From 03ccdecdf6145df10801a2bd46f70ae14ceae891 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Thu, 10 Aug 2023 04:14:01 +0000 Subject: [PATCH] build based on 305efff --- stable | 2 +- v0.13 | 2 +- v0.13.16/assets/documenter.js | 331 ++++++++++++++++++++ v0.13.16/assets/search.js | 267 ++++++++++++++++ v0.13.16/assets/themes/documenter-dark.css | 7 + v0.13.16/assets/themes/documenter-light.css | 9 + v0.13.16/assets/themeswap.js | 66 ++++ v0.13.16/assets/warner.js | 49 +++ v0.13.16/conversions/index.html | 54 ++++ v0.13.16/custom/index.html | 65 ++++ v0.13.16/eventloop/index.html | 2 + v0.13.16/gettingstarted/index.html | 123 ++++++++ v0.13.16/index.html | 2 + v0.13.16/installation/index.html | 10 + v0.13.16/internal/index.html | 14 + v0.13.16/known-issues/index.html | 2 + v0.13.16/search/index.html | 2 + v0.13.16/search_index.js | 3 + v0.13.16/siteinfo.js | 1 + versions.js | 2 +- 20 files changed, 1010 insertions(+), 3 deletions(-) create mode 100644 v0.13.16/assets/documenter.js create mode 100644 v0.13.16/assets/search.js create mode 100644 v0.13.16/assets/themes/documenter-dark.css create mode 100644 v0.13.16/assets/themes/documenter-light.css create mode 100644 v0.13.16/assets/themeswap.js create mode 100644 v0.13.16/assets/warner.js create mode 100644 v0.13.16/conversions/index.html create mode 100644 v0.13.16/custom/index.html create mode 100644 v0.13.16/eventloop/index.html create mode 100644 v0.13.16/gettingstarted/index.html create mode 100644 v0.13.16/index.html create mode 100644 v0.13.16/installation/index.html create mode 100644 v0.13.16/internal/index.html create mode 100644 v0.13.16/known-issues/index.html create mode 100644 v0.13.16/search/index.html create mode 100644 v0.13.16/search_index.js create mode 100644 v0.13.16/siteinfo.js diff --git a/stable b/stable index 1efddb08..00aed7e5 120000 --- a/stable +++ b/stable @@ -1 +1 @@ -v0.13.15 \ No newline at end of file +v0.13.16 \ No newline at end of file diff --git a/v0.13 b/v0.13 index 1efddb08..00aed7e5 120000 --- a/v0.13 +++ b/v0.13 @@ -1 +1 @@ -v0.13.15 \ No newline at end of file +v0.13.16 \ No newline at end of file diff --git a/v0.13.16/assets/documenter.js b/v0.13.16/assets/documenter.js new file mode 100644 index 00000000..6adfbbbf --- /dev/null +++ b/v0.13.16/assets/documenter.js @@ -0,0 +1,331 @@ +// Generated by Documenter.jl +requirejs.config({ + paths: { + 'highlight-julia': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.5.1/languages/julia.min', + 'headroom': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.12.0/headroom.min', + 'jqueryui': 'https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min', + 'katex-auto-render': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/contrib/auto-render.min', + 'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min', + 'headroom-jquery': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.12.0/jQuery.headroom.min', + 'katex': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min', + 'highlight': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.5.1/highlight.min', + 'highlight-julia-repl': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.5.1/languages/julia-repl.min', + }, + shim: { + "highlight-julia": { + "deps": [ + "highlight" + ] + }, + "katex-auto-render": { + "deps": [ + "katex" + ] + }, + "headroom-jquery": { + "deps": [ + "jquery", + "headroom" + ] + }, + "highlight-julia-repl": { + "deps": [ + "highlight" + ] + } +} +}); +//////////////////////////////////////////////////////////////////////////////// +require(['jquery', 'katex', 'katex-auto-render'], function($, katex, renderMathInElement) { +$(document).ready(function() { + renderMathInElement( + document.body, + { + "delimiters": [ + { + "left": "$", + "right": "$", + "display": false + }, + { + "left": "$$", + "right": "$$", + "display": true + }, + { + "left": "\\[", + "right": "\\]", + "display": true + } + ] +} + + ); +}) + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery', 'highlight', 'highlight-julia', 'highlight-julia-repl'], function($) { +$(document).ready(function() { + hljs.highlightAll(); +}) + +}) +//////////////////////////////////////////////////////////////////////////////// +require([], function() { +function addCopyButtonCallbacks() { + for (const el of document.getElementsByTagName("pre")) { + const