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1 |
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3 |
4 |
5 |
6 |
7 |
8 |
9 |
108 |
124 |
125 |
126 |
127 |
137 |
109 |
116 |
117 |
122 |
123 |
110 |
112 |
113 | Content not found. Please use links in the navbar.
114 |
115 | Page not found (404)
111 |`, 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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/docs/docsearch.css:
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1 | /* Docsearch -------------------------------------------------------------- */
2 | /*
3 | Source: https://github.com/algolia/docsearch/
4 | License: MIT
5 | */
6 |
7 | .algolia-autocomplete {
8 | display: block;
9 | -webkit-box-flex: 1;
10 | -ms-flex: 1;
11 | flex: 1
12 | }
13 |
14 | .algolia-autocomplete .ds-dropdown-menu {
15 | width: 100%;
16 | min-width: none;
17 | max-width: none;
18 | padding: .75rem 0;
19 | background-color: #fff;
20 | background-clip: padding-box;
21 | border: 1px solid rgba(0, 0, 0, .1);
22 | box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
23 | }
24 |
25 | @media (min-width:768px) {
26 | .algolia-autocomplete .ds-dropdown-menu {
27 | width: 175%
28 | }
29 | }
30 |
31 | .algolia-autocomplete .ds-dropdown-menu::before {
32 | display: none
33 | }
34 |
35 | .algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
36 | padding: 0;
37 | background-color: rgb(255,255,255);
38 | border: 0;
39 | max-height: 80vh;
40 | }
41 |
42 | .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
43 | margin-top: 0
44 | }
45 |
46 | .algolia-autocomplete .algolia-docsearch-suggestion {
47 | padding: 0;
48 | overflow: visible
49 | }
50 |
51 | .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
52 | padding: .125rem 1rem;
53 | margin-top: 0;
54 | font-size: 1.3em;
55 | font-weight: 500;
56 | color: #00008B;
57 | border-bottom: 0
58 | }
59 |
60 | .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
61 | float: none;
62 | padding-top: 0
63 | }
64 |
65 | .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
66 | float: none;
67 | width: auto;
68 | padding: 0;
69 | text-align: left
70 | }
71 |
72 | .algolia-autocomplete .algolia-docsearch-suggestion--content {
73 | float: none;
74 | width: auto;
75 | padding: 0
76 | }
77 |
78 | .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
79 | display: none
80 | }
81 |
82 | .algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
83 | padding-top: .75rem;
84 | margin-top: .75rem;
85 | border-top: 1px solid rgba(0, 0, 0, .1)
86 | }
87 |
88 | .algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
89 | display: block;
90 | padding: .1rem 1rem;
91 | margin-bottom: 0.1;
92 | font-size: 1.0em;
93 | font-weight: 400
94 | /* display: none */
95 | }
96 |
97 | .algolia-autocomplete .algolia-docsearch-suggestion--title {
98 | display: block;
99 | padding: .25rem 1rem;
100 | margin-bottom: 0;
101 | font-size: 0.9em;
102 | font-weight: 400
103 | }
104 |
105 | .algolia-autocomplete .algolia-docsearch-suggestion--text {
106 | padding: 0 1rem .5rem;
107 | margin-top: -.25rem;
108 | font-size: 0.8em;
109 | font-weight: 400;
110 | line-height: 1.25
111 | }
112 |
113 | .algolia-autocomplete .algolia-docsearch-footer {
114 | width: 110px;
115 | height: 20px;
116 | z-index: 3;
117 | margin-top: 10.66667px;
118 | float: right;
119 | font-size: 0;
120 | line-height: 0;
121 | }
122 |
123 | .algolia-autocomplete .algolia-docsearch-footer--logo {
124 | background-image: url("data:image/svg+xml;utf8,");
125 | background-repeat: no-repeat;
126 | background-position: 50%;
127 | background-size: 100%;
128 | overflow: hidden;
129 | text-indent: -9000px;
130 | width: 100%;
131 | height: 100%;
132 | display: block;
133 | transform: translate(-8px);
134 | }
135 |
136 | .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
137 | color: #FF8C00;
138 | background: rgba(232, 189, 54, 0.1)
139 | }
140 |
141 |
142 | .algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
143 | box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
144 | }
145 |
146 | .algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
147 | background-color: rgba(192, 192, 192, .15)
148 | }
149 |
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/docs/docsearch.js:
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1 | $(function() {
2 |
3 | // register a handler to move the focus to the search bar
4 | // upon pressing shift + "/" (i.e. "?")
5 | $(document).on('keydown', function(e) {
6 | if (e.shiftKey && e.keyCode == 191) {
7 | e.preventDefault();
8 | $("#search-input").focus();
9 | }
10 | });
11 |
12 | $(document).ready(function() {
13 | // do keyword highlighting
14 | /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
15 | var mark = function() {
16 |
17 | var referrer = document.URL ;
18 | var paramKey = "q" ;
19 |
20 | if (referrer.indexOf("?") !== -1) {
21 | var qs = referrer.substr(referrer.indexOf('?') + 1);
22 | var qs_noanchor = qs.split('#')[0];
23 | var qsa = qs_noanchor.split('&');
24 | var keyword = "";
25 |
26 | for (var i = 0; i < qsa.length; i++) {
27 | var currentParam = qsa[i].split('=');
28 |
29 | if (currentParam.length !== 2) {
30 | continue;
31 | }
32 |
33 | if (currentParam[0] == paramKey) {
34 | keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
35 | }
36 | }
37 |
38 | if (keyword !== "") {
39 | $(".contents").unmark({
40 | done: function() {
41 | $(".contents").mark(keyword);
42 | }
43 | });
44 | }
45 | }
46 | };
47 |
48 | mark();
49 | });
50 | });
51 |
52 | /* Search term highlighting ------------------------------*/
53 |
54 | function matchedWords(hit) {
55 | var words = [];
56 |
57 | var hierarchy = hit._highlightResult.hierarchy;
58 | // loop to fetch from lvl0, lvl1, etc.
59 | for (var idx in hierarchy) {
60 | words = words.concat(hierarchy[idx].matchedWords);
61 | }
62 |
63 | var content = hit._highlightResult.content;
64 | if (content) {
65 | words = words.concat(content.matchedWords);
66 | }
67 |
68 | // return unique words
69 | var words_uniq = [...new Set(words)];
70 | return words_uniq;
71 | }
72 |
73 | function updateHitURL(hit) {
74 |
75 | var words = matchedWords(hit);
76 | var url = "";
77 |
78 | if (hit.anchor) {
79 | url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
80 | } else {
81 | url = hit.url + '?q=' + escape(words.join(" "));
82 | }
83 |
84 | return url;
85 | }
86 |
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/docs/index.html:
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1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 | Generic template for data analysis projects structured as R packages • template
9 |
10 |
11 |
12 |
13 |
14 |
15 |
19 |
23 |
24 |
25 |
26 |
66 |
67 |
68 |
69 |
70 |
71 |
72 |
73 |
74 | template package
75 |
76 |
77 | Generic template for data analysis projects structured as R packages
78 |
79 | The template package automates creation of new projects with all the necessary scaffolding: different folders for data, scripts, and functions, plus (optionally) additional files required for an R package structure. It can simultaneously create and synchronise a new repository on GitHub so one can start working immediately.
