Content Changes following read-through

[kweav]

⚠️ There are stacked PRs on top of this one. This branch focused on reading through content and flagging things for questions/discussion. There are some figure additions, rewordings, and additional notes. Later PRs focus on style or rearranging content. This PR should be merged last ⚠️

[github-actions]

OTTR Check Results

Summary

• Spelling check: ✅ PASSED (0 errors found, threshold: 1)
• URL check: ✅ PASSED (3 errors found, threshold: 3)

🎉 All checks passed!

Last Updated: 2025-06-26-18:56:03

[kweav]

@cansavvy are you wanting to link to the ottrproject github discussions or a course specific one here instead of itcrtraining.org?

reproducibility_capstone/01-intro.Rmd

Line 74 in 4a3ecec

We also recommend that students leverage the broader ITCR Training Network community and resources, including the [GitHub repository discussions](https://www.itcrtraining.org/), course forums, and peer collaboration opportunities to enhance their learning experience and build lasting professional connections in the cancer informatics community.

[cansavvy]

@cansavvy are you wanting to link to the ottrproject github discussions or a course specific one here instead of itcrtraining.org?

reproducibility_capstone/01-intro.Rmd

Line 74 in 4a3ecec

We also recommend that students leverage the broader ITCR Training Network community and resources, including the [GitHub repository discussions](https://www.itcrtraining.org/), course forums, and peer collaboration opportunities to enhance their learning experience and build lasting professional connections in the cancer informatics community.

Oh the GitHub Discussions aren't really appropriate here we should remove that mention. But linking to ITCR in general is good.

[kweav]

@cansavvy Ok -- editing that now. What do you mean by course forums? Is there something I should link there?

[cansavvy]

@cansavvy Ok -- editing that now. What do you mean by course forums? Is there something I should link there?

I think this was AI going rogue. I don't remember writing this. But apparently didn't catch it when I was reviewing it.

[kweav]

@cansavvy from the slides, there's language about how this course will have students create docker images, but then in this intro chapter it discusses modifying. Is it creating or modifying or both?

[kweav]

The thing being flagged by the spell check appears to be a special character. And the url being flagged by the URL check is in the ignore file, but is still being flagged

[kweav]

@carriewright11 @cansavvy render preview isn't working here yet, but do we want checkboxes for the steps? And do we want tabs for the parallel steps (e.g., command line vs github desktop)?

[cansavvy]

@carriewright11 @cansavvy render preview isn't working here yet, but do we want checkboxes for the steps? And do we want tabs for the parallel steps (e.g., command line vs github desktop)?

Not all of them a strictly "steps" per se but where it applies sure! And drop downs would be great!

[carriewright11]

The thing being flagged by the spell check appears to be a special character. And the url being flagged by the URL check is in the ignore file, but is still being flagged

we can adjust the minimum errors then :)

[carriewright11]

@carriewright11 @cansavvy render preview isn't working here yet, but do we want checkboxes for the steps? And do we want tabs for the parallel steps (e.g., command line vs github desktop)?

Not all of them a strictly "steps" per se but where it applies sure! And drop downs would be great!

yeah we could have click to expand for command line

[carriewright11]

@cansavvy from the slides, there's language about how this course will have students create docker images, but then in this intro chapter it discusses modifying. Is it creating or modifying or both?

I think it is just modifying - right @cansavvy ?

[kweav]

As I'm going through the activity, it's creating the Docker file from scratch.... So I might adjust some language in the intro sections

[cansavvy]

As I'm going through the activity, it's creating the Docker file from scratch.... So I might adjust some language in the intro sections

Ah good point. I had changed that from before but forgot to update the words.

[github-actions]

Re-rendered previews from the latest commit:

• 👀 Quick preview of course website here *
• 🔬 Comprehensive download of the course website here
• Download the .docx file

* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea.

Updated at 2025-06-26 with changes from the latest commit 4afe370

[avahoffman]

Overall readability score: 47.79 (🟢 +0.03)

File	Readability
README.md	48.07 (🟢 +1.26)

View detailed metrics

🟢 - Shows an increase in readability
🔴 - Shows a decrease in readability

File	Readability	FRE	GF	ARI	CLI	DCRS
README.md	48.07	40.85	11.33	11.8	13.91	9.08
	🟢 +1.26	🟢 +1.82	🟢 +0.28	🟢 +0.7	🔴 -0.29	🔴 -0.04

Averages:

	Readability	FRE	GF	ARI	CLI	DCRS
Average	47.79	42.42	11.74	13.91	13.72	8.16
	🟢 +0.03	🟢 +0.05	🟢 +0.01	🟢 +0.02	🔴 -0.01	🟢 +0

View metric targets

Metric	Range	Ideal score
Flesch Reading Ease	100 (very easy read) to 0 (extremely difficult read)	60
Gunning Fog	6 (very easy read) to 17 (extremely difficult read)	8 or less
Auto. Read. Index	6 (very easy read) to 14 (extremely difficult read)	8 or less
Coleman Liau Index	6 (very easy read) to 17 (extremely difficult read)	8 or less
Dale-Chall Readability	4.9 (very easy read) to 9.9 (extremely difficult read)	6.9 or less

[kweav]

@carriewright11 do the screenshots in these sections look blurry to you?

• 4.4.1 Step 8: Trigger the Evaluation Action
• 1.4 Objectives --> Assessment Approach

@cansavvy @carriewright11 good to merge these changes to address Issue #8?