Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Initial draft update alpha diversity chapter #657

Merged
merged 15 commits into from
Jan 25, 2025
Merged

Initial draft update alpha diversity chapter #657

merged 15 commits into from
Jan 25, 2025

Conversation

thomazbastiaanssen
Copy link
Contributor

Hi!

Please find my first draft here. No code changes, only text (& refs)

antagomir
antagomir reviewed Jan 17, 2025
View reviewed changes
Copy link
Member

@antagomir antagomir left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Seems good!

inst/assets/bibliography.bib Outdated Show resolved Hide resolved
inst/assets/bibliography.bib Outdated Show resolved Hide resolved
inst/assets/bibliography.bib Outdated Show resolved Hide resolved
TuomasBorman
TuomasBorman requested changes Jan 20, 2025
View reviewed changes
Copy link
Contributor

@TuomasBorman TuomasBorman left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks very good!

You have apparently noticed, but I am not sure if we had said: try to keep lines under 80 characters long. That will help in maintenance and future Bioc submission process

inst/pages/alpha_diversity.qmd Outdated Show resolved Hide resolved
inst/pages/alpha_diversity.qmd Show resolved Hide resolved
@thomazbastiaanssen
According to PR comments:
c76e149 
Added Hill1973 to bibliography
Fixed the 80-line limit
Replaced figure with table
Re-emphasized diversity, richness & evenness, now referring to them in text and table.
TuomasBorman
TuomasBorman requested changes Jan 24, 2025
View reviewed changes
inst/pages/alpha_diversity.qmd Outdated Show resolved Hide resolved
inst/pages/alpha_diversity.qmd Show resolved Hide resolved
inst/pages/alpha_diversity.qmd Outdated Show resolved Hide resolved
inst/pages/alpha_diversity.qmd Show resolved Hide resolved
@TuomasBorman
Copy link
Contributor

I made some changes. The PR looks good. Final things to do:

  1. The diversity table is not rendering in my local computer. Can you check that it is correct?
  2. Check that every package that is utilized is listed in DESCRIPTION. (I added gt and katex as it seems that they are needed, please double-check)

@thomazbastiaanssen
fixed some duplicate labels for code chunks.
4e7336f 
BiocBook::preview(BiocBook::BiocBook('.')) renders the full book sucessfully.
@thomazbastiaanssen
BiocBook::preview(BiocBook::BiocBook('.')) renders the full book suce…
28661e9 
…ssfully.

minor edits:
- fixed some duplicate labels for code chunks.
- removed katex from dependencies in DESCRIPTION
@thomazbastiaanssen
Merge branch 'devel' of https://github.com/thomazbastiaanssen/OMA int…
ab57697 
…o devel
@thomazbastiaanssen
remove gt from DESCRIPTION
b868d76
@thomazbastiaanssen
restored gt - removed by mistake
d115f65
@thomazbastiaanssen
Copy link
Contributor Author

I made some changes. The PR looks good. Final things to do:

1. The diversity table is not rendering in my local computer. Can you check that it is correct?

2. Check that every package that is utilized is listed in DESCRIPTION. (I added gt and katex as it seems that they are needed, please double-check)

Many thanks! The book renders using the given call - katex is not necessary, but gt is.
I'd say it's ready :)

@TuomasBorman TuomasBorman merged commit 407b20a into microbiome:devel Jan 25, 2025
1 check passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@antagomir antagomir antagomir left review comments

@TuomasBorman TuomasBorman TuomasBorman approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@thomazbastiaanssen @TuomasBorman @antagomir