80 | template can create both projects with or without R package structure. Structuring data analysis projects as R packages (a.k.a. “research compendia”) can bring some advantages (e.g. see this blogpost, this repo, these and these slides or read Marwick et al.). But there are also good reasons why an R package structure may not always be needed or convenient.
81 |
82 |
83 |
84 | Installation
85 |
86 | # install.packages("remotes")
87 | remotes::install_github("Pakillo/template")
88 |
89 |
90 |
91 | Usage
92 | First, load the package:
93 |
94 | library("template")
95 | Now run the function new_project to create a directory with all the scaffolding (slightly modified from R package structure). For example, to start a new project about tree growth, just use:
96 |
97 | new_project("treegrowth")
98 | This will create a new Rstudio project with this structure:
99 | 
100 | You can create a GitHub repository for the project at the same time:
101 |
102 | new_project("treegrowth", github = TRUE, private.repo = FALSE)
103 | You could choose either public or private repository. Note that to create a GitHub repo you will need to have configured your system as explained in https://usethis.r-lib.org/articles/articles/usethis-setup.html.
104 | There are other options you could choose, like setting up testthat or continuous integration (Travis-CI, GitHub Actions…). Or skip R package structure altogether. See ?new_project for all options.
105 |
106 |
107 |
108 | Developing the project
109 |
110 | Now edit README.Rmd and the DESCRIPTION file with some basic information about your project: title, brief description, licence, package dependencies, etc.
Place original (raw) data in data-raw folder. Save all R scripts (or Rmarkdown documents) used for data preparation in the same folder.
Save final (clean, tidy) datasets in the data folder. You may write documentation for these data.
R scripts or Rmarkdown documents used for data analyses may be placed at the analyses folder. The final manuscript/report may be placed at the manuscript folder. You could use one of the many Rmarkdown templates available out there (e.g. rticles, rrtools or rmdTemplates).
If you write custom functions, place them in the R folder. Document all your functions with Roxygen. Write tests for your functions and place them in the tests folder.
If your analysis uses functions from other CRAN packages, include these as dependencies (Imports) in the DESCRIPTION file (e.g. using usethis::use_package() or rrtools::add_dependencies_to_description(). Also, use Roxygen @import or @importFrom in your function definitions, or alternatively package::function(), to import these dependencies in the namespace.
I recommend using an advanced tool like targets to manage your project workflow. A simpler alternative might be writing a makefile or master script to organise and execute all parts of the analysis. A template makefile is included with this package (use makefile = TRUE when calling new_project).
Render Rmarkdown reports using rmarkdown::render, and use Rstudio Build menu to create/update documentation, run tests, build package, etc.
Record the exact dependencies of your project. One option is simply running sessionInfo() but many more sophisticated alternatives exist. For example, automagic::make_deps_file() or renv::snapshot() will create a file recording the exact versions of all packages used, which can be used to recreate such environment in the future or in another computer. If you want to use Docker, you could use e.g. containerit::dockerfile() or rrtools::use_dockerfile().
Archive your repository (e.g. in Zenodo), get a DOI, and include citation information in your README.
121 |
122 |
123 |
124 | Thanks to:
125 |
126 | - Carl Boettiger and his template package
127 |
128 | - Jeff Hollister and his manuscriptPackage
129 |
130 | - Robert Flight: http://rmflight.github.io/posts/2014/07/analyses_as_packages.html
131 |
132 | - Hadley Wickham: http://r-pkgs.had.co.nz/
133 |
134 | - Yihui Xie: http://yihui.name/knitr/
135 |
136 | - Rstudio
137 |
138 |
139 |
150 |
151 |
152 |
153 |
183 |
184 |
185 |
186 |
195 |
196 |
197 |
198 |
199 |
200 |
201 |
202 |
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1 |
2 |
3 |
13 |
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/docs/pkgdown.css:
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1 | /* Sticky footer */
2 |
3 | /**
4 | * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
5 | * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
6 | *
7 | * .Site -> body > .container
8 | * .Site-content -> body > .container .row
9 | * .footer -> footer
10 | *
11 | * Key idea seems to be to ensure that .container and __all its parents__
12 | * have height set to 100%
13 | *
14 | */
15 |
16 | html, body {
17 | height: 100%;
18 | }
19 |
20 | body {
21 | position: relative;
22 | }
23 |
24 | body > .container {
25 | display: flex;
26 | height: 100%;
27 | flex-direction: column;
28 | }
29 |
30 | body > .container .row {
31 | flex: 1 0 auto;
32 | }
33 |
34 | footer {
35 | margin-top: 45px;
36 | padding: 35px 0 36px;
37 | border-top: 1px solid #e5e5e5;
38 | color: #666;
39 | display: flex;
40 | flex-shrink: 0;
41 | }
42 | footer p {
43 | margin-bottom: 0;
44 | }
45 | footer div {
46 | flex: 1;
47 | }
48 | footer .pkgdown {
49 | text-align: right;
50 | }
51 | footer p {
52 | margin-bottom: 0;
53 | }
54 |
55 | img.icon {
56 | float: right;
57 | }
58 |
59 | img {
60 | max-width: 100%;
61 | }
62 |
63 | /* Fix bug in bootstrap (only seen in firefox) */
64 | summary {
65 | display: list-item;
66 | }
67 |
68 | /* Typographic tweaking ---------------------------------*/
69 |
70 | .contents .page-header {
71 | margin-top: calc(-60px + 1em);
72 | }
73 |
74 | dd {
75 | margin-left: 3em;
76 | }
77 |
78 | /* Section anchors ---------------------------------*/
79 |
80 | a.anchor {
81 | margin-left: -30px;
82 | display:inline-block;
83 | width: 30px;
84 | height: 30px;
85 | visibility: hidden;
86 |
87 | background-image: url(./link.svg);
88 | background-repeat: no-repeat;
89 | background-size: 20px 20px;
90 | background-position: center center;
91 | }
92 |
93 | .hasAnchor:hover a.anchor {
94 | visibility: visible;
95 | }
96 |
97 | @media (max-width: 767px) {
98 | .hasAnchor:hover a.anchor {
99 | visibility: hidden;
100 | }
101 | }
102 |
103 |
104 | /* Fixes for fixed navbar --------------------------*/
105 |
106 | .contents h1, .contents h2, .contents h3, .contents h4 {
107 | padding-top: 60px;
108 | margin-top: -40px;
109 | }
110 |
111 | /* Navbar submenu --------------------------*/
112 |
113 | .dropdown-submenu {
114 | position: relative;
115 | }
116 |
117 | .dropdown-submenu>.dropdown-menu {
118 | top: 0;
119 | left: 100%;
120 | margin-top: -6px;
121 | margin-left: -1px;
122 | border-radius: 0 6px 6px 6px;
123 | }
124 |
125 | .dropdown-submenu:hover>.dropdown-menu {
126 | display: block;
127 | }
128 |
129 | .dropdown-submenu>a:after {
130 | display: block;
131 | content: " ";
132 | float: right;
