40 | 
43 |
44 | License
41 | 42 |YEAR: 2019 45 | COPYRIGHT HOLDER: Luis D. Verde Arregoita 46 |47 | 48 |
38 |
60 |
61 |
62 |
63 |
64 |
65 |
66 |
67 |
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/docs/deps/Rethink_Sans-0.4.9/font.css:
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1 | /* latin-ext */
2 | @font-face {
3 | font-family: 'Rethink Sans';
4 | font-style: italic;
5 | font-weight: 400;
6 | font-display: swap;
7 | src: url(https://fonts.gstatic.com/s/rethinksans/v5/AMOIz4SDuXOMCPfdoglY9JQEUWi769174g.woff2) format('woff2');
8 | unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
9 | }
10 | /* latin */
11 | @font-face {
12 | font-family: 'Rethink Sans';
13 | font-style: italic;
14 | font-weight: 400;
15 | font-display: swap;
16 | src: url(https://fonts.gstatic.com/s/rethinksans/v5/AMOIz4SDuXOMCPfdoglY9JQEUWi1690.woff2) format('woff2');
17 | unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
18 | }
19 | /* latin-ext */
20 | @font-face {
21 | font-family: 'Rethink Sans';
22 | font-style: italic;
23 | font-weight: 500;
24 | font-display: swap;
25 | src: url(https://fonts.gstatic.com/s/rethinksans/v5/AMOIz4SDuXOMCPfdoglY9JQEUWi769174g.woff2) format('woff2');
26 | unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
27 | }
28 | /* latin */
29 | @font-face {
30 | font-family: 'Rethink Sans';
31 | font-style: italic;
32 | font-weight: 500;
33 | font-display: swap;
34 | src: url(https://fonts.gstatic.com/s/rethinksans/v5/AMOIz4SDuXOMCPfdoglY9JQEUWi1690.woff2) format('woff2');
35 | unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
36 | }
37 | /* latin-ext */
38 | @font-face {
39 | font-family: 'Rethink Sans';
40 | font-style: italic;
41 | font-weight: 700;
42 | font-display: swap;
43 | src: url(https://fonts.gstatic.com/s/rethinksans/v5/AMOIz4SDuXOMCPfdoglY9JQEUWi769174g.woff2) format('woff2');
44 | unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
45 | }
46 | /* latin */
47 | @font-face {
48 | font-family: 'Rethink Sans';
49 | font-style: italic;
50 | font-weight: 700;
51 | font-display: swap;
52 | src: url(https://fonts.gstatic.com/s/rethinksans/v5/AMOIz4SDuXOMCPfdoglY9JQEUWi1690.woff2) format('woff2');
53 | unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
54 | }
55 | /* latin-ext */
56 | @font-face {
57 | font-family: 'Rethink Sans';
58 | font-style: normal;
59 | font-weight: 400;
60 | font-display: swap;
61 | src: url(https://fonts.gstatic.com/s/rethinksans/v5/AMOWz4SDuXOMCPfdoglY9JQEWli389k.woff2) format('woff2');
62 | unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
63 | }
64 | /* latin */
65 | @font-face {
66 | font-family: 'Rethink Sans';
67 | font-style: normal;
68 | font-weight: 400;
69 | font-display: swap;
70 | src: url(https://fonts.gstatic.com/s/rethinksans/v5/AMOWz4SDuXOMCPfdoglY9JQEVFi3.woff2) format('woff2');
71 | unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
72 | }
73 | /* latin-ext */
74 | @font-face {
75 | font-family: 'Rethink Sans';
76 | font-style: normal;
77 | font-weight: 500;
78 | font-display: swap;
79 | src: url(https://fonts.gstatic.com/s/rethinksans/v5/AMOWz4SDuXOMCPfdoglY9JQEWli389k.woff2) format('woff2');
80 | unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
81 | }
82 | /* latin */
83 | @font-face {
84 | font-family: 'Rethink Sans';
85 | font-style: normal;
86 | font-weight: 500;
87 | font-display: swap;
88 | src: url(https://fonts.gstatic.com/s/rethinksans/v5/AMOWz4SDuXOMCPfdoglY9JQEVFi3.woff2) format('woff2');
89 | unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
90 | }
91 | /* latin-ext */
92 | @font-face {
93 | font-family: 'Rethink Sans';
94 | font-style: normal;
95 | font-weight: 700;
96 | font-display: swap;
97 | src: url(https://fonts.gstatic.com/s/rethinksans/v5/AMOWz4SDuXOMCPfdoglY9JQEWli389k.woff2) format('woff2');
98 | unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
99 | }
100 | /* latin */
101 | @font-face {
102 | font-family: 'Rethink Sans';
103 | font-style: normal;
104 | font-weight: 700;
105 | font-display: swap;
106 | src: url(https://fonts.gstatic.com/s/rethinksans/v5/AMOWz4SDuXOMCPfdoglY9JQEVFi3.woff2) format('woff2');
107 | unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
108 | }
109 |
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/docs/pkgdown.js:
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1 | /* http://gregfranko.com/blog/jquery-best-practices/ */
2 | (function($) {
3 | $(function() {
4 |
5 | $('nav.navbar').headroom();
6 |
7 | Toc.init({
8 | $nav: $("#toc"),
9 | $scope: $("main h2, main h3, main h4, main h5, main h6")
10 | });
11 |
12 | if ($('#toc').length) {
13 | $('body').scrollspy({
14 | target: '#toc',
15 | offset: $("nav.navbar").outerHeight() + 1
16 | });
17 | }
18 |
19 | // Activate popovers
20 | $('[data-bs-toggle="popover"]').popover({
21 | container: 'body',
22 | html: true,
23 | trigger: 'focus',
24 | placement: "top",
25 | sanitize: false,
26 | });
27 |
28 | $('[data-bs-toggle="tooltip"]').tooltip();
29 |
30 | /* Clipboard --------------------------*/
31 |
32 | function changeTooltipMessage(element, msg) {
33 | var tooltipOriginalTitle=element.getAttribute('data-bs-original-title');
34 | element.setAttribute('data-bs-original-title', msg);
35 | $(element).tooltip('show');
36 | element.setAttribute('data-bs-original-title', tooltipOriginalTitle);
37 | }
38 |
39 | if(ClipboardJS.isSupported()) {
40 | $(document).ready(function() {
41 | var copyButton = "";
42 |
43 | $("div.sourceCode").addClass("hasCopyButton");
44 |
45 | // Insert copy buttons:
46 | $(copyButton).prependTo(".hasCopyButton");
47 |
48 | // Initialize tooltips:
49 | $('.btn-copy-ex').tooltip({container: 'body'});
50 |
51 | // Initialize clipboard:
52 | var clipboard = new ClipboardJS('[data-clipboard-copy]', {
53 | text: function(trigger) {
54 | return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, "");
55 | }
56 | });
57 |
58 | clipboard.on('success', function(e) {
59 | changeTooltipMessage(e.trigger, 'Copied!');
60 | e.clearSelection();
61 | });
62 |
63 | clipboard.on('error', function(e) {
64 | changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
65 | });
66 |
67 | });
68 | }
69 |
70 | /* Search marking --------------------------*/
71 | var url = new URL(window.location.href);
72 | var toMark = url.searchParams.get("q");
73 | var mark = new Mark("main#main");
74 | if (toMark) {
75 | mark.mark(toMark, {
76 | accuracy: {
77 | value: "complementary",
78 | limiters: [",", ".", ":", "/"],
79 | }
80 | });
81 | }
82 |
83 | /* Search --------------------------*/
84 | /* Adapted from https://github.com/rstudio/bookdown/blob/2d692ba4b61f1e466c92e78fd712b0ab08c11d31/inst/resources/bs4_book/bs4_book.js#L25 */
85 | // Initialise search index on focus
86 | var fuse;
87 | $("#search-input").focus(async function(e) {
88 | if (fuse) {
89 | return;
90 | }
91 |
92 | $(e.target).addClass("loading");
93 | var response = await fetch($("#search-input").data("search-index"));
94 | var data = await response.json();
95 |
96 | var options = {
97 | keys: ["what", "text", "code"],
98 | ignoreLocation: true,
99 | threshold: 0.1,
100 | includeMatches: true,
101 | includeScore: true,
102 | };
103 | fuse = new Fuse(data, options);
104 |
105 | $(e.target).removeClass("loading");
106 | });
107 |
108 | // Use algolia autocomplete
109 | var options = {
110 | autoselect: true,
111 | debug: true,
