To do list from beta pilot (2022-05-25-aucenter-online)

[ErinBecker]

Below is a summary of the 20 pages of notes the workshop observers took at the first beta pilot workshop teaching this lesson (2022-05-25-aucenter-online). Issues are listed by episode and are described in an actionable way wherever possible. In a few cases, more discussion may be needed within the developer team before an action can be decided.

Follow-up activity on the list below will be split among the lesson developers. To claim one or more of the items, place your name in bold at the start of the item. After you have created an PR for the item, add a link to your PR at the end of the item. Check off an item once a PR has been merged.

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Introduction to the example dataset and file type

• [x] #148

Introducing R and RStudio IDE

• [x] #181
• [x] #240
• [ ] Add a warning box that the AWS link may not work for some browsers (e.g. Edge). For those browsers, learner needs to copy link and paste into browser instead of clicking link in spreadsheet. If anyone is using VPN, please switch it off for this workshop.
• [x] #261
• [ ] Remove section in 01-introduction that uses ??geom_point as an example of what happens when you search for help on a package that isn’t installed on your system. This was unnecessarily confusing.
• [x] #264
• [x] #265

R Basics

• [ ] In R Basics - creating objects in R, add callout box about white space not being necessary but making code easier to read. Link to style guide?
• [ ] Should we add a callout box explaining why doing assignment operation with = is a problem? (Erin votes no but including for completeness)
• [ ] Get rid of the example in R basics that computes the golden ratio and replace with a less confusing mathematical equation (both in the code chunks and in the exercise)
• [ ] Add an example to the vectors section demonstrating that character vectors are case sensitive
• [ ] In R basics - creating and subsetting vectors, note to Instructor that they and learners should copy/paste the character vectors provided in the code chunk. There is nothing gained by the learners in having to type those out by hand.
• [x] #183
• [x] #184
• [x] #178
• [x] #175
• [x] #179
• [x] #258
• [x] #180
• [x] #182

R basics continued - factors and data frames

• [x] #149
• [ ] Improve the explanation of the difference between “base R” and “tidyverse” in a way that limits learner cognitive overhead. This explanation may need to come earlier in the lesson.
• [ ] At the end of “importing tabular data into R” include a table that describes what each of the column names means / stands for
• [ ] Change the note “put the first three columns of variants into a new data frame called subset” so that it matches code chunk, which also includes column 6
• [ ] Explain the order of columns and rows in two-dimensional subsetting
• [ ] str(subset) includes integer data, which hasn’t been introduced before. Explain this in the text.
• [ ] Instead of introducing snps <- c(alt_alleles . . . ), break this into smaller demos. First show alt_alleles[alt_alleles=="A"] then show a few variations before stringing them in within c().
• [ ] Might be good to show str(factor_snps) and summary(factor_snps) on a character vector to reinforce the difference between factors vs character vectors.

Using packages from Bioconductor

• [x] #170
• [x] #163
• [x] #168
• [x] #188
• [x] #173
• [x] #169
• [x] #185
• [x] #186
• [x] #187

Data wrangling and analysis with tidyverse

• [x] #150
• [x] #157
• [x] #158
• [x] #160
• [x] #162
• [x] #166
• [x] #165
• [x] #164
• [x] #172
• [x] #176
• [x] #177

Data visualization with ggplot2

• [x] Remove the period in the example doing facet_grid, as it hasn’t been explained. (but see PR #138)

[ytakemon]

• [x] Given our discussion today, we will be removing the Knitr lesson to ensure that we stay within time and instead will be pointing to other resources (eg. R for reproducible research).

[ytakemon]

One more section to go! We might finish this by the end of this year 😲 @naupaka @JasonJWilliamsNY