button = document.createElement("button"); + button.classList.add("copy-button", "fas", "fa-copy"); + el.appendChild(button); + + const success = function () { + button.classList.add("success", "fa-check"); + button.classList.remove("fa-copy"); + }; + + const failure = function () { + button.classList.add("error", "fa-times"); + button.classList.remove("fa-copy"); + }; + + button.addEventListener("click", function () { + copyToClipboard(el.innerText).then(success, failure); + + setTimeout(function () { + button.classList.add("fa-copy"); + button.classList.remove("success", "fa-check", "fa-times"); + }, 5000); + }); + } +} + +function copyToClipboard(text) { + // clipboard API is only available in secure contexts + if (window.navigator && window.navigator.clipboard) { + return window.navigator.clipboard.writeText(text); + } else { + return new Promise(function (resolve, reject) { + try { + const el = document.createElement("textarea"); + el.textContent = text; + el.style.position = "fixed"; + el.style.opacity = 0; + document.body.appendChild(el); + el.select(); + document.execCommand("copy"); + + resolve(); + } catch (err) { + reject(err); + } finally { + document.body.removeChild(el); + } + }); + } +} + +if (document.readyState === "loading") { + document.addEventListener("DOMContentLoaded", addCopyButtonCallbacks); +} else { + addCopyButtonCallbacks(); +} + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery', 'headroom', 'headroom-jquery'], function($, Headroom) { + +// Manages the top navigation bar (hides it when the user starts scrolling down on the +// mobile). +window.Headroom = Headroom; // work around buggy module loading? +$(document).ready(function() { + $('#documenter .docs-navbar').headroom({ + "tolerance": {"up": 10, "down": 10}, + }); +}) + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery'], function($) { + +// Modal settings dialog +$(document).ready(function() { + var settings = $('#documenter-settings'); + $('#documenter-settings-button').click(function(){ + settings.toggleClass('is-active'); + }); + // Close the dialog if X is clicked + $('#documenter-settings button.delete').click(function(){ + settings.removeClass('is-active'); + }); + // Close dialog if ESC is pressed + $(document).keyup(function(e) { + if (e.keyCode == 27) settings.removeClass('is-active'); + }); +}); + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery'], function($) { + +// Manages the showing and hiding of the sidebar. +$(document).ready(function() { + var sidebar = $("#documenter > .docs-sidebar"); + var sidebar_button = $("#documenter-sidebar-button") + sidebar_button.click(function(ev) { + ev.preventDefault(); + sidebar.toggleClass('visible'); + if (sidebar.hasClass('visible')) { + // Makes sure that the current menu item is visible in the sidebar. + $("#documenter .docs-menu a.is-active").focus(); + } + }); + $("#documenter > .docs-main").bind('click', function(ev) { + if ($(ev.target).is(sidebar_button)) { + return; + } + if (sidebar.hasClass('visible')) { + sidebar.removeClass('visible'); + } + }); +}) + +// Resizes the package name / sitename in the sidebar if it is too wide. +// Inspired by: https://github.com/davatron5000/FitText.js +$(document).ready(function() { + e = $("#documenter .docs-autofit"); + function resize() { + var L = parseInt(e.css('max-width'), 10); + var L0 = e.width(); + if(L0 > L) { + var h0 = parseInt(e.css('font-size'), 10); + e.css('font-size', L * h0 / L0); + // TODO: make sure it survives resizes? + } + } + // call once and then register events + resize(); + $(window).resize(resize); + $(window).on('orientationchange', resize); +}); + +// Scroll the navigation bar to the currently selected menu item +$(document).ready(function() { + var sidebar = $("#documenter .docs-menu").get(0); + var active = $("#documenter .docs-menu .is-active").get(0); + if(typeof active !== 'undefined') { + sidebar.scrollTop = active.offsetTop - sidebar.offsetTop - 15; + } +}) + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery'], function($) { + +function set_theme(theme) { + var active = null; + var disabled = []; + for (var i = 0; i < document.styleSheets.length; i++) { + var ss = document.styleSheets[i]; + var themename = ss.ownerNode.getAttribute("data-theme-name"); + if(themename === null) continue; // ignore non-theme stylesheets + // Find the active theme + if(themename === theme) active = ss; + else disabled.push(ss); + } + if(active !