112 | hint: false,
113 | minLength: 2,
114 | };
115 | var q;
116 | async function searchFuse(query, callback) {
117 | await fuse;
118 |
119 | var items;
120 | if (!fuse) {
121 | items = [];
122 | } else {
123 | q = query;
124 | var results = fuse.search(query, { limit: 20 });
125 | items = results
126 | .filter((x) => x.score <= 0.75)
127 | .map((x) => x.item);
128 | if (items.length === 0) {
129 | items = [{dir:"Sorry 😿",previous_headings:"",title:"No results found.",what:"No results found.",path:window.location.href}];
130 | }
131 | }
132 | callback(items);
133 | }
134 | $("#search-input").autocomplete(options, [
135 | {
136 | name: "content",
137 | source: searchFuse,
138 | templates: {
139 | suggestion: (s) => {
140 | if (s.title == s.what) {
141 | return `${s.dir} >
39 |
49 |
50 |
51 | ${s.title}
`;
142 | } else if (s.previous_headings == "") {
143 | return `${s.dir} > ${s.title}
> ${s.what}`;
144 | } else {
145 | return `${s.dir} > ${s.title}
> ${s.previous_headings} > ${s.what}`;
146 | }
147 | },
148 | },
149 | },
150 | ]).on('autocomplete:selected', function(event, s) {
151 | window.location.href = s.path + "?q=" + q + "#" + s.id;
152 | });
153 | });
154 | })(window.jQuery || window.$)
155 |
156 | document.addEventListener('keydown', function(event) {
157 | // Check if the pressed key is '/'
158 | if (event.key === '/') {
159 | event.preventDefault(); // Prevent any default action associated with the '/' key
160 | document.getElementById('search-input').focus(); // Set focus to the search input
161 | }
162 | });
163 |
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/docs/articles/index.html:
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1 |
2 |
38 |
62 |
63 |
64 |
65 |
66 |
67 |
68 |
69 |
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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 = $('');
64 | $li.append($a);
65 | return $li;
66 | },
67 |
68 | generateNavItem: function(headingEl) {
69 | var anchor = this.generateAnchor(headingEl);
70 | var $heading = $(headingEl);
71 | var text = $heading.data('toc-text') || $heading.text();
72 | return this.generateNavEl(anchor, text);
73 | },
74 |
75 | // Find the first heading level (`
39 |
51 |
52 |
53 |
40 | 
42 |
43 | Articles
41 |
44 |
50 | All vignettes
45 | 46 | 47 |- Introduction to annotater 48 |
- 49 |
`, then ``, etc.) that has more than one element. Defaults to 1 (for ``).
76 | getTopLevel: function($scope) {
77 | for (var i = 1; i <= 6; i++) {
78 | var $headings = this.findOrFilter($scope, 'h' + i);
79 | if ($headings.length > 1) {
80 | return i;
81 | }
82 | }
83 |
84 | return 1;
85 | },
86 |
87 | // returns the elements for the top level, and the next below it
88 | getHeadings: function($scope, topLevel) {
89 | var topSelector = 'h' + topLevel;
90 |
91 | var secondaryLevel = topLevel + 1;
92 | var secondarySelector = 'h' + secondaryLevel;
93 |
94 | return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
95 | },
96 |
97 | getNavLevel: function(el) {
98 | return parseInt(el.tagName.charAt(1), 10);
99 | },
100 |
101 | populateNav: function($topContext, topLevel, $headings) {
102 | var $context = $topContext;
103 | var $prevNav;
104 |
105 | var helpers = this;
106 | $headings.each(function(i, el) {
107 | var $newNav = helpers.generateNavItem(el);
108 | var navLevel = helpers.getNavLevel(el);
109 |
110 | // determine the proper $context
111 | if (navLevel === topLevel) {
112 | // use top level
113 | $context = $topContext;
114 | } else if ($prevNav && $context === $topContext) {
115 | // create a new level of the tree and switch to it
116 | $context = helpers.createChildNavList($prevNav);
117 | } // else use the current $context
118 |
119 | $context.append($newNav);
120 |
121 | $prevNav = $newNav;
122 | });
123 | },
124 |
125 | parseOps: function(arg) {
126 | var opts;
127 | if (arg.jquery) {
128 | opts = {
129 | $nav: arg
130 | };
131 | } else {
132 | opts = arg;
133 | }
134 | opts.$scope = opts.$scope || $(document.body);
135 | return opts;
136 | }
137 | },
138 |
139 | // accepts a jQuery object, or an options object
140 | init: function(opts) {
141 | opts = this.helpers.parseOps(opts);
142 |
143 | // ensure that the data attribute is in place for styling
144 | opts.$nav.attr('data-toggle', 'toc');
145 |
146 | var $topContext = this.helpers.createChildNavList(opts.$nav);
147 | var topLevel = this.helpers.getTopLevel(opts.$scope);
148 | var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
149 | this.helpers.populateNav($topContext, topLevel, $headings);
150 | }
151 | };
152 |
153 | $(function() {
154 | $('nav[data-toggle="toc"]').each(function(i, el) {
155 | var $nav = $(el);
156 | Toc.init($nav);
157 | });
158 | });
159 | })();
160 |
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/CODE_OF_CONDUCT.md:
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1 | # Contributor Covenant Code of Conduct
2 |
3 | ## Our Pledge
4 |
5 | We as members, contributors, and leaders pledge to make participation in our
6 | community a harassment-free experience for everyone, regardless of age, body
7 | size, visible or invisible disability, ethnicity, sex characteristics, gender
8 | identity and expression, level of experience, education, socio-economic status,
9 | nationality, personal appearance, race, caste, color, religion, or sexual
10 | identity and orientation.
11 |
12 | We pledge to act and interact in ways that contribute to an open, welcoming,
13 | diverse, inclusive, and healthy community.
14 |
15 | ## Our Standards
16 |
17 | Examples of behavior that contributes to a positive environment for our
18 | community include:
19 |
20 | * Demonstrating empathy and kindness toward other people
21 | * Being respectful of differing opinions, viewpoints, and experiences
22 | * Giving and gracefully accepting constructive feedback
23 | * Accepting responsibility and apologizing to those affected by our mistakes,
24 | and learning from the experience
25 | * Focusing on what is best not just for us as individuals, but for the overall
26 | community
27 |
28 | Examples of unacceptable behavior include:
29 |
30 | * The use of sexualized language or imagery, and sexual attention or advances of
31 | any kind
32 | * Trolling, insulting or derogatory comments, and personal or political attacks
33 | * Public or private harassment
34 | * Publishing others' private information, such as a physical or email address,
35 | without their explicit permission
36 | * Other conduct which could reasonably be considered inappropriate in a
37 | professional setting
38 |
39 | ## Enforcement Responsibilities
40 |
41 | Community leaders are responsible for clarifying and enforcing our standards of
42 | acceptable behavior and will take appropriate and fair corrective action in
43 | response to any behavior that they deem inappropriate, threatening, offensive,
44 | or harmful.
45 |
46 | Community leaders have the right and responsibility to remove, edit, or reject
47 | comments, commits, code, wiki edits, issues, and other contributions that are
48 | not aligned to this Code of Conduct, and will communicate reasons for moderation
49 | decisions when appropriate.
50 |
51 | ## Scope
52 |
53 | This Code of Conduct applies within all community spaces, and also applies when
54 | an individual is officially representing the community in public spaces.
