’t attend in person? Inform us before the lecture
  • Live streaming recording available
  • Missed classes: work through the material using the recording

Policies

Use of AI tools

  • Use it! (e.g. perplexity.ai has useful free features)
  • Refine your prompts to get good outcomes
  • Don’t trust anything it says
  • Include links to your prompts
  • Be thoughtful about when this tool is useful

AI Policy adapted from Ethan Mollick

Policies

Code of Conduct

Homework assignments module 1

Module 1 documentation

rbtl-fs24.github.io/website/modules/md-01.html

Homework due date

  • Homework is a pre-requsite for active participation in Module 2
  • Homework assignment due: Wednesday, 28th February

Wrap-up

Thanks! 🌻

Slides created via revealjs and Quarto: https://quarto.org/docs/presentations/revealjs/ Access slides as PDF on GitHub

All material is licensed under Creative Commons Attribution Share Alike 4.0 International.

rbtl-fs24.github.io/website/