== null) { + active.disabled = false; + if(active.ownerNode.getAttribute("data-theme-primary") === null) { + document.getElementsByTagName('html')[0].className = "theme--" + theme; + } else { + document.getElementsByTagName('html')[0].className = ""; + } + disabled.forEach(function(ss){ + ss.disabled = true; + }); + } + + // Store the theme in localStorage + if(typeof(window.localStorage) !== "undefined") { + window.localStorage.setItem("documenter-theme", theme); + } else { + console.error("Browser does not support window.localStorage"); + } +} + +// Theme picker setup +$(document).ready(function() { + // onchange callback + $('#documenter-themepicker').change(function themepick_callback(ev){ + var themename = $('#documenter-themepicker option:selected').attr('value'); + set_theme(themename); + }); + + // Make sure that the themepicker displays the correct theme when the theme is retrieved + // from localStorage + if(typeof(window.localStorage) !== "undefined") { + var theme = window.localStorage.getItem("documenter-theme"); + if(theme !== null) { + $('#documenter-themepicker option').each(function(i,e) { + e.selected = (e.value === theme); + }) + } else { + $('#documenter-themepicker option').each(function(i,e) { + e.selected = $("html").hasClass(`theme--${e.value}`); + }) + } + } +}) + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery'], function($) { + +// update the version selector with info from the siteinfo.js and ../versions.js files +$(document).ready(function() { + // If the version selector is disabled with DOCUMENTER_VERSION_SELECTOR_DISABLED in the + // siteinfo.js file, we just return immediately and not display the version selector. + if (typeof DOCUMENTER_VERSION_SELECTOR_DISABLED === 'boolean' && DOCUMENTER_VERSION_SELECTOR_DISABLED) { + return; + } + + var version_selector = $("#documenter .docs-version-selector"); + var version_selector_select = $("#documenter .docs-version-selector select"); + + version_selector_select.change(function(x) { + target_href = version_selector_select.children("option:selected").get(0).value; + window.location.href = target_href; + }); + + // add the current version to the selector based on siteinfo.js, but only if the selector is empty + if (typeof DOCUMENTER_CURRENT_VERSION !== 'undefined' && $('#version-selector > option').length == 0) { + var option = $(""); + version_selector_select.append(option); + } + + if (typeof DOC_VERSIONS !== 'undefined') { + var existing_versions = version_selector_select.children("option"); + var existing_versions_texts = existing_versions.map(function(i,x){return x.text}); + DOC_VERSIONS.forEach(function(each) { + var version_url = documenterBaseURL + "/../" + each; + var existing_id = $.inArray(each, existing_versions_texts); + // if not already in the version selector, add it as a new option, + // otherwise update the old option with the URL and enable it + if (existing_id == -1) { + var option = $(""); + version_selector_select.append(option); + } else { + var option = existing_versions[existing_id]; + option.value = version_url; + option.disabled = false; + } + }); + } + + // only show the version selector if the selector has been populated + if (version_selector_select.children("option").length > 0) { + version_selector.toggleClass("visible"); + } +}) + +}) diff --git a/v0.13.16/assets/search.js b/v0.13.16/assets/search.js new file mode 100644 index 00000000..c133f741 --- /dev/null +++ b/v0.13.16/assets/search.js @@ -0,0 +1,267 @@ +// Generated by Documenter.jl +requirejs.config({ + paths: { + 'lunr': 'https://cdnjs.cloudflare.com/ajax/libs/lunr.js/2.3.9/lunr.min', + 'lodash': 'https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.21/lodash.min', + 'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min', + } +}); +//////////////////////////////////////////////////////////////////////////////// +require(['jquery', 'lunr', 'lodash'], function($, lunr, _) { + +$(document).ready(function() { + // parseUri 1.2.2 + // (c) Steven Levithan + // MIT License + function parseUri (str) { + var o = parseUri.options, + m = o.parser[o.strictMode ? "strict" : "loose"].exec(str), + uri = {}, + i = 14; + + while (i--) uri[o.key[i]] = m[i] || ""; + + uri[o.q.name] = {}; + uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) { + if ($1) uri[o.q.name][$1] = $2; + }); + + return uri; + }; + parseUri.options = { + strictMode: false, + key: ["source","protocol","authority","userInfo","user","password","host","port","relative","path","directory","file","query","anchor"], + q: { + name: "queryKey", + parser: /(?:^|&)([^&=]*)=?