55 | Examples of representing our community include using an official e-mail address,
56 | posting via an official social media account, or acting as an appointed
57 | representative at an online or offline event.
58 |
59 | ## Enforcement
60 |
61 | Instances of abusive, harassing, or otherwise unacceptable behavior may be
62 | reported to the community leaders responsible for enforcement at luis@liomys.mx.
63 | All complaints will be reviewed and investigated promptly and fairly.
64 |
65 | All community leaders are obligated to respect the privacy and security of the
66 | reporter of any incident.
67 |
68 | ## Enforcement Guidelines
69 |
70 | Community leaders will follow these Community Impact Guidelines in determining
71 | the consequences for any action they deem in violation of this Code of Conduct:
72 |
73 | ### 1. Correction
74 |
75 | **Community Impact**: Use of inappropriate language or other behavior deemed
76 | unprofessional or unwelcome in the community.
77 |
78 | **Consequence**: A private, written warning from community leaders, providing
79 | clarity around the nature of the violation and an explanation of why the
80 | behavior was inappropriate. A public apology may be requested.
81 |
82 | ### 2. Warning
83 |
84 | **Community Impact**: A violation through a single incident or series of
85 | actions.
86 |
87 | **Consequence**: A warning with consequences for continued behavior. No
88 | interaction with the people involved, including unsolicited interaction with
89 | those enforcing the Code of Conduct, for a specified period of time. This
90 | includes avoiding interactions in community spaces as well as external channels
91 | like social media. Violating these terms may lead to a temporary or permanent
92 | ban.
93 |
94 | ### 3. Temporary Ban
95 |
96 | **Community Impact**: A serious violation of community standards, including
97 | sustained inappropriate behavior.
98 |
99 | **Consequence**: A temporary ban from any sort of interaction or public
100 | communication with the community for a specified period of time. No public or
101 | private interaction with the people involved, including unsolicited interaction
102 | with those enforcing the Code of Conduct, is allowed during this period.
103 | Violating these terms may lead to a permanent ban.
104 |
105 | ### 4. Permanent Ban
106 |
107 | **Community Impact**: Demonstrating a pattern of violation of community
108 | standards, including sustained inappropriate behavior, harassment of an
109 | individual, or aggression toward or disparagement of classes of individuals.
110 |
111 | **Consequence**: A permanent ban from any sort of public interaction within the
112 | community.
113 |
114 | ## Attribution
115 |
116 | This Code of Conduct is adapted from the [Contributor Covenant][homepage],
117 | version 2.1, available at
118 | .
119 |
120 | Community Impact Guidelines were inspired by
121 | [Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
122 |
123 | For answers to common questions about this code of conduct, see the FAQ at
124 | . Translations are available at .
125 |
126 | [homepage]: https://www.contributor-covenant.org
127 |
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8 | Page not found (404) • annotater
9 |
10 |
11 |
12 |
13 |
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15 |
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46 | Copyright (c) 2019 Luis D. Verde Arregoita
47 | Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
48 | The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
49 | THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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/R/annotate_repo_source.R:
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1 | #' Annotate repository sources
2 | #'
3 | #' @param string_og text string (script) with package load calls
4 | #'
5 | #' @return text string with package repository source annotations. Will make
6 | #' note of packages not currently installed. Lines with existing comments or
7 | #' annotations are ignored by the regular expression that matches package
8 | #' names. Also ignores base packages. Local installs now annotated as such.
9 | #'
10 | #' @examples
11 | #' test_string <- c("library(knitr)\nrequire(datasets)")
12 | #' annotate_repo_source(test_string)
13 | #' @importFrom rlang .data
14 | #' @export
15 | annotate_repo_source <- function(string_og) {
16 | out_tb <- match_pkg_names(string_og)
17 | if (nrow(out_tb) == 0) cat("no matching library load calls")
18 | if (nrow(out_tb) == 0) {
19 | return(string_og)
20 | }
21 | out_tb <- tibble::rowid_to_column(out_tb)
22 | pck_descs <- suppressWarnings(purrr::map(out_tb$pkgname_clean,
23 | utils::packageDescription,
24 | fields = c("Repository", "RemoteType", "biocViews")
25 | ))
26 | pck_descs <- purrr::map(pck_descs, as.list)
27 | pck_descs <-
28 | purrr::map(pck_descs, function(x) {
29 | if (
30 | !is.na(x$Repository) &&
31 | x$Repository == "CRAN" &&
32 | !is.na(x$RemoteType) &&
33 | x$RemoteType == "standard"
34 | ) {
35 | x$RemoteType <- NA
36 | }
37 | x
38 | })
39 | pck_descs <- tidyr::unnest(tibble::enframe(purrr::map(pck_descs, purrr::flatten_chr)), cols = c("value"))
40 | pck_descs <- dplyr::rename(pck_descs, rowid = 1, repo = 2)
41 | pck_descs <- dplyr::left_join(out_tb, pck_descs, by = "rowid")
42 | pck_descs <- dplyr::mutate(pck_descs, repo = ifelse(stringr::str_detect(.data$repo, ","), "Bioconductor", .data$repo))
43 | pck_descs <- dplyr::add_count(pck_descs, .data$package_name)
44 | pck_descs <- dplyr::mutate(pck_descs, repo = dplyr::if_else(.data$n == 1, "none", .data$repo))
45 | pck_descs <-
46 | suppressMessages(dplyr::ungroup(dplyr::summarize(
47 | dplyr::group_by(pck_descs,call,.data$package_name,.data$pkgname_clean),repo=dplyr::last(stats::na.omit(.data$repo)))))
48 | pck_descs <- dplyr::mutate(pck_descs, user_repo = dplyr::case_when(
49 | .data$repo ==
50 | "CRAN" ~ "CRAN",
51 | stringr::str_detect(.data$repo, "r-universe") ~ .data$repo,
52 | .data$repo == "Bioconductor" ~ "Bioconductor",
53 | .data$repo == "RSPM" ~ "Posit RSPM",
54 | .data$repo == "none" ~ "not installed on this machine",
55 | is.na(.data$repo) ~ "local install",
56 | TRUE ~ repo_details(.data$pkgname_clean)
57 | ), annotation = dplyr::case_when(stringr::str_detect(
58 | user_repo,
59 | "(?
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/R/annotate_repostitle.R:
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1 | #' Annotate package titles and repository sources
2 | #'
3 | #' @param string_og Text string (script) with package load calls.
4 | #'
5 | #' @return Text string with package titles and package repository source
6 | #' annotations. Will make note of packages not currently installed. Lines with
7 | #' existing comments or annotations are ignored by the regular expression that
8 | #' matches package names. Also ignores base packages.
9 | #'
10 | #' @details Some annotations may be long, check for possible line breaks
11 | #' introduced into your script.
