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AMR/pkgdown/extra.js
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/*
# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
*/
$(function () {
// add GPT assistant info
$('aside').prepend('<div class="amr-gpt-assistant"><a target="_blank" href="https://chat.amr-for-r.org"><img src="https://amr-for-r.org/AMRforRGPT.svg"></a></div>');
// split version number in navbar into main version and build number
$('.nav-text').each(function () {
const $el = $(this);
const text = $.trim($el.text());
const lastDotIndex = text.lastIndexOf('.');
if (lastDotIndex > -1) {
const main = text.substring(0, lastDotIndex);
const build = text.substring(lastDotIndex);
$el.html(`<span class="version-main">${main}</span><span class="version-build">${build}</span>`);
}
});
// replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
$(".developers h2").text("Maintainers");
$(".template-citation-authors h1:nth(0)").text("Contributors and Citation");
$(".template-citation-authors h2:nth(0)").text("All contributors");
$(".template-citation-authors h2:nth(1)").text("How to Cite");
// remove \donttest and \dontrun texts in Examples
if ($("#ref-examples ~ div pre").length > 0) {
$("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\donttest{", ""));
$("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\dontrun{", ""));
$("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# }", ""));
}
// rename 'Package index' to 'Manual' (weird design choice to pick 'Package index')
if ($(".template-reference-index").length > 0) {
$(".template-reference-index .page-header h1").text("Manual");
document.title = document.title.replace("Package index", "Manual");
}
// reference index ('Manual'): collapse long function lists and filter topics, see pkgdown/templates/content-reference-index.html
if ($(".amr-ref-item").length > 0) {
const maxAliases = 8;
const $body = $(".template-reference-index");
const $input = $("#amr-ref-filter-input");
const $status = $("#amr-ref-filter-status");
const $items = $(".amr-ref-item");
const pageText = {}; // full text per reference page, from search.json
let pageTextLoaded = false;
// keep the sticky filter field directly below the navbar, which hides when scrolling down
const navbar = document.querySelector(".navbar.fixed-top");
const filterBar = document.querySelector(".amr-ref-filter");
function placeFilter() {
const navBottom = navbar ? Math.max(0, navbar.getBoundingClientRect().bottom) : 0;
$body.css("--amr-navbar-height", navBottom + "px");
$(filterBar).toggleClass("amr-ref-stuck", filterBar.getBoundingClientRect().top <= navBottom + 1 && window.scrollY > 0);
}
let placing = false;
$(window).on("scroll resize", function () {
if (placing) return;
placing = true;
// follow the navbar during its slide transition
const start = performance.now();
(function step(now) {
placeFilter();
if (now - start < 400) requestAnimationFrame(step); else placing = false;
})(start);
});
placeFilter();
// headings that are jumped to (e.g. from 'On this page') must end up below the filter field, and below the navbar
// when jumping up, since the navbar only shows when scrolling up
$(document).on("click", 'a[href^="#"]', function () {
const target = document.getElementById(decodeURIComponent($(this).attr("href").slice(1)));
if (!target) return;
const up = target.getBoundingClientRect().top < 0;
document.documentElement.style.scrollPaddingTop = ((up && navbar ? navbar.offsetHeight : 0) + filterBar.offsetHeight + 8) + "px";
});
// the same when opening a link to a section, as the browser jumps before this script runs
if (window.location.hash) {
const target = document.getElementById(decodeURIComponent(window.location.hash.slice(1)));
if (target) {
document.documentElement.style.scrollPaddingTop = (filterBar.offsetHeight + 8) + "px";
target.scrollIntoView();
}
}
function updateMoreButton($item) {
const nHidden = $item.find("code.amr-ref-extra:not(.amr-ref-match)").length;
$item.find(".amr-ref-more").text("+ " + nHidden + " more").toggle(nHidden > 0);
}
$items.each(function () {
const $item = $(this);
const $codes = $item.find("dd code");
// pkgdown puts backticks around non-syntactic names, e.g. `%like%`
$codes.find("a").each(function () {
const name = $(this).text();
if (/^`.+`$/.test(name)) $(this).text(name.slice(1, -1));
});
$item.data("page", $item.find("dt a").attr("href"));
$item.data("text", ($item.find("dt").text() + " " + $item.find("dd").text()).toLowerCase());
// do not offer to show only one or two more
if ($codes.length > maxAliases + 2) {
$codes.slice(maxAliases).addClass("amr-ref-extra");