133 | width: 0;
134 | height: 0;
135 | border-color: transparent;
136 | border-style: solid;
137 | border-width: 5px 0 5px 5px;
138 | border-left-color: #cccccc;
139 | margin-top: 5px;
140 | margin-right: -10px;
141 | }
142 |
143 | .dropdown-submenu:hover>a:after {
144 | border-left-color: #ffffff;
145 | }
146 |
147 | .dropdown-submenu.pull-left {
148 | float: none;
149 | }
150 |
151 | .dropdown-submenu.pull-left>.dropdown-menu {
152 | left: -100%;
153 | margin-left: 10px;
154 | border-radius: 6px 0 6px 6px;
155 | }
156 |
157 | /* Sidebar --------------------------*/
158 |
159 | #pkgdown-sidebar {
160 | margin-top: 30px;
161 | position: -webkit-sticky;
162 | position: sticky;
163 | top: 70px;
164 | }
165 |
166 | #pkgdown-sidebar h2 {
167 | font-size: 1.5em;
168 | margin-top: 1em;
169 | }
170 |
171 | #pkgdown-sidebar h2:first-child {
172 | margin-top: 0;
173 | }
174 |
175 | #pkgdown-sidebar .list-unstyled li {
176 | margin-bottom: 0.5em;
177 | }
178 |
179 | /* bootstrap-toc tweaks ------------------------------------------------------*/
180 |
181 | /* All levels of nav */
182 |
183 | nav[data-toggle='toc'] .nav > li > a {
184 | padding: 4px 20px 4px 6px;
185 | font-size: 1.5rem;
186 | font-weight: 400;
187 | color: inherit;
188 | }
189 |
190 | nav[data-toggle='toc'] .nav > li > a:hover,
191 | nav[data-toggle='toc'] .nav > li > a:focus {
192 | padding-left: 5px;
193 | color: inherit;
194 | border-left: 1px solid #878787;
195 | }
196 |
197 | nav[data-toggle='toc'] .nav > .active > a,
198 | nav[data-toggle='toc'] .nav > .active:hover > a,
199 | nav[data-toggle='toc'] .nav > .active:focus > a {
200 | padding-left: 5px;
201 | font-size: 1.5rem;
202 | font-weight: 400;
203 | color: inherit;
204 | border-left: 2px solid #878787;
205 | }
206 |
207 | /* Nav: second level (shown on .active) */
208 |
209 | nav[data-toggle='toc'] .nav .nav {
210 | display: none; /* Hide by default, but at >768px, show it */
211 | padding-bottom: 10px;
212 | }
213 |
214 | nav[data-toggle='toc'] .nav .nav > li > a {
215 | padding-left: 16px;
216 | font-size: 1.35rem;
217 | }
218 |
219 | nav[data-toggle='toc'] .nav .nav > li > a:hover,
220 | nav[data-toggle='toc'] .nav .nav > li > a:focus {
221 | padding-left: 15px;
222 | }
223 |
224 | nav[data-toggle='toc'] .nav .nav > .active > a,
225 | nav[data-toggle='toc'] .nav .nav > .active:hover > a,
226 | nav[data-toggle='toc'] .nav .nav > .active:focus > a {
227 | padding-left: 15px;
228 | font-weight: 500;
229 | font-size: 1.35rem;
230 | }
231 |
232 | /* orcid ------------------------------------------------------------------- */
233 |
234 | .orcid {
235 | font-size: 16px;
236 | color: #A6CE39;
237 | /* margins are required by official ORCID trademark and display guidelines */
238 | margin-left:4px;
239 | margin-right:4px;
240 | vertical-align: middle;
241 | }
242 |
243 | /* Reference index & topics ----------------------------------------------- */
244 |
245 | .ref-index th {font-weight: normal;}
246 |
247 | .ref-index td {vertical-align: top; min-width: 100px}
248 | .ref-index .icon {width: 40px;}
249 | .ref-index .alias {width: 40%;}
250 | .ref-index-icons .alias {width: calc(40% - 40px);}
251 | .ref-index .title {width: 60%;}
252 |
253 | .ref-arguments th {text-align: right; padding-right: 10px;}
254 | .ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px}
255 | .ref-arguments .name {width: 20%;}
256 | .ref-arguments .desc {width: 80%;}
257 |
258 | /* Nice scrolling for wide elements --------------------------------------- */
259 |
260 | table {
261 | display: block;
262 | overflow: auto;
263 | }
264 |
265 | /* Syntax highlighting ---------------------------------------------------- */
266 |
267 | pre {
268 | word-wrap: normal;
269 | word-break: normal;
270 | border: 1px solid #eee;
271 | }
272 |
273 | pre, code {
274 | background-color: #f8f8f8;
275 | color: #333;
276 | }
277 |
278 | pre code {
279 | overflow: auto;
280 | word-wrap: normal;
281 | white-space: pre;
282 | }
283 |
284 | pre .img {
285 | margin: 5px 0;
286 | }
287 |
288 | pre .img img {
289 | background-color: #fff;
290 | display: block;
291 | height: auto;
292 | }
293 |
294 | code a, pre a {
295 | color: #375f84;
296 | }
297 |
298 | a.sourceLine:hover {
299 | text-decoration: none;
300 | }
301 |
302 | .fl {color: #1514b5;}
303 | .fu {color: #000000;} /* function */
304 | .ch,.st {color: #036a07;} /* string */
305 | .kw {color: #264D66;} /* keyword */
306 | .co {color: #888888;} /* comment */
307 |
308 | .message { color: black; font-weight: bolder;}
309 | .error { color: orange; font-weight: bolder;}
310 | .warning { color: #6A0366; font-weight: bolder;}
311 |
312 | /* Clipboard --------------------------*/
313 |
314 | .hasCopyButton {
315 | position: relative;
316 | }
317 |
318 | .btn-copy-ex {
319 | position: absolute;
320 | right: 0;
321 | top: 0;
322 | visibility: hidden;
323 | }
324 |
325 | .hasCopyButton:hover button.btn-copy-ex {
326 | visibility: visible;
327 | }
328 |
329 | /* headroom.js ------------------------ */
330 |
331 | .headroom {
332 | will-change: transform;
333 | transition: transform 200ms linear;
334 | }
335 | .headroom--pinned {
336 | transform: translateY(0%);
337 | }
338 | .headroom--unpinned {
339 | transform: translateY(-100%);
340 | }
341 |
342 | /* mark.js ----------------------------*/
343 |
344 | mark {
345 | background-color: rgba(255, 255, 51, 0.5);
346 | border-bottom: 2px solid rgba(255, 153, 51, 0.3);
347 | padding: 1px;
348 | }
349 |
350 | /* vertical spacing after htmlwidgets */
351 | .html-widget {
352 | margin-bottom: 10px;
353 | }
354 |
355 | /* fontawesome ------------------------ */
356 |
357 | .fab {
358 | font-family: "Font Awesome 5 Brands" !important;
359 | }
360 |
361 | /* don't display links in code chunks when printing */
362 | /* source: https://stackoverflow.com/a/10781533 */
363 | @media print {
364 | code a:link:after, code a:visited:after {
365 | content: "";
366 | }
367 | }
368 |
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/docs/pkgdown.js:
--------------------------------------------------------------------------------
1 | /* http://gregfranko.com/blog/jquery-best-practices/ */
2 | (function($) {
3 | $(function() {
4 |
5 | $('.navbar-fixed-top').headroom();
6 |
7 | $('body').css('padding-top', $('.navbar').height() + 10);
8 | $(window).resize(function(){
9 | $('body').css('padding-top', $('.navbar').height() + 10);
10 | });
11 |
12 | $('[data-toggle="tooltip"]').tooltip();
13 |
14 | var cur_path = paths(location.pathname);
15 | var links = $("#navbar ul li a");
16 | var max_length = -1;
17 | var pos = -1;
18 | for (var i = 0; i < links.length; i++) {
19 | if (links[i].getAttribute("href") === "#")
20 | continue;
21 | // Ignore external links
22 | if (links[i].host !== location.host)
23 | continue;
24 |
25 | var nav_path = paths(links[i].pathname);
26 |
27 | var length = prefix_length(nav_path, cur_path);
28 | if (length > max_length) {
29 | max_length = length;
30 | pos = i;
31 | }
32 | }
33 |
34 | // Add class to parent
`).