12 | #' @examples
13 | #' test_string <- c("library(knitr)\nrequire(datasets)")
14 | #' annotate_repostitle(test_string)
15 | #' @importFrom rlang .data
16 | #' @export
17 | annotate_repostitle <- function(string_og) {
18 | out_tb <- match_pkg_names(string_og)
19 | if (nrow(out_tb) == 0) cat("no matching library load calls")
20 | if (nrow(out_tb) == 0) {
21 | return(string_og)
22 | }
23 | out_tb <- tibble::rowid_to_column(out_tb)
24 | # get pkg titles
25 | out_tb$pck_title <- purrr::map_chr(out_tb$pkgname_clean, utils::packageDescription, fields = "Title")
26 | out_tb$pck_title <- stringi::stri_replace_na(out_tb$pck_title, "not installed on this machine")
27 | # new title variable
28 | out_tb$title <- paste(out_tb$pck_title)
29 | # repo descriptions
30 | pck_descs <- purrr::map(out_tb$pkgname_clean, utils::packageDescription,
31 | fields = c("Repository", "RemoteType", "biocViews")
32 | )
33 | pck_descs <- purrr::map(pck_descs, as.list)
34 | pck_descs <-
35 | purrr::map(pck_descs, function(x) {
36 | if (
37 | !is.na(x$Repository) &&
38 | x$Repository == "CRAN" &&
39 | !is.na(x$RemoteType) &&
40 | x$RemoteType == "standard"
41 | ) {
42 | x$RemoteType <- NA
43 | }
44 | x
45 | })
46 | pck_descs <- tidyr::unnest(tibble::enframe(purrr::map(pck_descs, purrr::flatten_chr)), cols = c("value"))
47 | pck_descs <- dplyr::rename(pck_descs, rowid = 1, repo = 2)
48 | pck_descs <- dplyr::left_join(out_tb, pck_descs, by = "rowid")
49 | pck_descs <- dplyr::mutate(pck_descs, repo = ifelse(stringr::str_detect(.data$repo, ","), "Bioconductor", .data$repo))
50 | pck_descs <- dplyr::add_count(pck_descs, .data$package_name)
51 |
52 | pck_descs <- dplyr::mutate(pck_descs, repo = dplyr::if_else(!is.na(.data$repo) & .data$n == 1, "none", .data$repo)) # Ensure we only check n if repo is not NA
53 | pck_descs <- dplyr::mutate(pck_descs, user_repo = dplyr::case_when(
54 | is.na(.data$repo) ~ "details not available", # Handle NA repo explicitly
55 | .data$repo == "CRAN" ~ "CRAN",
56 | .data$repo == "Bioconductor" ~ "Bioconductor",
57 | .data$repo == "RSPM" ~ "Posit RSPM",
58 | .data$repo == "none" ~ "not installed on this machine",
59 | stringr::str_detect(.data$repo,"universe")~ .data$repo, # for Runiverse pkgs
60 | TRUE ~ repo_details(.data$pkgname_clean) # Ensure repo_details handles missing packages gracefully
61 | ), annotation = dplyr::case_when(
62 | user_repo == "details not available" ~ user_repo, # Handle cases where details weren't found
63 | user_repo == "not installed on this machine" ~ user_repo, # Handle not installed cases
64 | stringr::str_detect(user_repo, "/(?!.+r-universe.+)") ~ paste0("[", .data$repo, "::", user_repo, "]"),
65 | TRUE ~ user_repo
66 | ))
67 | pck_descs <- dplyr::mutate(pck_descs, version = pkg_version(gsub("[\'\"]", "", .data$package_name)))
68 |
69 |
70 | # build annotations
71 | if (all(!grepl("p_load", pck_descs$call))) { # no pacman calls
72 | pck_descs <- dplyr::mutate(pck_descs,annotated=dplyr::case_when(
73 | stringr::str_detect(title,"not installed")~paste0(call, " # ", annotation, " vNA"),
74 | TRUE~ paste0(call, " # ", title, " ", annotation, " v", version)
75 | ))
76 | return(
77 | stringi::stri_replace_all_fixed(
78 | str = string_og, pattern = pck_descs$call,
79 | replacement = pck_descs$annotated, vectorize_all = FALSE
80 | )
81 | )
82 | }
83 |
84 | if (all(grepl("p_load", pck_descs$call))) { # only pacman calls
85 | pacld <- pck_descs[which(stringr::str_detect(pck_descs$call, ".+load\\(")), ]
86 | pacld$pkgnamesep <- paste0(pacld$package_name, ", ")
87 | pacld <- dplyr::mutate(dplyr::group_by(pacld, call), pkgnamesep = ifelse(dplyr::row_number() == dplyr::n(), gsub(",", "", .data$pkgnamesep), .data$pkgnamesep))
88 | pacld$annotatedpac <- paste0(pacld$pkgnamesep, "# ", pacld$title, " ", pacld$annotation, " v", pacld$version)
89 | pacld <- dplyr::summarize(dplyr::group_by(pacld, call), pkgs = paste(.data$annotatedpac, collapse = "\n"))
90 | pacld$ldcalls <- stringr::str_extract(pacld$call, ".+\\(")
91 | pacld <- dplyr::mutate(pacld, annotpac = paste(.data$ldcalls, .data$pkgs, ")", sep = "\n "))
92 | return(
93 | stringi::stri_replace_all_fixed(
94 | str = string_og, pattern = pacld$call,
95 | replacement = pacld$annotpac, vectorize_all = FALSE
96 | )
97 | )
98 | }
99 |
100 | if (any(grepl("p_load", pck_descs$call)) & any(grepl("libr|req", out_tb$call))) { # pacman and base calls
101 | pacld <- pck_descs[which(stringr::str_detect(pck_descs$call, ".+load\\(")), ]
102 | pacld$pkgnamesep <- paste0(pacld$package_name, ", ")
103 | pacld <- dplyr::mutate(dplyr::group_by(pacld, call), pkgnamesep = ifelse(dplyr::row_number() == dplyr::n(), gsub(",", "", .data$pkgnamesep), .data$pkgnamesep))
104 | pacld$annotatedpac <- paste0(pacld$pkgnamesep, "# ", pacld$title, " ", pacld$annotation, " v", pacld$version)
105 | pacld <- dplyr::summarize(dplyr::group_by(pacld, call), pkgs = paste(.data$annotatedpac, collapse = "\n "))
106 | pacld$ldcalls <- stringr::str_extract(pacld$call, ".+\\(")
107 | pacld <- dplyr::mutate(pacld, annotpac = paste(.data$ldcalls, .data$pkgs, ")", sep = "\n "))
108 | string_og <- stringi::stri_replace_all_fixed(
109 | str = string_og, pattern = pacld$call,
110 | replacement = pacld$annotpac, vectorize_all = FALSE
111 | )
112 | pck_descs <- pck_descs[which(!stringr::str_detect(pck_descs$call, ".+load\\(")), ]
113 | pck_descs <- dplyr::mutate(pck_descs,annotated=dplyr::case_when(
114 | stringr::str_detect(title,"not installed")~paste0(call, " #", " ", annotation, " vNA"),
115 | TRUE~ paste0(call, " # ", title, " ", annotation, " v", version)
116 | ))
117 |
118 | return(
119 | stringi::stri_replace_all_fixed(
120 | str = string_og,
121 | pattern = pck_descs$call, # Changed
122 | replacement = pck_descs$annotated,
123 | vectorize_all = FALSE
124 | )
125 | )
126 | }
127 | }
128 |
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40 | Annotate loaded data in active file
41 | Source: R/annotate_pkg_datasets_active.R
42 | annotate_data_active_file.Rd
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40 | Annotate repositories in active file
41 | Source: R/annotate_repos_active_file.R
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40 | Authors and Citation
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60 |
61 | Citation
62 | Source: DESCRIPTION
63 |
64 | Verde Arregoitia L (2025).
65 | annotater: Annotate Package Load Calls.
66 | R package version 0.2.3.9000, https://annotater.liomys.mx, https://github.com/luisDVA/annotater.
67 |
68 | @Manual{,
69 | title = {annotater: Annotate Package Load Calls},
70 | author = {Luis D. {Verde Arregoitia}},
71 | year = {2025},
72 | note = {R package version 0.2.3.9000, https://annotater.liomys.mx},
73 | url = {https://github.com/luisDVA/annotater},
74 | }
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41 |
42 | Annotate function calls in active file
43 | Source: R/annotate_fun_calls_active_file.R
44 | annotate_fun_calls_active_file.Rd
45 |
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47 |
48 | Annotates package load calls with the used functions of each package in the
49 | active .R file
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42 | Annotate titles and repositories in active file
43 | Source: R/annotate_repostitle_active.R
44 | annotate_repostitle_active.Rd
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49 | the active .R file
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`).
