4 Day 5 - workflows, loops, packages, and help
Important links:
- The Syllabus / Notes - you are here!
- The Worksheet for Day 5 - save it, and open it from inside RStudio ( control/combo + o key, usually). You can also go here and then click “Raw”, and save that as a file. Open that inside Rstudio.
Today we’re going to learn about applying R skills to repeat, reproduce, extend, and share your analyses.
Here’s some broad questions to reflect on the previous two days:
- Crack open your code - can you use it again?
- Can you adapt it to modify your question, feed in new data, and modify the scientifically-important bits easily?
- Can you share it with someone and they follow along?
Our goals are to learn:
- Why and how to organize work in a folder and rmarkdown files
- How look at character strings, to look for patterns and calculate lengths of strings
- Why and how to write loops to do many analyses in a scalable way
- What packages are for, how to find them, and how to install them
- How to find help and tackle new problems with a learning community
Preparing for Today: Please make sure you have completed all readings and activities from the previous days. If you have not found the time to do so, go ahead and join us to start on this material today.
This site will stay up for at least several months (if not years), so these notes and worksheets (and us!) will be available long after.
Today’s Schedule:
| Start Time | End Time | Activity | Description | Facilitator |
|---|---|---|---|---|
| 10:00 AM PDT | 10:15 AM PDT | Synchronous - lecture | 4.1 organizing workflows | Darach, Melissa, Samson, Margaret, Zac |
| 10:15 AM PDT | 10:45 AM PDT | Synchronous - breakout rooms, then lecture | 4.1 exercises | Darach, Melissa, Samson, Margaret, Zac |
| 10:45 AM PDT | 12:15 PM PDT | Asynchronous - video, slack, etc | 4.2 Project - analyze viral protein sequences | Darach, Samson, Margaret, Zac |
| 12:15 PM PDT | 12:30 PM PDT | Synchronous - lecture | 4.2 Modular, extendable workflows | Darach, Melissa, Samson, Margaret |
| 12:30 PM PDT | 01:00 PM PDT | Break | Lunch. Take a computer break! | N/A |
| 01:00 PM PDT | 01:15 PM PDT | Synchronous - lecture | 4.3 Packages - why and how | Darach, Samson, Margaret, Zac |
| 01:15 PM PDT | 02:00 PM PDT | Asynchronous - video, slack, etc | 4.3 exericses | Darach, Samson, Margaret, Zac |
| 02:00 PM PDT | 02:15 PM PDT | Synchronous - lecture | 4.3 wrapup | Darach, Samson, Margaret, Zac |
| 02:15 PM PDT | 02:30 PM PDT | Break | Take a computer break! | N/A |
| 02:30 PM PDT | 02:45 PM PDT | Synchronous - lecture | 4.4 Demo/discuss some places to find help | Darach, Samson, Margaret |
| 02:45 PM PDT | 03:15 PM PDT | Synchronous - groups | 4.4 projects - attempt ambitious projects | Darach, Samson, Margaret, Zac |
| 03:15 PM PDT | 03:30 PM PDT | Synchronous - lecture | 4.5 Wrapping up | Darach, Samson, Margaret, Zac |
Licensed Creative Commons Attribution-NonCommercial-ShareAlike 4.0