Update pkgdown documentation

[sdhutchins]

ToDo

• Add our custom pkgdown theme (https://github.com/vallenderlab/vallender-pkgdown-theme)
• Add vignettes
• Ensure changelog/news.md is added
• Order functions into groups for the reference page i.e. data wrangling, visualization, utils etc.

More ToDos via @grabear #15 (comment)

• Add an About tab on the navbar
  • Add a leaflet widget
• Add vignette's for shaurita's functions
  • Stacked Bar
  • Ordination
  • Permanova
  • Alpha Diversity
• Hunt down pkgdown warnings:
  • 
  • 
• Add search
• Look at some of the pkgdown articles to get any other ideas

[sdhutchins]

Rebuild pkgdown docs

library(pkgdown)
build_site()

To build or create a new vignette

library(pkgdown)
build_article("vignette_name")

[grabear]

Can we merge the "test" branch? @sdhutchins I'm working on vignettes on my current branch "pkg-doc-branch" and I wanted to start messing with pkgdown.

[grabear]

Or can I merge the dev-master into test, and then test into my own branch?

[sdhutchins]

I think the test branch might be too messy to merge - I did a lot of weird things over there if I recall correctly (non pkgdown things)...

If you want I can do a quick pkgdown branch with just some of the base pkgdown things I implemented in the test branch.

[grabear]

That would be legit!

[sdhutchins]

Also, check out this package's pkgdown. Nice example imo.

https://valr.hesselberthlab.org/index.html

[grabear]

Do you know if there is a quicker way to build the reference based on the roxygen tag @family?? @sdhutchins

That's what I'm going to do anyway, but I can't find anything in the docs (so far).

[sdhutchins]

Yes/kinda? check out this link: https://pkgdown.r-lib.org/reference/build_reference.html#yaml-config

[sdhutchins]

[sdhutchins]

reference:
- title: Data Visualization
  contents:
  - ends_with("_plot")

I don't know how helpful that will be....

[grabear]

Yea, I was hoping I could port all of the @family Data Visualization functions and make that a reference section, but it seems that pkgdown doesn't do that out of the box..

I filed an issue, so we should hopefully get some insight. r-lib/pkgdown#954

[sdhutchins]

Reference r-lib/pkgdown#248 as well. Someone asked there.

[sdhutchins]

They made it where you can base it on the @concept tag.

[grabear]

So do we need to do that with roxygen? @sdhutchins

[sdhutchins]

So do we need to do that with roxygen? @sdhutchins

Yeah, but it may be that it's easy enough to implement selecting by @family instead of us having to go back and add the @concept tag to all of our functions.

About the @concept tag:

Aliases form the index that ? searches. Use @aliases space separated aliases to add additional aliases.

@concept add extra keywords that will be found with help.search()

[grabear]

Hrmmm... I'm just going to use RStudio to get all of the functions with the family tag:

Edit > Find in Files "@family"

It actually works nicely and it points out the inconsistencies in family names:

[sdhutchins]

Oh dear! lol Does work though!

[sdhutchins]

I bet there is a regex that lets you do this and you could build a function for it but....

[grabear]

More Todos:

• Add an About tab on the navbar
  • Add a leaflet widget
• Add vignette's for shaurita's functions
  • Stacked Bar
  • Ordination
• Hunt down pkgdown warnings:
  • 
  • 
• Add search
• Look at some of the pkgdown articles to get any other ideas

[grabear]

Should I commit all of the build_site() files? @sdhutchins

[sdhutchins]

Should I commit all of the build_site() files? @sdhutchins

Yeah, go ahead and do so.

On the warnings, typically the topic must be a valid R expression means the function does not exist or there is no .rd file for it.

I don't know if pkgdown supports the pretty print tag. The seealso is self-explanatory.

[sdhutchins]

FYI @grabear

This week, I'm going to try to add more in-depth documentation to the alpha_diversity and ordination functions. I'm also going to integrate the search box for our docs.