76 | getTopLevel: function($scope) {
77 | for (var i = 1; i <= 6; i++) {
78 | var $headings = this.findOrFilter($scope, 'h' + i);
79 | if ($headings.length > 1) {
80 | return i;
81 | }
82 | }
83 |
84 | return 1;
85 | },
86 |
87 | // returns the elements for the top level, and the next below it
88 | getHeadings: function($scope, topLevel) {
89 | var topSelector = 'h' + topLevel;
90 |
91 | var secondaryLevel = topLevel + 1;
92 | var secondarySelector = 'h' + secondaryLevel;
93 |
94 | return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
95 | },
96 |
97 | getNavLevel: function(el) {
98 | return parseInt(el.tagName.charAt(1), 10);
99 | },
100 |
101 | populateNav: function($topContext, topLevel, $headings) {
102 | var $context = $topContext;
103 | var $prevNav;
104 |
105 | var helpers = this;
106 | $headings.each(function(i, el) {
107 | var $newNav = helpers.generateNavItem(el);
108 | var navLevel = helpers.getNavLevel(el);
109 |
110 | // determine the proper $context
111 | if (navLevel === topLevel) {
112 | // use top level
113 | $context = $topContext;
114 | } else if ($prevNav && $context === $topContext) {
115 | // create a new level of the tree and switch to it
116 | $context = helpers.createChildNavList($prevNav);
117 | } // else use the current $context
118 |
119 | $context.append($newNav);
120 |
121 | $prevNav = $newNav;
122 | });
123 | },
124 |
125 | parseOps: function(arg) {
126 | var opts;
127 | if (arg.jquery) {
128 | opts = {
129 | $nav: arg
130 | };
131 | } else {
132 | opts = arg;
133 | }
134 | opts.$scope = opts.$scope || $(document.body);
135 | return opts;
136 | }
137 | },
138 |
139 | // accepts a jQuery object, or an options object
140 | init: function(opts) {
141 | opts = this.helpers.parseOps(opts);
142 |
143 | // ensure that the data attribute is in place for styling
144 | opts.$nav.attr('data-toggle', 'toc');
145 |
146 | var $topContext = this.helpers.createChildNavList(opts.$nav);
147 | var topLevel = this.helpers.getTopLevel(opts.$scope);
148 | var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
149 | this.helpers.populateNav($topContext, topLevel, $headings);
150 | }
151 | };
152 |
153 | $(function() {
154 | $('nav[data-toggle="toc"]').each(function(i, el) {
155 | var $nav = $(el);
156 | Toc.init($nav);
157 | });
158 | });
159 | })();
160 |
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/CODE_OF_CONDUCT.md:
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1 | # Contributor Covenant Code of Conduct
2 |
3 | ## Our Pledge
4 |
5 | We as members, contributors, and leaders pledge to make participation in our
6 | community a harassment-free experience for everyone, regardless of age, body
7 | size, visible or invisible disability, ethnicity, sex characteristics, gender
8 | identity and expression, level of experience, education, socio-economic status,
9 | nationality, personal appearance, race, caste, color, religion, or sexual
10 | identity and orientation.
11 |
12 | We pledge to act and interact in ways that contribute to an open, welcoming,
13 | diverse, inclusive, and healthy community.
14 |
15 | ## Our Standards
16 |
17 | Examples of behavior that contributes to a positive environment for our
18 | community include:
19 |
20 | * Demonstrating empathy and kindness toward other people
21 | * Being respectful of differing opinions, viewpoints, and experiences
22 | * Giving and gracefully accepting constructive feedback
23 | * Accepting responsibility and apologizing to those affected by our mistakes,
24 | and learning from the experience
25 | * Focusing on what is best not just for us as individuals, but for the overall
26 | community
27 |
28 | Examples of unacceptable behavior include:
29 |
30 | * The use of sexualized language or imagery, and sexual attention or advances of
31 | any kind
32 | * Trolling, insulting or derogatory comments, and personal or political attacks
33 | * Public or private harassment
34 | * Publishing others' private information, such as a physical or email address,
35 | without their explicit permission
36 | * Other conduct which could reasonably be considered inappropriate in a
37 | professional setting
38 |
39 | ## Enforcement Responsibilities
40 |
41 | Community leaders are responsible for clarifying and enforcing our standards of
42 | acceptable behavior and will take appropriate and fair corrective action in
43 | response to any behavior that they deem inappropriate, threatening, offensive,
44 | or harmful.
45 |
46 | Community leaders have the right and responsibility to remove, edit, or reject
47 | comments, commits, code, wiki edits, issues, and other contributions that are
48 | not aligned to this Code of Conduct, and will communicate reasons for moderation
49 | decisions when appropriate.
50 |
51 | ## Scope
52 |
53 | This Code of Conduct applies within all community spaces, and also applies when
54 | an individual is officially representing the community in public spaces.
55 | Examples of representing our community include using an official e-mail address,
56 | posting via an official social media account, or acting as an appointed
57 | representative at an online or offline event.
58 |
59 | ## Enforcement
60 |
61 | Instances of abusive, harassing, or otherwise unacceptable behavior may be
62 | reported to the community leaders responsible for enforcement at luis@liomys.mx.
63 | All complaints will be reviewed and investigated promptly and fairly.
64 |
65 | All community leaders are obligated to respect the privacy and security of the
66 | reporter of any incident.
67 |
68 | ## Enforcement Guidelines
69 |
70 | Community leaders will follow these Community Impact Guidelines in determining
71 | the consequences for any action they deem in violation of this Code of Conduct:
72 |
73 | ### 1. Correction
74 |
75 | **Community Impact**: Use of inappropriate language or other behavior deemed
76 | unprofessional or unwelcome in the community.
77 |
78 | **Consequence**: A private, written warning from community leaders, providing
79 | clarity around the nature of the violation and an explanation of why the
80 | behavior was inappropriate. A public apology may be requested.
81 |
82 | ### 2. Warning
83 |
84 | **Community Impact**: A violation through a single incident or series of
85 | actions.
86 |
87 | **Consequence**: A warning with consequences for continued behavior. No
88 | interaction with the people involved, including unsolicited interaction with
89 | those enforcing the Code of Conduct, for a specified period of time. This
90 | includes avoiding interactions in community spaces as well as external channels
91 | like social media. Violating these terms may lead to a temporary or permanent
92 | ban.
93 |
94 | ### 3. Temporary Ban
95 |
96 | **Community Impact**: A serious violation of community standards, including
97 | sustained inappropriate behavior.
98 |
99 | **Consequence**: A temporary ban from any sort of interaction or public
100 | communication with the community for a specified period of time. No public or
101 | private interaction with the people involved, including unsolicited interaction
102 | with those enforcing the Code of Conduct, is allowed during this period.
103 | Violating these terms may lead to a permanent ban.
104 |
105 | ### 4. Permanent Ban
106 |
107 | **Community Impact**: Demonstrating a pattern of violation of community
108 | standards, including sustained inappropriate behavior, harassment of an
109 | individual, or aggression toward or disparagement of classes of individuals.
110 |
111 | **Consequence**: A permanent ban from any sort of public interaction within the
112 | community.
113 |
114 | ## Attribution
115 |
116 | This Code of Conduct is adapted from the [Contributor Covenant][homepage],
117 | version 2.1, available at
118 | .
119 |
120 | Community Impact Guidelines were inspired by
121 | [Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
122 |
123 | For answers to common questions about this code of conduct, see the FAQ at
124 | . Translations are available at .
125 |
126 | [homepage]: https://www.contributor-covenant.org
127 |
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46 | Copyright (c) 2019 Luis D. Verde Arregoita
47 | Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
48 | The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
49 | THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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1 | #' Annotate repository sources
2 | #'
3 | #' @param string_og text string (script) with package load calls
4 | #'
5 | #' @return text string with package repository source annotations. Will make
6 | #' note of packages not currently installed. Lines with existing comments or
7 | #' annotations are ignored by the regular expression that matches package
8 | #' names. Also ignores base packages. Local installs now annotated as such.