$item.find("dd").append('<button type="button" class="amr-ref-more"></button>');
updateMoreButton($item);
}
});
let h2Title = "";
$(".template-reference-index main").find("h2, h3").each(function () {
if (this.tagName === "H2") h2Title = $(this).text().trim();
else $(this).attr("data-amr-parent", h2Title);
});
$(".amr-ref-more").on("click", function () {
$(this).closest(".amr-ref-item").addClass("amr-ref-expanded");
$(this).remove();
});
function loadPageText() {
if (pageTextLoaded) return;
pageTextLoaded = true;
$.getJSON($("#search-input").data("search-index") || "../search.json", function (data) {
data.forEach(function (x) {
if (x.dir !== "Reference") return;
const page = x.path.split("/").pop();
pageText[page] = (pageText[page] || "") + " " + (x.what + " " + x.text + " " + x.code).toLowerCase();
});
filter();
});
}
function filter() {
const terms = $.trim($input.val()).toLowerCase().split(/\s+/).filter(Boolean);
$body.toggleClass("amr-ref-filtering", terms.length > 0);
let nDirect = 0;
let nText = 0;
$items.each(function () {
const $item = $(this);
const $codes = $item.find("dd code");
const direct = terms.length > 0 && terms.every(t => $item.data("text").includes(t));
const text = terms.length > 0 && !direct && terms.every(t => (pageText[$item.data("page")] || "").includes(t));
$item.toggleClass("amr-ref-hidden", terms.length > 0 && !direct && !text);
$item.toggleClass("amr-ref-textmatch", text);
// highlight the function names that match, which also reveals them if collapsed
$codes.each(function () {
const name = $(this).text().toLowerCase();
$(this).toggleClass("amr-ref-match", direct && terms.some(t => name.includes(t)));
});
updateMoreButton($item);
if (direct) nDirect++;
if (text) nText++;
});
// hide headings (with their descriptions) that have no visible topic before the next heading of the same or a higher level;
// this follows the document order, since pkgdown puts a heading and its topics in separate sibling blocks
const nVisible = new Map();
let h2 = null;
let h3 = null;
$(".template-reference-index main").find("h2, h3, .amr-ref-item").each(function () {
if (this.tagName === "H2") {
h2 = this;
h3 = null;
nVisible.set(this, 0);
} else if (this.tagName === "H3") {
h3 = this;
nVisible.set(this, 0);
} else if (!$(this).hasClass("amr-ref-hidden")) {
if (h2) nVisible.set(h2, nVisible.get(h2) + 1);
if (h3) nVisible.set(h3, nVisible.get(h3) + 1);
}
});
nVisible.forEach((n, heading) => $(heading).closest(".section").toggleClass("amr-ref-hidden", n === 0));
// blocks that only hold topics
$(".template-reference-index main .section").not(":has(h2, h3)").each(function () {
$(this).toggleClass("amr-ref-hidden", $(this).find(".amr-ref-item:not(.amr-ref-hidden)").length === 0);
});
const topics = n => n + (n === 1 ? " topic" : " topics");
if (terms.length === 0) {
$status.text("");
} else if (nDirect + nText === 0) {
$status.text(pageTextLoaded ? "No topics found" : "Searching...");
} else if (nText === 0) {
$status.text(topics(nDirect) + " found by name or title");
} else if (nDirect === 0) {
$status.text("No topics found by name or title, but " + topics(nText) + " mention it");
} else {
$status.text(topics(nDirect) + " found by name or title, and " + nText + " more mention it");
}
placeFilter();
}
$input.on("input", function () {
loadPageText();
filter();
});
$input.on("keydown", function (e) {
if (e.key === "Escape") {
$input.val("");
filter();
}
});
// press '/' anywhere to focus the filter field
$(document).on("keydown", function (e) {
if (e.key === "/" && !$(e.target).is("input, textarea")) {
e.preventDefault();
$input.trigger("focus");
}
});
}
// remove leading newline in code examples on changelog
if ($("body .template-news").length > 0) {
$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R"><span></span>\n<span', 'sourceCode R"><span'));
}
// make Python part more fancy - prepare for CSS
if (window.location.href.includes('AMR_for_Python')) {
$('body').addClass('amr-for-python'); /* to set colours in CSS */
$('img[src="../logo.svg"]').attr('src', '../logo_python.svg'); /* replace base logo */
$('img[src="https://amr-for-r.org/AMRforRGPT.svg"]').attr('src', 'https://amr-for-r.org/AMRforRGPT_python.svg'); /* replace GPT logo */
}
// add country flags
function country_flag(x) {
if (typeof(x) != "undefined") {
const prefix = '<img src="lang_';
const suffix = '.svg" style="height: 13px !important; border: 1px solid #cccccc; aspect-ratio: 1 / 0.6; object-fit: cover; vertical-align: initial !important;"> ';
// bit weird, but we refer to languages here! So "uk" is Ukrain, not UK - take "en" for that.