76 | getTopLevel: function($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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/docs/docsearch.css:
--------------------------------------------------------------------------------
1 | /* Docsearch -------------------------------------------------------------- */
2 | /*
3 | Source: https://github.com/algolia/docsearch/
4 | License: MIT
5 | */
6 |
7 | .algolia-autocomplete {
8 | display: block;
9 | -webkit-box-flex: 1;
10 | -ms-flex: 1;
11 | flex: 1
12 | }
13 |
14 | .algolia-autocomplete .ds-dropdown-menu {
15 | width: 100%;
16 | min-width: none;
17 | max-width: none;
18 | padding: .75rem 0;
19 | background-color: #fff;
20 | background-clip: padding-box;
21 | border: 1px solid rgba(0, 0, 0, .1);
22 | box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
23 | }
24 |
25 | @media (min-width:768px) {
26 | .algolia-autocomplete .ds-dropdown-menu {
27 | width: 175%
28 | }
29 | }
30 |
31 | .algolia-autocomplete .ds-dropdown-menu::before {
32 | display: none
33 | }
34 |
35 | .algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
36 | padding: 0;
37 | background-color: rgb(255,255,255);
38 | border: 0;
39 | max-height: 80vh;
40 | }
41 |
42 | .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
43 | margin-top: 0
44 | }
45 |
46 | .algolia-autocomplete .algolia-docsearch-suggestion {
47 | padding: 0;
48 | overflow: visible
49 | }
50 |
51 | .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
52 | padding: .125rem 1rem;
53 | margin-top: 0;
54 | font-size: 1.3em;
55 | font-weight: 500;
56 | color: #00008B;
57 | border-bottom: 0
58 | }
59 |
60 | .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
61 | float: none;
62 | padding-top: 0
63 | }
64 |
65 | .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
66 | float: none;
67 | width: auto;
68 | padding: 0;
69 | text-align: left
70 | }
71 |
72 | .algolia-autocomplete .algolia-docsearch-suggestion--content {
73 | float: none;
74 | width: auto;
75 | padding: 0
76 | }
77 |
78 | .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
79 | display: none
80 | }
81 |
82 | .algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
83 | padding-top: .75rem;
84 | margin-top: .75rem;
85 | border-top: 1px solid rgba(0, 0, 0, .1)
86 | }
87 |
88 | .algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
89 | display: block;
90 | padding: .1rem 1rem;
91 | margin-bottom: 0.1;
92 | font-size: 1.0em;
93 | font-weight: 400
94 | /* display: none */
95 | }
96 |
97 | .algolia-autocomplete .algolia-docsearch-suggestion--title {
98 | display: block;
99 | padding: .25rem 1rem;
100 | margin-bottom: 0;
101 | font-size: 0.9em;
102 | font-weight: 400
103 | }
104 |
105 | .algolia-autocomplete .algolia-docsearch-suggestion--text {
106 | padding: 0 1rem .5rem;
107 | margin-top: -.25rem;
108 | font-size: 0.8em;
109 | font-weight: 400;
110 | line-height: 1.25
111 | }
112 |
113 | .algolia-autocomplete .algolia-docsearch-footer {
114 | width: 110px;
115 | height: 20px;
116 | z-index: 3;
117 | margin-top: 10.66667px;
118 | float: right;
119 | font-size: 0;
120 | line-height: 0;
121 | }
122 |
123 | .algolia-autocomplete .algolia-docsearch-footer--logo {
124 | background-image: url("data:image/svg+xml;utf8,");
125 | background-repeat: no-repeat;
126 | background-position: 50%;
127 | background-size: 100%;
128 | overflow: hidden;
129 | text-indent: -9000px;
130 | width: 100%;
131 | height: 100%;
132 | display: block;
133 | transform: translate(-8px);
134 | }
135 |
136 | .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
137 | color: #FF8C00;
138 | background: rgba(232, 189, 54, 0.1)
139 | }
140 |
141 |
142 | .algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
143 | box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
144 | }
145 |
146 | .algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
147 | background-color: rgba(192, 192, 192, .15)
148 | }
149 |
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/docs/docsearch.js:
--------------------------------------------------------------------------------
1 | $(function() {
2 |
3 | // register a handler to move the focus to the search bar
4 | // upon pressing shift + "/" (i.e. "?")
5 | $(document).on('keydown', function(e) {
6 | if (e.shiftKey && e.keyCode == 191) {
7 | e.preventDefault();
8 | $("#search-input").focus();
9 | }
10 | });
11 |
12 | $(document).ready(function() {
13 | // do keyword highlighting
14 | /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
15 | var mark = function() {
16 |
17 | var referrer = document.URL ;
18 | var paramKey = "q" ;
19 |
20 | if (referrer.indexOf("?") !== -1) {
21 | var qs = referrer.substr(referrer.indexOf('?') + 1);
22 | var qs_noanchor = qs.split('#')[0];
23 | var qsa = qs_noanchor.split('&');
24 | var keyword = "";
25 |
26 | for (var i = 0; i < qsa.length; i++) {
27 | var currentParam = qsa[i].split('=');
28 |
29 | if (currentParam.length !== 2) {
30 | continue;
31 | }
32 |
33 | if (currentParam[0] == paramKey) {
34 | keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
35 | }
36 | }
37 |
38 | if (keyword !== "") {
39 | $(".contents").unmark({
40 | done: function() {
41 | $(".contents").mark(keyword);
42 | }
43 | });
44 | }
45 | }
46 | };
47 |
48 | mark();
49 | });
50 | });
51 |
52 | /* Search term highlighting ------------------------------*/
53 |
54 | function matchedWords(hit) {
55 | var words = [];
56 |
57 | var hierarchy = hit._highlightResult.hierarchy;
58 | // loop to fetch from lvl0, lvl1, etc.
59 | for (var idx in hierarchy) {
60 | words = words.concat(hierarchy[idx].matchedWords);
61 | }
62 |
63 | var content = hit._highlightResult.content;
64 | if (content) {
65 | words = words.concat(content.matchedWords);
66 | }
67 |
68 | // return unique words
69 | var words_uniq = [...new Set(words)];
70 | return words_uniq;
71 | }
72 |
73 | function updateHitURL(hit) {
74 |
75 | var words = matchedWords(hit);
76 | var url = "";
77 |
78 | if (hit.anchor) {
79 | url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
80 | } else {
81 | url = hit.url + '?q=' + escape(words.join(" "));
82 | }
83 |
84 | return url;
85 | }
86 |
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/docs/index.html:
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1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 | Generic template for data analysis projects structured as R packages • template
9 |
10 |
11 |
12 |
13 |
14 |
15 |
19 |
23 |
24 |
25 |
26 |
66 |
67 |
68 |
69 |
70 |
71 |
72 |
73 |
74 | template package
75 |
76 |
77 | Generic template for data analysis projects structured as R packages
78 |
79 | The template package automates creation of new projects with all the necessary scaffolding: different folders for data, scripts, and functions, plus (optionally) additional files required for an R package structure. It can simultaneously create and synchronise a new repository on GitHub so one can start working immediately.