9 | #'
10 | #' @examples
11 | #' test_string <- c("library(knitr)\nrequire(datasets)")
12 | #' annotate_repo_source(test_string)
13 | #' @importFrom rlang .data
14 | #' @export
15 | annotate_repo_source <- function(string_og) {
16 | out_tb <- match_pkg_names(string_og)
17 | if (nrow(out_tb) == 0) cat("no matching library load calls")
18 | if (nrow(out_tb) == 0) {
19 | return(string_og)
20 | }
21 | out_tb <- tibble::rowid_to_column(out_tb)
22 | pck_descs <- suppressWarnings(purrr::map(out_tb$pkgname_clean,
23 | utils::packageDescription,
24 | fields = c("Repository", "RemoteType", "biocViews")
25 | ))
26 | pck_descs <- purrr::map(pck_descs, as.list)
27 | pck_descs <-
28 | purrr::map(pck_descs, function(x) {
29 | if (
30 | !is.na(x$Repository) &&
31 | x$Repository == "CRAN" &&
32 | !is.na(x$RemoteType) &&
33 | x$RemoteType == "standard"
34 | ) {
35 | x$RemoteType <- NA
36 | }
37 | x
38 | })
39 | pck_descs <- tidyr::unnest(tibble::enframe(purrr::map(pck_descs, purrr::flatten_chr)), cols = c("value"))
40 | pck_descs <- dplyr::rename(pck_descs, rowid = 1, repo = 2)
41 | pck_descs <- dplyr::left_join(out_tb, pck_descs, by = "rowid")
42 | pck_descs <- dplyr::mutate(pck_descs, repo = ifelse(stringr::str_detect(.data$repo, ","), "Bioconductor", .data$repo))
43 | pck_descs <- dplyr::add_count(pck_descs, .data$package_name)
44 | pck_descs <- dplyr::mutate(pck_descs, repo = dplyr::if_else(.data$n == 1, "none", .data$repo))
45 | pck_descs <-
46 | suppressMessages(dplyr::ungroup(dplyr::summarize(
47 | dplyr::group_by(pck_descs,call,.data$package_name,.data$pkgname_clean),repo=dplyr::last(stats::na.omit(.data$repo)))))
48 | pck_descs <- dplyr::mutate(pck_descs, user_repo = dplyr::case_when(
49 | .data$repo ==
50 | "CRAN" ~ "CRAN",
51 | stringr::str_detect(.data$repo, "r-universe") ~ .data$repo,
52 | .data$repo == "Bioconductor" ~ "Bioconductor",
53 | .data$repo == "RSPM" ~ "Posit RSPM",
54 | .data$repo == "none" ~ "not installed on this machine",
55 | is.na(.data$repo) ~ "local install",
56 | TRUE ~ repo_details(.data$pkgname_clean)
57 | ), annotation = dplyr::case_when(stringr::str_detect(
58 | user_repo,
59 | "(?
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1 | #' Annotate package titles and repository sources
2 | #'
3 | #' @param string_og Text string (script) with package load calls.
4 | #'
5 | #' @return Text string with package titles and package repository source
6 | #' annotations. Will make note of packages not currently installed. Lines with
7 | #' existing comments or annotations are ignored by the regular expression that
8 | #' matches package names. Also ignores base packages.
9 | #'
10 | #' @details Some annotations may be long, check for possible line breaks
11 | #' introduced into your script.
12 | #' @examples
13 | #' test_string <- c("library(knitr)\nrequire(datasets)")
14 | #' annotate_repostitle(test_string)
15 | #' @importFrom rlang .data
16 | #' @export
17 | annotate_repostitle <- function(string_og) {
18 | out_tb <- match_pkg_names(string_og)
19 | if (nrow(out_tb) == 0) cat("no matching library load calls")
20 | if (nrow(out_tb) == 0) {
21 | return(string_og)
22 | }
23 | out_tb <- tibble::rowid_to_column(out_tb)
24 | # get pkg titles
25 | out_tb$pck_title <- purrr::map_chr(out_tb$pkgname_clean, utils::packageDescription, fields = "Title")
26 | out_tb$pck_title <- stringi::stri_replace_na(out_tb$pck_title, "not installed on this machine")
27 | # new title variable
28 | out_tb$title <- paste(out_tb$pck_title)
29 | # repo descriptions
30 | pck_descs <- purrr::map(out_tb$pkgname_clean, utils::packageDescription,
31 | fields = c("Repository", "RemoteType", "biocViews")
32 | )
33 | pck_descs <- purrr::map(pck_descs, as.list)
34 | pck_descs <-
35 | purrr::map(pck_descs, function(x) {
36 | if (
37 | !is.na(x$Repository) &&
38 | x$Repository == "CRAN" &&
39 | !is.na(x$RemoteType) &&
40 | x$RemoteType == "standard"
41 | ) {
42 | x$RemoteType <- NA
43 | }
44 | x
45 | })
46 | pck_descs <- tidyr::unnest(tibble::enframe(purrr::map(pck_descs, purrr::flatten_chr)), cols = c("value"))
47 | pck_descs <- dplyr::rename(pck_descs, rowid = 1, repo = 2)
48 | pck_descs <- dplyr::left_join(out_tb, pck_descs, by = "rowid")
49 | pck_descs <- dplyr::mutate(pck_descs, repo = ifelse(stringr::str_detect(.data$repo, ","), "Bioconductor", .data$repo))
50 | pck_descs <- dplyr::add_count(pck_descs, .data$package_name)
51 |
52 | pck_descs <- dplyr::mutate(pck_descs, repo = dplyr::if_else(!is.na(.data$repo) & .data$n == 1, "none", .data$repo)) # Ensure we only check n if repo is not NA
53 | pck_descs <- dplyr::mutate(pck_descs, user_repo = dplyr::case_when(
54 | is.na(.data$repo) ~ "details not available", # Handle NA repo explicitly
55 | .data$repo == "CRAN" ~ "CRAN",
56 | .data$repo == "Bioconductor" ~ "Bioconductor",
57 | .data$repo == "RSPM" ~ "Posit RSPM",
58 | .data$repo == "none" ~ "not installed on this machine",
59 | stringr::str_detect(.data$repo,"universe")~ .data$repo, # for Runiverse pkgs
60 | TRUE ~ repo_details(.data$pkgname_clean) # Ensure repo_details handles missing packages gracefully
61 | ), annotation = dplyr::case_when(
62 | user_repo == "details not available" ~ user_repo, # Handle cases where details weren't found
63 | user_repo == "not installed on this machine" ~ user_repo, # Handle not installed cases
64 | stringr::str_detect(user_repo, "/(?!.+r-universe.+)") ~ paste0("[", .data$repo, "::", user_repo, "]"),
65 | TRUE ~ user_repo
66 | ))
67 | pck_descs <- dplyr::mutate(pck_descs, version = pkg_version(gsub("[\'\"]", "", .data$package_name)))
68 |
69 |
70 | # build annotations
71 | if (all(!grepl("p_load", pck_descs$call))) { # no pacman calls
72 | pck_descs <- dplyr::mutate(pck_descs,annotated=dplyr::case_when(
73 | stringr::str_detect(title,"not installed")~paste0(call, " # ", annotation, " vNA"),
74 | TRUE~ paste0(call, " # ", title, " ", annotation, " v", version)
75 | ))
76 | return(
77 | stringi::stri_replace_all_fixed(
78 | str = string_og, pattern = pck_descs$call,
79 | replacement = pck_descs$annotated, vectorize_all = FALSE
80 | )
81 | )
82 | }
83 |
84 | if (all(grepl("p_load", pck_descs$call))) { # only pacman calls
85 | pacld <- pck_descs[which(stringr::str_detect(pck_descs$call, ".+load\\(")), ]
86 | pacld$pkgnamesep <- paste0(pacld$package_name, ", ")
87 | pacld <- dplyr::mutate(dplyr::group_by(pacld, call), pkgnamesep = ifelse(dplyr::row_number() == dplyr::n(), gsub(",", "", .data$pkgnamesep), .data$pkgnamesep))
88 | pacld$annotatedpac <- paste0(pacld$pkgnamesep, "# ", pacld$title, " ", pacld$annotation, " v", pacld$version)
89 | pacld <- dplyr::summarize(dplyr::group_by(pacld, call), pkgs = paste(.data$annotatedpac, collapse = "\n"))
