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We will be recording this workshop via Zoom. Please see the Recording Notice: https://ucla-data-archive.github.io/2020-04-10-ucla/#recording-notice
Recordings will be uploaded here: https://doi.org/10.25346/S6/ZJKUAC
* Recordings from Week 1 & 2 are already there
* Code from Week 1 & 2 is here: https://github.com/ucla-data-archive/2020-ucla-r
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Workshop Info
Workshop website: https://ucla-data-archive.github.io/2020-04-10-ucla/
Zoom link: https://ucla.zoom.us/j/942467827 OR
https://ucla.zoom.us/my/ucladatascience
Lesson: http://swcarpentry.github.io/r-novice-gapminder/
In case you get knocked off Zoom or have issues logging in, email timdennis@ucla.edu
Setting up software & interfaces
Needed Software
Zoom & Rstudio - Interface
- Helpers will aid learners in how to get this interface < https://tinyurl.com/qnqm2l6> (so that instructor UI will mirror learners’ UI). During screen-sharing, (at top of screen) make sure:
- “Fit-to-screen” is checked ☑️
- Side-by-side is UNchecked ?
Zoom - Nametags
- Learners, please add your name to the Zoom Room so it reflects what you registered with. If you also prefer to use a pseudonym instead of your name, please let us know so we can match you with the registration.
Zoom Course Norms
- Stay on mute unless you need to talk.
- Stay on video if you can, esp. during small group work.
- Use the chat to ask a question and the helpers will respond. You can also direct message a helper.
- We will be using the Zoom breakout rooms. You will be prompted to enter a breakout room.
------------------- Day 3 -------------------
Sign-In: Name / Affiliation / Email
Leigh Phan / UCLA Library Data Science Center / leighphan@library.ucla.edu
Kristian Allen (helper) he,him,his / UCLA Library / kallen2@library.ucla.edu
Tim Dennis (helper) / UCLA Library / tdennis@library.ucla.edu
Scott Gruber (helper) / UCLA Institute of the Environment and Sustainability / scott.gruber@ucla.edu
Jamie Jamison (helper) / UCLA Library Data Science Center / jamison@library.ucla.edu
Ibraheem Ali (helper) / UCLA Library / ibraheemali@library.ucla.edu
Dave George (helper) / UCLA Anderson / dave.george@anderson.ucla.edu
Geno Sanchez (helper) / he,him,his / UCLA Library / genosanchez@library.ucla.edu
Keerthi Kocherlakota/ UCLA Anderson/ keerthi.k.2021@anderson.ucla.edu
Holly Huang/ UCLA Dept of Medicine/ hollykthuang@ucla.edu
Charlotte Fagan / UCLA Luskin, UCLA Anderson / charlotte.fagan.2021@anderson.ucla.edu
Radon Liang/ UCLA Anderson/ radon.liang.2021@anderson.ucla.edu
Cytlalli Gonzalez/UCLA Institute of Environment and Sustainability/ csglez99@gmail.com
Doug Daniels / UCLA Library DSC / dougdaniels@library.ucla.edu
Taylor Mobley, Fielding School of Public Health / tmmobley@ucla.edu
Fan Zhao, Epidemiology, zhaofan1996@g.ucla.edu
Phatharajit Phatharodom, UCLA Epidemiology, praephatjit@gmail.com
Tony Lun, tony.lun.2021@anderson.ucla.edu
Jennifer Lin, UCLA Epidemiology, ichunlinbebe@gmail.com
Francisco Avalos Jr. / UCLA Stats / fraval@ucla.edu
Sungwon Han, sungwon.han.2021@anderson.ucla.edu
Joy Guey/UCLA Social Sciences Center for Education Research & Technology /joy@sscert.ucla.edu
Ted Lee
Soizic Riche/ UCLA Neurobiology/ soizic.riche@gmail.com
Jayne Vidheecharoen / UCLA Luskin / jaynev@ucla.edu
Anthony Linares/UCLA SOM/alinares@mednet.ucla.edu
Terence Lam / UCLA ANderson / terence.lam.2021@anderson.ucla.edu
Maryam Ghajar/Civil Eng/maryamghajar@ucla.edu
Emily Martinez/emart615@g.ucla.edu
Ankita Sharma / UCLA Anderson / ankita.sharma.2021@anderson.ucla.edu
Leigh-Michil George (she, her, hers)/ Geffen Academy at UCLA / lgeorge@geffenacademy.ucla.edu
Shawnt Issakhanian / UCLA Dept of Medicine / shawnti@g.ucla.edu
Zhan Shu, UCLA Psychiatry, zhanshu@ucla.edu
Sebastian Suarez, Master's of Social Sciences, ssuarez3@g.ucla.edu
Lesson:
https://swcarpentry.github.io/r-novice-gapminder/08-plot-ggplot2/index.html
https://raw.githubusercontent.com/ucla-data-archive/2020-ucla-r/master/03_r-markdown_ggplot.Rmd
- * right-click and save > open in Rstudio (we'll use this in the 2nd phase of class)
Schedule:
9:15-9:40 - What is RMarkdown? How to setup an RMarkdown document
9:40-10:15 - Creating charts and graphics with ggplot2 + Exercises
10:15-10:25 - Break
10:30-11:00 - Exercises (Breakout rooms)
11:00-11:15 - Review & Discussion
11:15-11:45 - Exercises (Breakout rooms)
11:45-12:00 - Feedback survey + wrap up
For access to recordings for previous sessions email any of the instructors or helpers denoted at the the top of the document.