80 | template can create both projects with or without R package structure. Structuring data analysis projects as R packages (a.k.a. “research compendia”) can bring some advantages (e.g. see this blogpost, this repo, these and these slides or read Marwick et al.). But there are also good reasons why an R package structure may not always be needed or convenient.
81 |
82 |
83 |
84 | Installation
85 |
86 | # install.packages("remotes")
87 | remotes::install_github("Pakillo/template")
88 |
89 |
90 |
91 | Usage
92 | First, load the package:
93 |
94 | library("template")
95 | Now run the function new_project to create a directory with all the scaffolding (slightly modified from R package structure). For example, to start a new project about tree growth, just use:
96 |
97 | new_project("treegrowth")
98 | This will create a new Rstudio project with this structure:
99 |
100 | You can create a GitHub repository for the project at the same time:
101 |
102 | new_project("treegrowth", github = TRUE, private.repo = FALSE)
103 | You could choose either public or private repository. Note that to create a GitHub repo you will need to have configured your system as explained in https://usethis.r-lib.org/articles/articles/usethis-setup.html.
104 | There are other options you could choose, like setting up testthat or continuous integration (Travis-CI, GitHub Actions…). Or skip R package structure altogether. See ?new_project for all options.
105 |
106 |
107 |
108 | Developing the project
109 |
110 | Now edit README.Rmd and the DESCRIPTION file with some basic information about your project: title, brief description, licence, package dependencies, etc.
Place original (raw) data in data-raw folder. Save all R scripts (or Rmarkdown documents) used for data preparation in the same folder.
Save final (clean, tidy) datasets in the data folder. You may write documentation for these data.
R scripts or Rmarkdown documents used for data analyses may be placed at the analyses folder. The final manuscript/report may be placed at the manuscript folder. You could use one of the many Rmarkdown templates available out there (e.g. rticles, rrtools or rmdTemplates).
If you write custom functions, place them in the R folder. Document all your functions with Roxygen. Write tests for your functions and place them in the tests folder.
If your analysis uses functions from other CRAN packages, include these as dependencies (Imports) in the DESCRIPTION file (e.g. using usethis::use_package() or rrtools::add_dependencies_to_description(). Also, use Roxygen @import or @importFrom in your function definitions, or alternatively package::function(), to import these dependencies in the namespace.
I recommend using an advanced tool like targets to manage your project workflow. A simpler alternative might be writing a makefile or master script to organise and execute all parts of the analysis. A template makefile is included with this package (use makefile = TRUE when calling new_project).
Render Rmarkdown reports using rmarkdown::render, and use Rstudio Build menu to create/update documentation, run tests, build package, etc.
Record the exact dependencies of your project. One option is simply running sessionInfo() but many more sophisticated alternatives exist. For example, automagic::make_deps_file() or renv::snapshot() will create a file recording the exact versions of all packages used, which can be used to recreate such environment in the future or in another computer. If you want to use Docker, you could use e.g. containerit::dockerfile() or rrtools::use_dockerfile().
Archive your repository (e.g. in Zenodo), get a DOI, and include citation information in your README.
121 |
122 |
123 |
124 | Thanks to:
125 |
126 | - Carl Boettiger and his template package
127 |
128 | - Jeff Hollister and his manuscriptPackage
129 |
130 | - Robert Flight: http://rmflight.github.io/posts/2014/07/analyses_as_packages.html
131 |
132 | - Hadley Wickham: http://r-pkgs.had.co.nz/
133 |
134 | - Yihui Xie: http://yihui.name/knitr/
135 |
136 | - Rstudio
137 |
138 |
139 |
150 |
151 |
152 |
153 |
183 |
184 |
185 |
186 |
195 |
196 |
197 |
198 |
199 |
200 |
201 |
202 |
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/docs/link.svg:
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1 |
2 |
3 |
13 |
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/docs/pkgdown.css:
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1 | /* Sticky footer */
2 |
3 | /**
4 | * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
5 | * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
6 | *
7 | * .Site -> body > .container
8 | * .Site-content -> body > .container .row
9 | * .footer -> footer
10 | *
11 | * Key idea seems to be to ensure that .container and __all its parents__
12 | * have height set to 100%
13 | *
14 | */
15 |
16 | html, body {
17 | height: 100%;
18 | }
19 |
20 | body {
21 | position: relative;
22 | }
23 |
24 | body > .container {
25 | display: flex;
26 | height: 100%;
27 | flex-direction: column;
28 | }
29 |
30 | body > .container .row {
31 | flex: 1 0 auto;
32 | }
33 |
34 | footer {
35 | margin-top: 45px;
36 | padding: 35px 0 36px;
37 | border-top: 1px solid #e5e5e5;
38 | color: #666;
39 | display: flex;
40 | flex-shrink: 0;
41 | }
42 | footer p {
43 | margin-bottom: 0;
44 | }
45 | footer div {
46 | flex: 1;
47 | }
48 | footer .pkgdown {
49 | text-align: right;
50 | }
51 | footer p {
52 | margin-bottom: 0;
53 | }
54 |
55 | img.icon {
56 | float: right;
57 | }
58 |
59 | img {
60 | max-width: 100%;
61 | }
62 |
63 | /* Fix bug in bootstrap (only seen in firefox) */
64 | summary {
65 | display: list-item;
66 | }
67 |
68 | /* Typographic tweaking ---------------------------------*/
69 |
70 | .contents .page-header {
71 | margin-top: calc(-60px + 1em);
72 | }
73 |
74 | dd {
75 | margin-left: 3em;
76 | }
77 |
78 | /* Section anchors ---------------------------------*/
79 |
80 | a.anchor {
81 | margin-left: -30px;
82 | display:inline-block;
83 | width: 30px;
84 | height: 30px;
85 | visibility: hidden;
86 |
87 | background-image: url(./link.svg);
88 | background-repeat: no-repeat;
89 | background-size: 20px 20px;
90 | background-position: center center;
91 | }
92 |
93 | .hasAnchor:hover a.anchor {
94 | visibility: visible;
95 | }
96 |
97 | @media (max-width: 767px) {
98 | .hasAnchor:hover a.anchor {
99 | visibility: hidden;
100 | }
101 | }
102 |
103 |
104 | /* Fixes for fixed navbar --------------------------*/
105 |
106 | .contents h1, .contents h2, .contents h3, .contents h4 {
107 | padding-top: 60px;
108 | margin-top: -40px;
109 | }
110 |
111 | /* Navbar submenu --------------------------*/
112 |
113 | .dropdown-submenu {
114 | position: relative;
115 | }
116 |
117 | .dropdown-submenu>.dropdown-menu {
118 | top: 0;
119 | left: 100%;
120 | margin-top: -6px;
121 | margin-left: -1px;
122 | border-radius: 0 6px 6px 6px;
123 | }
124 |
125 | .dropdown-submenu:hover>.dropdown-menu {
126 | display: block;
127 | }
128 |
129 | .dropdown-submenu>a:after {
130 | display: block;
131 | content: " ";
132 | float: right;
133 | width: 0;
134 | height: 0;
135 | border-color: transparent;
136 | border-style: solid;
137 | border-width: 5px 0 5px 5px;
138 | border-left-color: #cccccc;
139 | margin-top: 5px;
140 | margin-right: -10px;
141 | }
142 |
143 | .dropdown-submenu:hover>a:after {
144 | border-left-color: #ffffff;
145 | }
146 |
147 | .dropdown-submenu.pull-left {
148 | float: none;
149 | }
150 |