90 | pacld$ldcalls <- stringr::str_extract(pacld$call, ".+\\(")
91 | pacld <- dplyr::mutate(pacld, annotpac = paste(.data$ldcalls, .data$pkgs, ")", sep = "\n "))
92 | return(
93 | stringi::stri_replace_all_fixed(
94 | str = string_og, pattern = pacld$call,
95 | replacement = pacld$annotpac, vectorize_all = FALSE
96 | )
97 | )
98 | }
99 |
100 | if (any(grepl("p_load", pck_descs$call)) & any(grepl("libr|req", out_tb$call))) { # pacman and base calls
101 | pacld <- pck_descs[which(stringr::str_detect(pck_descs$call, ".+load\\(")), ]
102 | pacld$pkgnamesep <- paste0(pacld$package_name, ", ")
103 | pacld <- dplyr::mutate(dplyr::group_by(pacld, call), pkgnamesep = ifelse(dplyr::row_number() == dplyr::n(), gsub(",", "", .data$pkgnamesep), .data$pkgnamesep))
104 | pacld$annotatedpac <- paste0(pacld$pkgnamesep, "# ", pacld$title, " ", pacld$annotation, " v", pacld$version)
105 | pacld <- dplyr::summarize(dplyr::group_by(pacld, call), pkgs = paste(.data$annotatedpac, collapse = "\n "))
106 | pacld$ldcalls <- stringr::str_extract(pacld$call, ".+\\(")
107 | pacld <- dplyr::mutate(pacld, annotpac = paste(.data$ldcalls, .data$pkgs, ")", sep = "\n "))
108 | string_og <- stringi::stri_replace_all_fixed(
109 | str = string_og, pattern = pacld$call,
110 | replacement = pacld$annotpac, vectorize_all = FALSE
111 | )
112 | pck_descs <- pck_descs[which(!stringr::str_detect(pck_descs$call, ".+load\\(")), ]
113 | pck_descs <- dplyr::mutate(pck_descs,annotated=dplyr::case_when(
114 | stringr::str_detect(title,"not installed")~paste0(call, " #", " ", annotation, " vNA"),
115 | TRUE~ paste0(call, " # ", title, " ", annotation, " v", version)
116 | ))
117 |
118 | return(
119 | stringi::stri_replace_all_fixed(
120 | str = string_og,
121 | pattern = pck_descs$call, # Changed
122 | replacement = pck_descs$annotated,
123 | vectorize_all = FALSE
124 | )
125 | )
126 | }
127 | }
128 |
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41 | Source: R/annotate_pkg_datasets_active.R
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41 | Source: R/annotate_repos_active_file.R
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61 | Citation
62 | Source: DESCRIPTION
63 |
64 | Verde Arregoitia L (2025).
65 | annotater: Annotate Package Load Calls.
66 | R package version 0.2.3.9000, https://annotater.liomys.mx, https://github.com/luisDVA/annotater.
67 |
68 | @Manual{,
69 | title = {annotater: Annotate Package Load Calls},
70 | author = {Luis D. {Verde Arregoitia}},
71 | year = {2025},
72 | note = {R package version 0.2.3.9000, https://annotater.liomys.mx},
73 | url = {https://github.com/luisDVA/annotater},
74 | }
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42 | Annotate function calls in active file
43 | Source: R/annotate_fun_calls_active_file.R
44 | annotate_fun_calls_active_file.Rd
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48 | Annotates package load calls with the used functions of each package in the
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42 | Annotate titles and repositories in active file
43 | Source: R/annotate_repostitle_active.R
44 | annotate_repostitle_active.Rd
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/R/annotate_repo_source.R:
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1 | #' Annotate repository sources
2 | #'
3 | #' @param string_og text string (script) with package load calls
4 | #'
5 | #' @return text string with package repository source annotations. Will make
6 | #' note of packages not currently installed. Lines with existing comments or
7 | #' annotations are ignored by the regular expression that matches package
8 | #' names. Also ignores base packages. Local installs now annotated as such.
9 | #'
10 | #' @examples
11 | #' test_string <- c("library(knitr)\nrequire(datasets)")
12 | #' annotate_repo_source(test_string)
13 | #' @importFrom rlang .data
14 | #' @export
15 | annotate_repo_source <- function(string_og) {
16 | out_tb <- match_pkg_names(string_og)
17 | if (nrow(out_tb) == 0) cat("no matching library load calls")
18 | if (nrow(out_tb) == 0) {
19 | return(string_og)
20 | }
21 | out_tb <- tibble::rowid_to_column(out_tb)
22 | pck_descs <- suppressWarnings(purrr::map(out_tb$pkgname_clean,
23 | utils::packageDescription,
24 | fields = c("Repository", "RemoteType", "biocViews")
25 | ))
26 | pck_descs <- purrr::map(pck_descs, as.list)
27 | pck_descs <-
28 | purrr::map(pck_descs, function(x) {
29 | if (
30 | !is.na(x$Repository) &&
31 | x$Repository == "CRAN" &&
32 | !is.na(x$RemoteType) &&
33 | x$RemoteType == "standard"
34 | ) {
35 | x$RemoteType <- NA
36 | }
37 | x
38 | })
39 | pck_descs <- tidyr::unnest(tibble::enframe(purrr::map(pck_descs, purrr::flatten_chr)), cols = c("value"))
40 | pck_descs <- dplyr::rename(pck_descs, rowid = 1, repo = 2)
41 | pck_descs <- dplyr::left_join(out_tb, pck_descs, by = "rowid")
42 | pck_descs <- dplyr::mutate(pck_descs, repo = ifelse(stringr::str_detect(.data$repo, ","), "Bioconductor", .data$repo))
43 | pck_descs <- dplyr::add_count(pck_descs, .data$package_name)
44 | pck_descs <- dplyr::mutate(pck_descs, repo = dplyr::if_else(.data$n == 1, "none", .data$repo))
45 | pck_descs <-
46 | suppressMessages(dplyr::ungroup(dplyr::summarize(
47 | dplyr::group_by(pck_descs,call,.data$package_name,.data$pkgname_clean),repo=dplyr::last(stats::na.omit(.data$repo)))))
48 | pck_descs <- dplyr::mutate(pck_descs, user_repo = dplyr::case_when(
49 | .data$repo ==
50 | "CRAN" ~ "CRAN",
51 | stringr::str_detect(.data$repo, "r-universe") ~ .data$repo,
52 | .data$repo == "Bioconductor" ~ "Bioconductor",
53 | .data$repo == "RSPM" ~ "Posit RSPM",
54 | .data$repo == "none" ~ "not installed on this machine",
55 | is.na(.data$repo) ~ "local install",
56 | TRUE ~ repo_details(.data$pkgname_clean)
57 | ), annotation = dplyr::case_when(stringr::str_detect(
58 | user_repo,
59 | "(?
2 |
39 |
43 |
44 |
53 |
54 |
55 |
45 |
46 |
51 |
52 | Copyright (c) 2019 Luis D. Verde Arregoita
47 |Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
48 |The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
49 |THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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1 | #' Annotate package titles and repository sources
2 | #'
3 | #' @param string_og Text string (script) with package load calls.
4 | #'
5 | #' @return Text string with package titles and package repository source
6 | #' annotations. Will make note of packages not currently installed. Lines with
7 | #' existing comments or annotations are ignored by the regular expression that
8 | #' matches package names. Also ignores base packages.
9 | #'
10 | #' @details Some annotations may be long, check for possible line breaks
11 | #' introduced into your script.