Examples of R Markdown
# Headers
# This is an `<h1>` tag
### This is an `<h3>` tag
#### My name is name-goes-here
Link to R Markdown cheatsheet which has list of most common formatt
https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf
Adding a code chunk:
mac cmd + alt + i
in order to create some space between lines in the .Rmd file add <br> after the line of text. I usually add it twice to give some space between lines.
library(gapminde
# to look at ou
Grammer of graphics visual representation of 'layers' that we are manipulating using these commands
https://www.science-craft.com/wp-content/uploads/2014/06/ggplot-1.png
ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point()
ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp, by=country, color=continent)) + geom_point()
Challenge Set
1. Modify the example so that the figure shows how life expectancy has changed over time.
2. In the previous examples and challenge we used the `aes` function to tell the scatterplot **geom** about the **x** and **y** locations of each point. Another _aesthetic_ property we can modify is the point _color_. Modify the code from the previous challenge to **color** the points by the "continent" column. What trends do you see in the data? Are they what you expected?
Common Breakout Room Questions
- Is there a way to average the data and plot it? -->
```{r}
```
To get averages by continent and plot, we need to use group_by continent & year first, then summarize to add a mean:
```{r}
gapminder %>%
group_by(continent, year) %>%
summarize(mean_gdpPercap = mean(gdpPercap)) %>%
ggplot(aes(x=year, y = mean_gdpPercap, color=continent)) + geom_point()
```
Challenge Set 2
1. Switch the order of the point and line layers from the previous example. What happened?
Challenge Set
1. Modify the color and size of the points on the point layer in the previous example.
Hint: do not use the `aes` function.
2. Modify your solution to Challenge above so that the points are now a different shape and are colored by continent with new trendlines. Hint: The color argument can be used inside the aesthetic.
Extra material for GGPLOT - if you want to continue: https://ucla-data-archive.github.io/2020-ucla-r/03b_ggplot-extras.html
DAY 4 - R Markdown
Tim Dennis / UCLA Library Data Science Center / timdennis@ucla.edu
Leigh Phan (she, her, hers) / UCLA Library Data Science Center / leighphan@library.ucla.edu
Geno Sanchez (he, him, his,) / UCLA Digital Library / genosanchez@library.ucla.edu
Kristian Allen (he, him, his) / UCLA Digital Library / kallen2@library.ucla.edu
Ibraheem Ali (he, they) / UCLA Biomedical Library / ibraheemali@library.ucla.edu
Phatharajit Phatharodom, UCLA Epidemiology, praephatjit@gmail.com
Scott Gruber / UCLA Institute of the Environment and Sustainability / scott.gruber@ucla.edu
Shawnt Issakhanian / UCLA Dept of Medicine / shawnti@g.ucla.edu
Holly Huang/ UCLA Dept of Medicine/ hollykthuang@g.ucla.edu
Taylor Mobley / UCLA Fielding School of Public Health / tmmobley@ucla.edu
Jayne Vidheecharoen / UCLA Luskin / jaynev@ucla.edu
Soizic Riche / UCLA Neurobiology/ soizic.riche@gmail.com
Zhan Shu, UCLA Psychiatry, zhanshu@ucla.edu
Tony Lun, UCLA Anderson, tony.lun.2021@anderson.ucla.edu
Charlotte Fagan (she/her), UCLA Anderson/Luskin, charlotte.fagan.2021@anderson.ucla.edu
Terence Lam, UCLA ANderson, terence.lam.2021@anderson.ucla.edu
Joy Guey/UCLA Social Sciences Center for Education Research & Technology /joy@sscert.ucla.edu
Fan Zhao/ Epidemiology/ fanzhao1996@g.ucla.edu
Francisco Avalos Jr. / statistics / fraval@ucla.edu
Download files for today: https://github.com/ucla-data-archive/2020-05-01-rmd/archive/master.zip
* Download above zip file and unzip on your desktop
* You can typically double click on the .Rproj file inside that directory and it will open the folder in Rstudio
* if that doesn't work, from R Studio, you can `open project' and navigate to that folder and open the Rproj file
Schedule:
9:10-9:30 - Why use R Markdown (slides) https://ucla-data-archive.github.io/2020-ucla-r/04a_r-markdown_slides.html
9:30-10:00 -Creating a R Markdown document, components of a R Markdown file, Markdown, code chunks
10:00 - 10:5 Exercises (Breakout room)
10:15-10:25 - Break
10:25-10:40 - How things get compiled, chunk options, & inline code
10:40-11:00 - Exercises (Breakout rooms)
11:00-11:15 - Composed example, sharing and rticles
11:15-11:45 - Exercises (Breakout rooms)
11:45-12:00 - Feedback survey + wrap up
https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf
One way to change image size in Rstudio:
<img src="smiley.jpg width=300>
If the image is not in the current directory, it may have issues loading. So you can specify the exact file path. For example
https://stackoverflow.com/a/15626317
ADD your Netlify links:
Leigh: http://elastic-jones-57ad64.netlify.app
Kristian: https://keen-newton-6db01b.netlify.app/
Terence: https://trusting-lovelace-7e21f6.netlify.app/
Joy: https://nifty-goldstine-c56a93.netlify.app/
Shawnt: http://serene-roentgen-32e1dd.netlify.app