• remove report output/source folders since we cannot change render output directory.
• remove rendered Quarto files
• remove Rmd file

Add information about the renv branch to the workshop instructor notes

it's an unwieldy name, should rename before adding link to lesson repository

so when we add them into code chunks it just generates the plot

under values of data:

"making the aggregation of evidence challenging@nitch202b"

add space after "challenging"

ReadMe starting at line 16

- tidyverse 1.3.0
- stringi 1.4.6
- BayesFactor 0.9.12-4.2.
- patchwork 1.0.0
  

What are the current version numbers?

“(Carpentry Workshop Version)” is already in the Rmd file’s YAML heading

line 143 "For 8 participants (out of N = 144 participants)"

add in FIXMEs for exercises to do during workshop , may need to "undo" the markdown code in some spots to add those exercises.

start with "FIXME: description of edit"

at end of workshop have full list with answer code?

see line 153 on and right after yaml

Leave FIXMEs for instructions purposes

but remove code chunk (and global code chunk options ) from file for teaching after episode is outlined

see lines 130-132

For some reason the alt-text from the fig is visible after rendering as well as the text in the actual paper (which is a repeat)

Are we using this code in any of the episodes? It looks like it was removed from the lesson.
Investigate if that is indeed an issue:

if (raw_data == "error")

"==" is a vector operation and "if" expects a single value. R might have become stricter about this in a recent version? I suggest using:

if (identical(raw_data, "error"))

the two figures at the end of the document.

See: https://ucsbcarpentry.github.io/R-markdown/10-publish/index.html

modify for this workshop

Main branch should be: https://github.com/carpentries-incubator/quarto-project-example/tree/ucsbcarpentry/main
We still need to add the renv branch https://github.com/UCSBCarpentry/Quarto-Project-Example/tree/renv

Since RStudio can be run in a Jupyter Hub environment like UCSB Library did for Nov 2022 workshop it would be nice to add the temporary files that come with running in that environment.

I think adding:

.ipynb_checkpoints/

to the .gitignore file would do the trick.

Probably just nitpicking but I like report better as a directory name.

May be too annoying to change at this point

Can decide later after development is finished.

address change in package for working directory.

remove rprojroot package

with this is the yaml:

knit: (function(rmdFile, encoding) {
out_dir <- '../output';
rmarkdown::render(rmdFile,
encoding=encoding,
output_file=file.path(dirname(rmdFile),
out_dir,
'DataPaper-ReproducibilityWorkshop.html'))})

knit button options are grayed out:

this messed with knit working directory changes (but addressed in carpentries-incubator/reproducible-publications-quarto#125 and commit 141a1e9c)

However, it will still mess with one of the challenges in episode 2 or 3.