12 | #' @examples
13 | #' test_string <- c("library(knitr)\nrequire(datasets)")
14 | #' annotate_repostitle(test_string)
15 | #' @importFrom rlang .data
16 | #' @export
17 | annotate_repostitle <- function(string_og) {
18 | out_tb <- match_pkg_names(string_og)
19 | if (nrow(out_tb) == 0) cat("no matching library load calls")
20 | if (nrow(out_tb) == 0) {
21 | return(string_og)
22 | }
23 | out_tb <- tibble::rowid_to_column(out_tb)
24 | # get pkg titles
25 | out_tb$pck_title <- purrr::map_chr(out_tb$pkgname_clean, utils::packageDescription, fields = "Title")
26 | out_tb$pck_title <- stringi::stri_replace_na(out_tb$pck_title, "not installed on this machine")
27 | # new title variable
28 | out_tb$title <- paste(out_tb$pck_title)
29 | # repo descriptions
30 | pck_descs <- purrr::map(out_tb$pkgname_clean, utils::packageDescription,
31 | fields = c("Repository", "RemoteType", "biocViews")
32 | )
33 | pck_descs <- purrr::map(pck_descs, as.list)
34 | pck_descs <-
35 | purrr::map(pck_descs, function(x) {
36 | if (
37 | !is.na(x$Repository) &&
38 | x$Repository == "CRAN" &&
39 | !is.na(x$RemoteType) &&
40 | x$RemoteType == "standard"
41 | ) {
42 | x$RemoteType <- NA
43 | }
44 | x
45 | })
46 | pck_descs <- tidyr::unnest(tibble::enframe(purrr::map(pck_descs, purrr::flatten_chr)), cols = c("value"))
47 | pck_descs <- dplyr::rename(pck_descs, rowid = 1, repo = 2)
48 | pck_descs <- dplyr::left_join(out_tb, pck_descs, by = "rowid")
49 | pck_descs <- dplyr::mutate(pck_descs, repo = ifelse(stringr::str_detect(.data$repo, ","), "Bioconductor", .data$repo))
50 | pck_descs <- dplyr::add_count(pck_descs, .data$package_name)
51 |
52 | pck_descs <- dplyr::mutate(pck_descs, repo = dplyr::if_else(!is.na(.data$repo) & .data$n == 1, "none", .data$repo)) # Ensure we only check n if repo is not NA
53 | pck_descs <- dplyr::mutate(pck_descs, user_repo = dplyr::case_when(
54 | is.na(.data$repo) ~ "details not available", # Handle NA repo explicitly
55 | .data$repo == "CRAN" ~ "CRAN",
56 | .data$repo == "Bioconductor" ~ "Bioconductor",
57 | .data$repo == "RSPM" ~ "Posit RSPM",
58 | .data$repo == "none" ~ "not installed on this machine",
59 | stringr::str_detect(.data$repo,"universe")~ .data$repo, # for Runiverse pkgs
60 | TRUE ~ repo_details(.data$pkgname_clean) # Ensure repo_details handles missing packages gracefully
61 | ), annotation = dplyr::case_when(
62 | user_repo == "details not available" ~ user_repo, # Handle cases where details weren't found
63 | user_repo == "not installed on this machine" ~ user_repo, # Handle not installed cases
64 | stringr::str_detect(user_repo, "/(?!.+r-universe.+)") ~ paste0("[", .data$repo, "::", user_repo, "]"),
65 | TRUE ~ user_repo
66 | ))
67 | pck_descs <- dplyr::mutate(pck_descs, version = pkg_version(gsub("[\'\"]", "", .data$package_name)))
68 |
69 |
70 | # build annotations
71 | if (all(!grepl("p_load", pck_descs$call))) { # no pacman calls
72 | pck_descs <- dplyr::mutate(pck_descs,annotated=dplyr::case_when(
73 | stringr::str_detect(title,"not installed")~paste0(call, " # ", annotation, " vNA"),
74 | TRUE~ paste0(call, " # ", title, " ", annotation, " v", version)
75 | ))
76 | return(
77 | stringi::stri_replace_all_fixed(
78 | str = string_og, pattern = pck_descs$call,
79 | replacement = pck_descs$annotated, vectorize_all = FALSE
80 | )
81 | )
82 | }
83 |
84 | if (all(grepl("p_load", pck_descs$call))) { # only pacman calls
85 | pacld <- pck_descs[which(stringr::str_detect(pck_descs$call, ".+load\\(")), ]
86 | pacld$pkgnamesep <- paste0(pacld$package_name, ", ")
87 | pacld <- dplyr::mutate(dplyr::group_by(pacld, call), pkgnamesep = ifelse(dplyr::row_number() == dplyr::n(), gsub(",", "", .data$pkgnamesep), .data$pkgnamesep))
88 | pacld$annotatedpac <- paste0(pacld$pkgnamesep, "# ", pacld$title, " ", pacld$annotation, " v", pacld$version)
89 | pacld <- dplyr::summarize(dplyr::group_by(pacld, call), pkgs = paste(.data$annotatedpac, collapse = "\n"))
90 | pacld$ldcalls <- stringr::str_extract(pacld$call, ".+\\(")
91 | pacld <- dplyr::mutate(pacld, annotpac = paste(.data$ldcalls, .data$pkgs, ")", sep = "\n "))
92 | return(
93 | stringi::stri_replace_all_fixed(
94 | str = string_og, pattern = pacld$call,
95 | replacement = pacld$annotpac, vectorize_all = FALSE
96 | )
97 | )
98 | }
99 |
100 | if (any(grepl("p_load", pck_descs$call)) & any(grepl("libr|req", out_tb$call))) { # pacman and base calls
101 | pacld <- pck_descs[which(stringr::str_detect(pck_descs$call, ".+load\\(")), ]
102 | pacld$pkgnamesep <- paste0(pacld$package_name, ", ")
103 | pacld <- dplyr::mutate(dplyr::group_by(pacld, call), pkgnamesep = ifelse(dplyr::row_number() == dplyr::n(), gsub(",", "", .data$pkgnamesep), .data$pkgnamesep))
104 | pacld$annotatedpac <- paste0(pacld$pkgnamesep, "# ", pacld$title, " ", pacld$annotation, " v", pacld$version)
105 | pacld <- dplyr::summarize(dplyr::group_by(pacld, call), pkgs = paste(.data$annotatedpac, collapse = "\n "))
106 | pacld$ldcalls <- stringr::str_extract(pacld$call, ".+\\(")
107 | pacld <- dplyr::mutate(pacld, annotpac = paste(.data$ldcalls, .data$pkgs, ")", sep = "\n "))
108 | string_og <- stringi::stri_replace_all_fixed(
109 | str = string_og, pattern = pacld$call,
110 | replacement = pacld$annotpac, vectorize_all = FALSE
111 | )
112 | pck_descs <- pck_descs[which(!stringr::str_detect(pck_descs$call, ".+load\\(")), ]
113 | pck_descs <- dplyr::mutate(pck_descs,annotated=dplyr::case_when(
114 | stringr::str_detect(title,"not installed")~paste0(call, " #", " ", annotation, " vNA"),
115 | TRUE~ paste0(call, " # ", title, " ", annotation, " v", version)
116 | ))
117 |
118 | return(
119 | stringi::stri_replace_all_fixed(
120 | str = string_og,
121 | pattern = pck_descs$call, # Changed
122 | replacement = pck_descs$annotated,
123 | vectorize_all = FALSE
124 | )
125 | )
126 | }
127 | }
128 |
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41 | Source:R/annotate_pkg_datasets_active.R
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62 |Source: DESCRIPTION
Verde Arregoitia L (2025). 65 | annotater: Annotate Package Load Calls. 66 | R package version 0.2.3.9000, https://annotater.liomys.mx, https://github.com/luisDVA/annotater. 67 |
68 |@Manual{,
69 | title = {annotater: Annotate Package Load Calls},
70 | author = {Luis D. {Verde Arregoitia}},
71 | year = {2025},
72 | note = {R package version 0.2.3.9000, https://annotater.liomys.mx},
73 | url = {https://github.com/luisDVA/annotater},
74 | }
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