151 | .dropdown-submenu.pull-left>.dropdown-menu {
152 | left: -100%;
153 | margin-left: 10px;
154 | border-radius: 6px 0 6px 6px;
155 | }
156 |
157 | /* Sidebar --------------------------*/
158 |
159 | #pkgdown-sidebar {
160 | margin-top: 30px;
161 | position: -webkit-sticky;
162 | position: sticky;
163 | top: 70px;
164 | }
165 |
166 | #pkgdown-sidebar h2 {
167 | font-size: 1.5em;
168 | margin-top: 1em;
169 | }
170 |
171 | #pkgdown-sidebar h2:first-child {
172 | margin-top: 0;
173 | }
174 |
175 | #pkgdown-sidebar .list-unstyled li {
176 | margin-bottom: 0.5em;
177 | }
178 |
179 | /* bootstrap-toc tweaks ------------------------------------------------------*/
180 |
181 | /* All levels of nav */
182 |
183 | nav[data-toggle='toc'] .nav > li > a {
184 | padding: 4px 20px 4px 6px;
185 | font-size: 1.5rem;
186 | font-weight: 400;
187 | color: inherit;
188 | }
189 |
190 | nav[data-toggle='toc'] .nav > li > a:hover,
191 | nav[data-toggle='toc'] .nav > li > a:focus {
192 | padding-left: 5px;
193 | color: inherit;
194 | border-left: 1px solid #878787;
195 | }
196 |
197 | nav[data-toggle='toc'] .nav > .active > a,
198 | nav[data-toggle='toc'] .nav > .active:hover > a,
199 | nav[data-toggle='toc'] .nav > .active:focus > a {
200 | padding-left: 5px;
201 | font-size: 1.5rem;
202 | font-weight: 400;
203 | color: inherit;
204 | border-left: 2px solid #878787;
205 | }
206 |
207 | /* Nav: second level (shown on .active) */
208 |
209 | nav[data-toggle='toc'] .nav .nav {
210 | display: none; /* Hide by default, but at >768px, show it */
211 | padding-bottom: 10px;
212 | }
213 |
214 | nav[data-toggle='toc'] .nav .nav > li > a {
215 | padding-left: 16px;
216 | font-size: 1.35rem;
217 | }
218 |
219 | nav[data-toggle='toc'] .nav .nav > li > a:hover,
220 | nav[data-toggle='toc'] .nav .nav > li > a:focus {
221 | padding-left: 15px;
222 | }
223 |
224 | nav[data-toggle='toc'] .nav .nav > .active > a,
225 | nav[data-toggle='toc'] .nav .nav > .active:hover > a,
226 | nav[data-toggle='toc'] .nav .nav > .active:focus > a {
227 | padding-left: 15px;
228 | font-weight: 500;
229 | font-size: 1.35rem;
230 | }
231 |
232 | /* orcid ------------------------------------------------------------------- */
233 |
234 | .orcid {
235 | font-size: 16px;
236 | color: #A6CE39;
237 | /* margins are required by official ORCID trademark and display guidelines */
238 | margin-left:4px;
239 | margin-right:4px;
240 | vertical-align: middle;
241 | }
242 |
243 | /* Reference index & topics ----------------------------------------------- */
244 |
245 | .ref-index th {font-weight: normal;}
246 |
247 | .ref-index td {vertical-align: top; min-width: 100px}
248 | .ref-index .icon {width: 40px;}
249 | .ref-index .alias {width: 40%;}
250 | .ref-index-icons .alias {width: calc(40% - 40px);}
251 | .ref-index .title {width: 60%;}
252 |
253 | .ref-arguments th {text-align: right; padding-right: 10px;}
254 | .ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px}
255 | .ref-arguments .name {width: 20%;}
256 | .ref-arguments .desc {width: 80%;}
257 |
258 | /* Nice scrolling for wide elements --------------------------------------- */
259 |
260 | table {
261 | display: block;
262 | overflow: auto;
263 | }
264 |
265 | /* Syntax highlighting ---------------------------------------------------- */
266 |
267 | pre {
268 | word-wrap: normal;
269 | word-break: normal;
270 | border: 1px solid #eee;
271 | }
272 |
273 | pre, code {
274 | background-color: #f8f8f8;
275 | color: #333;
276 | }
277 |
278 | pre code {
279 | overflow: auto;
280 | word-wrap: normal;
281 | white-space: pre;
282 | }
283 |
284 | pre .img {
285 | margin: 5px 0;
286 | }
287 |
288 | pre .img img {
289 | background-color: #fff;
290 | display: block;
291 | height: auto;
292 | }
293 |
294 | code a, pre a {
295 | color: #375f84;
296 | }
297 |
298 | a.sourceLine:hover {
299 | text-decoration: none;
300 | }
301 |
302 | .fl {color: #1514b5;}
303 | .fu {color: #000000;} /* function */
304 | .ch,.st {color: #036a07;} /* string */
305 | .kw {color: #264D66;} /* keyword */
306 | .co {color: #888888;} /* comment */
307 |
308 | .message { color: black; font-weight: bolder;}
309 | .error { color: orange; font-weight: bolder;}
310 | .warning { color: #6A0366; font-weight: bolder;}
311 |
312 | /* Clipboard --------------------------*/
313 |
314 | .hasCopyButton {
315 | position: relative;
316 | }
317 |
318 | .btn-copy-ex {
319 | position: absolute;
320 | right: 0;
321 | top: 0;
322 | visibility: hidden;
323 | }
324 |
325 | .hasCopyButton:hover button.btn-copy-ex {
326 | visibility: visible;
327 | }
328 |
329 | /* headroom.js ------------------------ */
330 |
331 | .headroom {
332 | will-change: transform;
333 | transition: transform 200ms linear;
334 | }
335 | .headroom--pinned {
336 | transform: translateY(0%);
337 | }
338 | .headroom--unpinned {
339 | transform: translateY(-100%);
340 | }
341 |
342 | /* mark.js ----------------------------*/
343 |
344 | mark {
345 | background-color: rgba(255, 255, 51, 0.5);
346 | border-bottom: 2px solid rgba(255, 153, 51, 0.3);
347 | padding: 1px;
348 | }
349 |
350 | /* vertical spacing after htmlwidgets */
351 | .html-widget {
352 | margin-bottom: 10px;
353 | }
354 |
355 | /* fontawesome ------------------------ */
356 |
357 | .fab {
358 | font-family: "Font Awesome 5 Brands" !important;
359 | }
360 |
361 | /* don't display links in code chunks when printing */
362 | /* source: https://stackoverflow.com/a/10781533 */
363 | @media print {
364 | code a:link:after, code a:visited:after {
365 | content: "";
366 | }
367 | }
368 |
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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 | $('.navbar-fixed-top').headroom();
6 |
7 | $('body').css('padding-top', $('.navbar').height() + 10);
8 | $(window).resize(function(){
9 | $('body').css('padding-top', $('.navbar').height() + 10);
10 | });
11 |
12 | $('[data-toggle="tooltip"]').tooltip();
13 |
14 | var cur_path = paths(location.pathname);
15 | var links = $("#navbar ul li a");
16 | var max_length = -1;
17 | var pos = -1;
18 | for (var i = 0; i < links.length; i++) {
19 | if (links[i].getAttribute("href") === "#")
20 | continue;
21 | // Ignore external links
22 | if (links[i].host !== location.host)
23 | continue;
24 |
25 | var nav_path = paths(links[i].pathname);
26 |
27 | var length = prefix_length(nav_path, cur_path);
28 | if (length > max_length) {
29 | max_length = length;
30 | pos = i;
31 | }
32 | }
33 |
34 | // Add class to parent
71 |
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185 |
186 |
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72 |
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73 |
74 |
75 |
151 |
74 | template package
75 |
76 |
82 | 77 | Generic template for data analysis projects structured as R packages
78 | 79 |The template package automates creation of new projects with all the necessary scaffolding: different folders for data, scripts, and functions, plus (optionally) additional files required for an R package structure. It can simultaneously create and synchronise a new repository on GitHub so one can start working immediately.
template can create both projects with or without R package structure. Structuring data analysis projects as R packages (a.k.a. “research compendia”) can bring some advantages (e.g. see this blogpost, this repo, these and these slides or read Marwick et al.). But there are also good reasons why an R package structure may not always be needed or convenient.
