10 |
11 |
12 | [](https://github.com/RVerse-Tutorials/DataProduct/releases)
13 | [](https://github.com/RVerse-Tutorials/DataProduct/actions/workflows/R-CMD-check.yaml)
14 |
15 |
16 | This is a template for a NMFS branded R package and pkgdown website. It will have a NMFS palette, appropriate license and disclaimer, and a NMFS footer with logo.
17 |
18 | The instructions will use the **usethis** and **pkgdown** packages. So install those.
19 |
20 | ## Step 1 Make sure the package builds
21 |
22 | 1. Clone this GitHub repository and then open the new repository (on your computer).
23 | 2. Set-up your RStudio project to use Roxygen for documentation and NAMESPACE
24 | * Tools > Project Options... > Build Tools Click the checkbox that says "Build documentation with Roxygen".
25 | * The Configure popup box for Roxygen will probably appear, if not click the Configure button. Check all the checkboxes.
26 | 3. On the Build tab, click Install and Restart to make sure it builds.
27 | 4. On the Build tab, click Check to make sure it passes all the checks.
28 | 5. Type the code `pkgdown::build_site()` and make sure the **pkgdown** building works. If on RStudio Cloud, you will need to use `pkgdown::build_site(override = list(destination = "~/docs"))` to see the webpage.
29 |
30 | Note steps 3 and 4 are to make sure your computer is set up to build and check packages. As long as you haven't edited the package yet, it will build and pass check.
31 |
32 | ## Step 2 Customize your package
33 |
34 | 1. Edit the DESCRIPTION file (change Title, Description, urls for repo, Authors)
35 | 2. Add any required packages to Depends (or Imports* or Suggests*).
36 | 3. Edit the Readme.Rmd file.
37 | 4. Add your functions to the R folder. There are some template functions there already.
38 | 5. Don't touch the man folder. Roxygen2 will make your Rd files.
39 |
40 | ## Step 3 Make some vignettes (optional)
41 |
42 | Vignettes are longform examples and are Rmd files in the `vignettes` folder. Easiest way to start a new vignette is `usethis::use_vignette("vignettename")`.
43 |
44 | ## Step 4 Customize your **pkgdown** site and build
45 |
46 | 1. Structure of the upper navbar. Edit `_pkgdown.yml` in the `pkddown` folder to change the look of the upper navbar. There are endless options. Find examples from other peoples' pkgdown sites.
47 | 2. Update your logo and favicons. Logo is in `man/figures`. After updating run `pkgdown::build_favicon()` to remake the favicons.
48 | 3. Add material to the `docs` folder as needed. See the example for the References tab in the `_pkgdown.yml`.
49 | 4. Build your site with `pkgdown::build_site()`.
50 |
51 | ## Step 5 Make your site live on GitHub
52 |
53 | 1. Push the changes to GitHub.
54 | 2. Click on Settings for the repository.
55 | 3. Scroll way down to the GitHub Pages section.
56 | 4. In the **Source** section, change branch to Main and folder to `docs`. There are other ways to set up GitHub Pages but this will get you started.
57 | 5. I always add my GitHub Pages URL to the repo description (on right when on your main repo page).
58 |
59 | ## NMFS Branding
60 |
61 | This template has the following branding elements.
62 |
63 | 1. `extra.css` in the `pkgdown` folder sources the **nmfspalette** css. This get you the colors.
64 | 2. The `Readme.Rmd` file sources the NMFS Disclaimer and footer with NMFS logo from the [FIT Resources](https://github.com/nmfs-fish-tools/Resources).
65 | 3. The LICENSE is set to that used by [FIT packages](https://github.com/nmfs-fish-tools).
66 |
67 | ## GitHub Actions and Badges
68 |
69 | In the `.github` folder is just one action, to run R CMD check on the package.
70 |
71 | ## Readme File
72 |
73 | **pkgdown** uses `Readme.md` but to pull in the Disclaimer and footer from FIT, you need a Rmd file. When you update the `Readme.Rmd` file, **you need to remember to knit the file** to update `Readme.md`.
74 |
75 |
76 |
77 | ****
78 |
79 | ```{r add-disclaimer, echo=FALSE, results='asis'}
80 | url <- "https://raw.githubusercontent.com/nmfs-fish-tools/Resources/master/Disclaimer.md"
81 | childtext <- readLines(url)
82 | cat(childtext, sep="\n")
83 | ```
84 |
85 | ****
86 |
87 | ```{r footer, echo=FALSE, results='asis'}
88 | url <- "https://raw.githubusercontent.com/nmfs-fish-tools/Resources/master/footer.md"
89 | childtext <- readLines(url)
90 | cat(childtext, sep="\n")
91 | ```
92 |
93 |
94 |
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/docs/bootstrap-toc.js:
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1 | /*!
2 | * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
3 | * Copyright 2015 Aidan Feldman
4 | * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
5 | (function() {
6 | 'use strict';
7 |
8 | window.Toc = {
9 | helpers: {
10 | // return all matching elements in the set, or their descendants
11 | findOrFilter: function($el, selector) {
12 | // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/
13 | // http://stackoverflow.com/a/12731439/358804
14 | var $descendants = $el.find(selector);
15 | return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])');
16 | },
17 |
18 | generateUniqueIdBase: function(el) {
19 | var text = $(el).text();
20 | var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-');
21 | return anchor || el.tagName.toLowerCase();
22 | },
23 |
24 | generateUniqueId: function(el) {
25 | var anchorBase = this.generateUniqueIdBase(el);
26 | for (var i = 0; ; i++) {
27 | var anchor = anchorBase;
28 | if (i > 0) {
29 | // add suffix
30 | anchor += '-' + i;
31 | }
32 | // check if ID already exists
33 | if (!document.getElementById(anchor)) {
34 | return anchor;
35 | }
36 | }
37 | },
38 |
39 | generateAnchor: function(el) {
40 | if (el.id) {
41 | return el.id;
42 | } else {
43 | var anchor = this.generateUniqueId(el);
44 | el.id = anchor;
45 | return anchor;
46 | }
47 | },
48 |
49 | createNavList: function() {
50 | return $('');
51 | },
52 |
53 | createChildNavList: function($parent) {
54 | var $childList = this.createNavList();
55 | $parent.append($childList);
56 | return $childList;
57 | },
58 |
59 | generateNavEl: function(anchor, text) {
60 | var $a = $('');
61 | $a.attr('href', '#' + anchor);
62 | $a.text(text);
63 | var $li = $('
126 |
127 | [U.S. Department of Commerce](https://www.commerce.gov/) \| [National
128 | Oceanographic and Atmospheric Administration](https://www.noaa.gov) \|
129 | [NOAA Fisheries](https://www.fisheries.noaa.gov/)
130 |
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1 |
2 | 