x = x.replace("Aislinn", prefix + "en" + suffix + "Aislinn");
x = x.replace("Alex", prefix + "de" + suffix + "Alex");
x = x.replace("Andrew", prefix + "us" + suffix + "Andrew");
x = x.replace("Anita", prefix + "au" + suffix + "Anita");
x = x.replace("Annick", prefix + "nl" + suffix + "Annick");
x = x.replace("Anthony", prefix + "en" + suffix + "Anthony");
x = x.replace("Anton", prefix + "uk" + suffix + "Anton");
x = x.replace("Bart", prefix + "nl" + suffix + "Bart");
x = x.replace("Bhanu", prefix + "nl" + suffix + "Bhanu");
x = x.replace("Casper", prefix + "nl" + suffix + "Casper");
x = x.replace("Christian", prefix + "de" + suffix + "Christian");
x = x.replace("Corinna", prefix + "nl" + suffix + "Corinna");
x = x.replace("Dennis", prefix + "nl" + suffix + "Dennis");
x = x.replace("Dmytro", prefix + "uk" + suffix + "Dmytro");
x = x.replace("Eric", prefix + "nl" + suffix + "Eric");
x = x.replace("Erwin", prefix + "nl" + suffix + "Erwin");
x = x.replace("Gwen", prefix + "en" + suffix + "Gwen");
x = x.replace("Jane", prefix + "au" + suffix + "Jane");
x = x.replace("Jason", prefix + "ca" + suffix + "Jason");
x = x.replace("Javier", prefix + "ca" + suffix + "Javier");
x = x.replace("Jonas", prefix + "de" + suffix + "Jonas");
x = x.replace("Judith", prefix + "nl" + suffix + "Judith");
x = x.replace("Kathryn", prefix + "en" + suffix + "Kathryn");
x = x.replace("Larisse", prefix + "sa" + suffix + "Larisse");
x = x.replace("Matthew", prefix + "ca" + suffix + "Matthew");
x = x.replace("Matthijs", prefix + "nl" + suffix + "Matthijs");
x = x.replace("Natacha", prefix + "en" + suffix + "Natacha");
x = x.replace("Peter", prefix + "en" + suffix + "Peter");
x = x.replace("Rogier", prefix + "nl" + suffix + "Rogier");
x = x.replace("Sofia", prefix + "sv" + suffix + "Sofia");
}
return(x);
}
$(".template-authors").html(country_flag($(".template-authors").html()));
$(".template-citation-authors").html(country_flag($(".template-citation-authors").html()));
// add doctoral titles to authors
function doct_tit(x) {
if (typeof(x) != "undefined") {
x = x.replace(/Author, maintainer/g, "Project founder and lead developer");
x = x.replace(/Author, contributor/g, "Package maintainer");
x = x.replace(/Thesis advisor/g, "Former doctoral advisor");
// contributors
x = x.replace("Alex", "Prof. Alex");
x = x.replace("Andrew", "Dr. Andrew");
x = x.replace("Annick", "Dr. Annick");
x = x.replace("Anthony", "Dr. Anthony");
x = x.replace("Bart", "Dr. Bart");
x = x.replace("Bhanu", "Prof. Bhanu");
x = x.replace("Casper", "Prof. Casper");
x = x.replace("Christian", "Dr. Christian");
x = x.replace("Corinna", "Dr. Corinna");
x = x.replace("Dennis", "Dr. Dennis");
x = x.replace("Gwen", "Prof. Gwen");
x = x.replace("Jane", "Dr. Jane");
x = x.replace("Jason", "Dr. Jason");
x = x.replace("Javier", "Prof. Javier");
x = x.replace("Jonas", "Dr. Jonas");
x = x.replace("Judith", "Dr. Judith");
x = x.replace("Kathryn", "Prof. Kathryn");
x = x.replace("Larisse", "Dr. Larisse");
x = x.replace("Matthijs", "Dr. Matthijs");
x = x.replace("Natacha", "Prof. Natacha");
x = x.replace("Peter", "Dr. Peter");
x = x.replace("Rogier", "Dr. Rogier");
x = x.replace("Sofia", "Dr. Sofia");
}
return(x);
}
$(".template-authors").html(doct_tit($(".template-authors").html()));
$(".template-citation-authors").html(doct_tit($(".template-citation-authors").html()));
$(".developers").html(doct_tit($(".developers").html()));
$(".developers a[href='authors.html']").text("All contributors...");
// add lines between collaborator types
$('.template-citation-authors li:contains("Contributor")').first().before('<hr>');
$('.template-citation-authors li:contains("Former doctoral advisor")').first().before('<hr>');
// dark variants of figures: list a file name here and put a file with '_dark' before its extension next to it in pkgdown/assets,
// e.g. "logo_umcg.svg" requires "logo_umcg_dark.svg"; images are swapped when the theme is dark, also after switching theme
const darkVariants = [];
function applyDarkVariants() {
const dark = document.documentElement.getAttribute("data-bs-theme") === "dark";
$("img").each(function () {
const src = $(this).attr("src") || "";
const file = src.split(/[?#]/)[0].split("/").pop();
const base = file.replace(/_dark(\.\w+)$/, "$1");
if (!darkVariants.includes(base)) return;
const target = dark ? base.replace(/(\.\w+)$/, "_dark$1") : base;
if (file !== target) $(this).attr("src", src.replace(file, target));
});
}
applyDarkVariants();
new MutationObserver(applyDarkVariants).observe(document.documentElement, { attributes: true, attributeFilter: ["data-bs-theme"] });
});
$('head').append("<!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.amr-for-r.org']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s); })();</script><!-- End Matomo Code -->");
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