Update documentation for pkgdown site (and just in general)

[kelliemac]

Builds off previous work by Claudio (#118) and Dave (#119).

Local site build can be accomplished with pkgdown::build_site() but changes will need to make their way into main branch to be deployed onto the github.io website.

Related to issues: #104, #64, #126

[cyurdadon]

@kelliemac Thank you for doing this Kellie! Apologies that its taken me a while to follow-up on this, could you direct me to where I can see what the roxygen render would look like?

[kelliemac]

hi all - this one has been in the works for a while, trying to push these updates to documentation through! any and all feedback welcome.

[kelliemac]

in particular: curious what people think about leaving notes about the functions in the README file and/or Overview vignette vs. moving them to roxygen documentation so that it shows up on the pkgdown site (https://fredhutch.github.io/VISCfunctions/)?

[lemireg]

Hi @kelliemac , to confirm you're referring to the descriptions at the link: https://fredhutch.github.io/VISCfunctions/ ?

Would the alternative be to simply list the functions with no description?

# Statistical testing and estimates

Compare two groups, return a p-value:

    two_sample_bin_test() for a Barnard, Fisher’s Exact, Chi-Square or McNemar test.
    two_samp_cont_test() for a t.test (paired or unpaired), Wilcox Rank-Sum, or Wilcox Signed-Rank test.
    cor_test() for a Spearman, Pearson, or Kendall correlation test.

--->

# Statistical testing and estimates

Compare two groups, return a p-value:

    two_sample_bin_test()
    two_samp_cont_test()
    cor_test()

If that's the question, my two cents is that I like these descriptions and I'd vote to keep them. I think it's ok they're also in the roxygen documentation.

[slager]

My vote would be for having function documentation per se live only in the roxygen2 skeletons of the functions. The vignettes ideally are used to put the functions in broader story/context. Both of these sources of info are auto-included in the website.

[cyurdadon]

Thanks @kelliemac, I also agree with @lemireg and it looks good to go for me!

[kelliemac]

@lemireg so there is currently duplication on the pkgdown website in terms of what is on the main page (https://fredhutch.github.io/VISCfunctions/) and the reference page (https://fredhutch.github.io/VISCfunctions/reference/index.html). what @slager is pointing out is that if we drop the function list from the main page, it will still exist on the reference page, and updating/maintaining the list on the reference page will be easier because it automatically generates from the roxygen documentation.

[kelliemac]

My vote would be for having function documentation per se live only in the roxygen2 skeletons of the functions. The vignettes ideally are used to put the functions in broader story/context. Both of these sources of info are auto-included in the website.

I also have this same vote :)

[kelliemac]

@lemireg if you are ok with that, I can remove the function list in the README / main page BUT at the same time make sure all of those details are included in the roxygen / reference page, so we won't be losing any information.

[lemireg]

@lemireg so there is currently duplication on the pkgdown website in terms of what is on the main page (https://fredhutch.github.io/VISCfunctions/) and the reference page (https://fredhutch.github.io/VISCfunctions/reference/index.html). what @slager is pointing out is that if we drop the function list from the main page, it will still exist on the reference page, and updating/maintaining the list on the reference page will be easier because it automatically generates from the roxygen documentation.

Thanks for clarifying @kelliemac, this sounds good to me

[mayerbry]

Note for Kellie, consolidate the readme md and rmd file. Move key overview text to pkgdown/website @kelliemac

[kelliemac]

@mayerbry and @slager will you take a look at this when you have a chance, following up on our conversation yesterday? in particular: @mayerbry to review the changes to function documentation for accuracy, @slager to review the pkgdown site formatting changes

[kelliemac]

@mayerbry and @slager will you take a look at this when you have a chance, following up on our conversation yesterday? in particular: @mayerbry to review the changes to function documentation for accuracy, @slager to review the pkgdown site formatting changes

@mayerbry and @slager tagging you in this again to review when you have a chance