83 |
88 |
89 | 84 | Installation
85 |
86 | # install.packages("remotes")
87 | remotes::install_github("Pakillo/template")
90 |
95 |
98 |
103 |
106 | 91 | Usage
92 |First, load the package:
93 |
94 | library("template")Now run the function new_project to create a directory with all the scaffolding (slightly modified from R package structure). For example, to start a new project about tree growth, just use:
97 | new_project("treegrowth")This will create a new Rstudio project with this structure:
99 |
You can create a GitHub repository for the project at the same time:
101 |
102 | new_project("treegrowth", github = TRUE, private.repo = FALSE)You could choose either public or private repository. Note that to create a GitHub repo you will need to have configured your system as explained in https://usethis.r-lib.org/articles/articles/usethis-setup.html.
104 |There are other options you could choose, like setting up testthat or continuous integration (Travis-CI, GitHub Actions…). Or skip R package structure altogether. See ?new_project for all options.
107 |
122 | 108 | Developing the project
109 |-
110 |
Now edit
README.Rmdand theDESCRIPTIONfile with some basic information about your project: title, brief description, licence, package dependencies, etc.
111 | Place original (raw) data in
data-rawfolder. Save all R scripts (or Rmarkdown documents) used for data preparation in the same folder.
112 | Save final (clean, tidy) datasets in the
datafolder. You may write documentation for these data.
113 | R scripts or Rmarkdown documents used for data analyses may be placed at the
analysesfolder. The final manuscript/report may be placed at themanuscriptfolder. You could use one of the many Rmarkdown templates available out there (e.g. rticles, rrtools or rmdTemplates).
114 | If you write custom functions, place them in the
Rfolder. Document all your functions withRoxygen. Write tests for your functions and place them in thetestsfolder.
115 | If your analysis uses functions from other CRAN packages, include these as dependencies (
Imports) in theDESCRIPTIONfile (e.g. usingusethis::use_package()orrrtools::add_dependencies_to_description(). Also, useRoxygen@importor@importFromin your function definitions, or alternativelypackage::function(), to import these dependencies in the namespace.
116 | I recommend using an advanced tool like
targetsto manage your project workflow. A simpler alternative might be writing amakefileor master script to organise and execute all parts of the analysis. A template makefile is included with this package (usemakefile = TRUEwhen callingnew_project).
117 | Render Rmarkdown reports using
rmarkdown::render, and use RstudioBuildmenu to create/update documentation, run tests, build package, etc.
118 | Record the exact dependencies of your project. One option is simply running
sessionInfo()but many more sophisticated alternatives exist. For example,automagic::make_deps_file()orrenv::snapshot()will create a file recording the exact versions of all packages used, which can be used to recreate such environment in the future or in another computer. If you want to use Docker, you could use e.g.containerit::dockerfile()orrrtools::use_dockerfile().
119 | Archive your repository (e.g. in Zenodo), get a DOI, and include citation information in your README.
120 |
123 |
139 |
150 | 124 | Thanks to:
125 |-
126 |
- Carl Boettiger and his template package 127 | 128 |
- Jeff Hollister and his manuscriptPackage 129 | 130 |
- Robert Flight: http://rmflight.github.io/posts/2014/07/analyses_as_packages.html 131 | 132 |
- Hadley Wickham: http://r-pkgs.had.co.nz/ 133 | 134 |
- Yihui Xie: http://yihui.name/knitr/ 135 | 136 |
- Rstudio 137 |
66 |
67 |
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/docs/reference/examplefunction.html:
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128 | This is an example showing how to document datasets included in the package (in data folder):
121 | you must specify docType and name; do not forget NULL in the end.
122 | Can include other fields, like citation.
123 | See http://r-pkgs.had.co.nz/data.html for further explanations.
Format
129 | 130 |A numeric vector.
131 |Source
132 | 133 |This example modified from C. Boettiger's template package https://github.com/cboettig/template.
134 | 135 |Examples
136 |141 |
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120 | This is an example showing how to document functions to be included in the package.
118 |examplefunction(text)121 | 122 |
Arguments
123 || text | 127 |Message to print. |
128 |
|---|
See also
132 | 133 | 134 |Author
135 | 136 |Francisco Rodriguez-Sanchez
137 | 138 |Examples
139 |141 |examplefunction('Hello world!') 140 |#> [1] "Hello world!"
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/docs/reference/template-package.html:
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120 | Create all the scaffolding for a new project in a new directory. The scaffolding includes a README file, different folders to hold raw data, analyses, etc, and optionally also testthat infrastructure. Also, optionally, set a private or public GitHub repo with continuous integration (Travis-CI, GitHub Actions...).
new_project( 121 | name, 122 | path = ".", 123 | package = TRUE, 124 | github = FALSE, 125 | private.repo = TRUE, 126 | ci = "none", 127 | makefile = TRUE, 128 | pipe = TRUE, 129 | testthat = FALSE, 130 | verbose = FALSE, 131 | open.project = TRUE 132 | )133 | 134 |
Arguments
135 || name | 139 |Character. Name of the new project. A new folder will be created with that name. |
140 |
|---|---|
| path | 143 |Character. Path where the new project should be created (default is the current working directory). |
144 |
| package | 147 |Logical. Create package structure or a simple project? |
148 |
| github | 151 |Logical. Create GitHub repository? Note this requires some working infrastructure like |
152 |
| private.repo | 155 |Logical. Default is TRUE. |
156 |
| ci | 159 |Logical. Use continuous integration in your GitHub repository? Current options are "none" (default), "travis" (uses Travis-CI), "circle" (uses Circle-CI), "appveyor" (uses AppVeyor), or "gh-actions" (uses GitHub Actions). |
160 |
| makefile | 163 |Logical. If TRUE, adds a template |
164 |
| pipe | 167 |Logical. Use magrittr's pipe in your package? |
168 |
| testthat | 171 |Logical. Add testthat infrastructure? |
172 |
| verbose | 175 |Print verbose output in the console while creating the new project? Default is FALSE. |
176 |
| open.project | 179 |Logical. If TRUE (the default) will open the newly created Rstudio project in a new session. |
180 |
Value
184 | 185 |A new directory with R package structure, slightly modified.
186 |Details
187 | 188 |If using github = TRUE, you will be asked if you want to commit some files. Reply positively to continue.
189 | 190 |Examples
191 |197 |if (FALSE) { 192 | library("template") 193 | new_project("myproject") 194 | new_project("myproject", github = TRUE, private.repo = TRUE) 195 | } 196 |
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/files.png:
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https://raw.githubusercontent.com/Pakillo/template/349e5201c6952831e22fc346503d3ac4bb15ae40/files.png
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/inst/makefile/makefile.R:
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1 |
2 | #### Template of a master script for the project ####
3 |
4 | ## Using an advanced tool like {drake} or {targets} is recommended,
5 | ## but this can work as a simple alternative.
6 |
7 |
8 | ### if you have written specific functions in R/, load the package:
9 | # library("myproject")
10 |
11 |
12 | ### Source data cleaning scripts
13 | # source("data-raw/datacleaning.R")
14 | ### Could also be Rmarkdown:
15 | # rmarkdown::render("data-raw/datacleaning.Rmd")
16 |
17 |
18 | ### Render manuscript
19 | # rmarkdown::render("manuscript/ms_project.Rmd")
20 |
21 |
22 | ## Check your code ##
23 | # goodpractice::gp()
24 |
25 |
26 |
27 | #### Control package dependencies ####
28 |
29 | # Many alternatives available, for example:
30 |
31 | # sessionInfo()
32 |
33 | # automagic::make_deps_file()
34 |
35 | # Or using renv:
36 | # renv::init()
37 | # renv::snapshot()
38 |
39 | # Or use Docker, see e.g. {containerit} or {liftr}
40 |
41 |
42 | ## Make a website for your project?
43 | ## see https://pkgdown.r-lib.org/
44 | # usethis::use_pkgdown()
45 | # pkgdown::build_site()
46 |
47 |
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/man/exampledataset.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/dataset.R
3 | \docType{data}
4 | \name{exampledataset}
5 | \alias{exampledataset}
6 | \title{How to document datasets.}
7 | \format{
8 | A numeric vector.
9 | }
10 | \source{
11 | This example modified from C. Boettiger's template package \url{https://github.com/cboettig/template}.
12 | }
13 | \description{
14 | This is an example showing how to document datasets included in the package (in \code{data} folder):
15 | you must specify docType and name; do not forget NULL in the end.
16 | Can include other fields, like citation.
17 | See \url{http://r-pkgs.had.co.nz/data.html} for further explanations.
18 | }
19 | \examples{
20 | \dontrun{
21 | data(exampledataset)
22 | str(exampledataset)
23 | }
24 | }
25 |
--------------------------------------------------------------------------------
/man/examplefunction.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/function.R
3 | \name{examplefunction}
4 | \alias{examplefunction}
5 | \title{How to document functions.}
6 | \usage{
7 | examplefunction(text)
8 | }
9 | \arguments{
10 | \item{text}{Message to print.}
11 | }
12 | \description{
13 | This is an example showing how to document functions to be included in the package.
14 | }
15 | \examples{
16 | examplefunction('Hello world!')
17 | }
18 | \seealso{
19 | \url{http://r-pkgs.had.co.nz/man.html}
20 | }
21 | \author{
22 | Francisco Rodriguez-Sanchez
23 | }
24 |
--------------------------------------------------------------------------------
/man/new_project.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/new_project.R
3 | \name{new_project}
4 | \alias{new_project}
5 | \title{Create new project scaffolding}
6 | \usage{
7 | new_project(
8 | name,
9 | path = ".",
10 | package = TRUE,
11 | github = FALSE,
12 | private.repo = TRUE,
13 | ci = "none",
14 | makefile = TRUE,
15 | pipe = TRUE,
16 | testthat = FALSE,
17 | verbose = FALSE,
18 | open.project = TRUE
19 | )
20 | }
21 | \arguments{
22 | \item{name}{Character. Name of the new project. A new folder will be created with that name.}
23 |
24 | \item{path}{Character. Path where the new project should be created (default is the current working directory).}
25 |
26 | \item{package}{Logical. Create package structure or a simple project?}
27 |
28 | \item{github}{Logical. Create GitHub repository? Note this requires some working infrastructure like \code{git} and a \code{GITHUB_PAT}. See instructions here \url{https://usethis.r-lib.org/articles/articles/usethis-setup.html}.}
29 |
30 | \item{private.repo}{Logical. Default is TRUE.}
31 |
32 | \item{ci}{Logical. Use continuous integration in your GitHub repository? Current options are "none" (default), "travis" (uses Travis-CI), "circle" (uses Circle-CI), "appveyor" (uses AppVeyor), or "gh-actions" (uses GitHub Actions).}
33 |
34 | \item{makefile}{Logical. If TRUE, adds a template \code{makefile.R} file to the project.}
35 |
36 | \item{pipe}{Logical. Use magrittr's pipe in your package?}
37 |
38 | \item{testthat}{Logical. Add testthat infrastructure?}
39 |
40 | \item{verbose}{Print verbose output in the console while creating the new project? Default is FALSE.}
41 |
42 | \item{open.project}{Logical. If TRUE (the default) will open the newly created Rstudio project in a new session.}
43 | }
44 | \value{
45 | A new directory with R package structure, slightly modified.
46 | }
47 | \description{
48 | Create all the scaffolding for a new project in a new directory. The scaffolding includes a README file, different folders to hold raw data, analyses, etc, and optionally also \code{testthat} infrastructure. Also, optionally, set a private or public GitHub repo with continuous integration (Travis-CI, GitHub Actions...).
49 | }
50 | \details{
51 | If using github = TRUE, you will be asked if you want to commit some files. Reply positively to continue.
52 | }
53 | \examples{
54 | \dontrun{
55 | library("template")
56 | new_project("myproject")
57 | new_project("myproject", github = TRUE, private.repo = TRUE)
58 | }
59 | }
60 |
--------------------------------------------------------------------------------
/man/template-package.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/template-package.R
3 | \docType{package}
4 | \name{template-package}
5 | \alias{template-package}
6 | \title{template package}
7 | \description{
8 | Generic template for research projects structured as R packages.
9 | This package works as a template for new research projects,
10 | under the idea of having everything (data, R scripts, functions and manuscripts)
11 | contained in the same package to promote reproducibility.
12 | }
13 | \details{
14 | For detailed steps on how to use the package see \url{https://github.com/Pakillo/template/blob/master/README.md}.
15 | }
16 | \author{
17 | Francisco Rodriguez-Sanchez
18 | }
19 | \keyword{package}
20 |
--------------------------------------------------------------------------------
/manuscript/README.md:
--------------------------------------------------------------------------------
1 | Put here the master Rmarkdown document with the final analyses and figures.
2 |
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/tests/testthat.R:
--------------------------------------------------------------------------------
1 | library(testthat)
2 | library(template)
3 |
4 | test_check("template")
5 |
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/tests/testthat/test_fake.R:
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1 | library(template)
2 |
3 | context("Fake test")
4 |
5 | test_that("examplefunction can be run", {
6 | output <- examplefunction("testing")
7 | expect_match(output, "testing")
8 | })
9 |
--------------------------------------------------------------------------------
112 |
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125 |
126 |
127 |
128 | Generic template for research projects structured as R packages. 121 | This package works as a template for new research projects, 122 | under the idea of having everything (data, R scripts, functions and manuscripts) 123 | contained in the same package to promote reproducibility.
124 |Details
129 | 130 |For detailed steps on how to use the package see https://github.com/Pakillo/template/blob/master/README.md.
131 |Author
132 | 133 |Francisco Rodriguez-Sanchez
134 | 135 |