([^&]*)/g + }, + parser: { + strict: /^(?:([^:\/?#]+):)?(?:\/\/((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?))?((((?:[^?#\/]*\/)*)([^?#]*))(?:\?([^#]*))?(?:#(.*))?)/, + loose: /^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.[^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/ + } + }; + + $("#search-form").submit(function(e) { + e.preventDefault() + }) + + // list below is the lunr 2.1.3 list minus the intersect with names(Base) + // (all, any, get, in, is, only, which) and (do, else, for, let, where, while, with) + // ideally we'd just filter the original list but it's not available as a variable + lunr.stopWordFilter = lunr.generateStopWordFilter([ + 'a', + 'able', + 'about', + 'across', + 'after', + 'almost', + 'also', + 'am', + 'among', + 'an', + 'and', + 'are', + 'as', + 'at', + 'be', + 'because', + 'been', + 'but', + 'by', + 'can', + 'cannot', + 'could', + 'dear', + 'did', + 'does', + 'either', + 'ever', + 'every', + 'from', + 'got', + 'had', + 'has', + 'have', + 'he', + 'her', + 'hers', + 'him', + 'his', + 'how', + 'however', + 'i', + 'if', + 'into', + 'it', + 'its', + 'just', + 'least', + 'like', + 'likely', + 'may', + 'me', + 'might', + 'most', + 'must', + 'my', + 'neither', + 'no', + 'nor', + 'not', + 'of', + 'off', + 'often', + 'on', + 'or', + 'other', + 'our', + 'own', + 'rather', + 'said', + 'say', + 'says', + 'she', + 'should', + 'since', + 'so', + 'some', + 'than', + 'that', + 'the', + 'their', + 'them', + 'then', + 'there', + 'these', + 'they', + 'this', + 'tis', + 'to', + 'too', + 'twas', + 'us', + 'wants', + 'was', + 'we', + 'were', + 'what', + 'when', + 'who', + 'whom', + 'why', + 'will', + 'would', + 'yet', + 'you', + 'your' + ]) + + // add . as a separator, because otherwise "title": "Documenter.Anchors.add!" + // would not find anything if searching for "add!", only for the entire qualification + lunr.tokenizer.separator = /[\s\-\.]+/ + + // custom trimmer that doesn't strip @ and !, which are used in julia macro and function names + lunr.trimmer = function (token) { + return token.update(function (s) { + return s.replace(/^[^a-zA-Z0-9@!]+/, '').replace(/[^a-zA-Z0-9@!]+$/, '') + }) + } + + lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'juliaStopWordFilter') + lunr.Pipeline.registerFunction(lunr.trimmer, 'juliaTrimmer') + + var index = lunr(function () { + this.ref('location') + this.field('title',{boost: 100}) + this.field('text') + documenterSearchIndex['docs'].forEach(function(e) { + this.add(e) + }, this) + }) + var store = {} + + documenterSearchIndex['docs'].forEach(function(e) { + store[e.location] = {title: e.title, category: e.category, page: e.page} + }) + + $(function(){ + searchresults = $('#documenter-search-results'); + searchinfo = $('#documenter-search-info'); + searchbox = $('#documenter-search-query'); + searchform = $('.docs-search'); + sidebar = $('.docs-sidebar'); + function update_search(querystring) { + tokens = lunr.tokenizer(querystring) + results = index.query(function (q) { + tokens.forEach(function (t) { + q.term(t.toString(), { + fields: ["title"], + boost: 100, + usePipeline: true, + editDistance: 0, + wildcard: lunr.Query.wildcard.NONE + }) + q.term(t.toString(), { + fields: ["title"], + boost: 10, + usePipeline: true, + editDistance: 2, + wildcard: lunr.Query.wildcard.NONE + }) + q.term(t.toString(), { + fields: ["text"], + boost: 1, + usePipeline: true, + editDistance: 0, + wildcard: lunr.Query.wildcard.NONE + }) + }) + }) + searchinfo.text("Number of results: " + results.length) + searchresults.empty() + results.forEach(function(result) { + data = store[result.ref] + link = $(''+data.title+'') + link.attr('href', documenterBaseURL+'/'+result.ref) + if (data.category != "page"){ + cat = $('('+data.category+', '+data.page+')') + } else { + cat = $('('+data.category+')') + } + li = $('
  • ').append(link).append(" ").append(cat) + searchresults.append(li) + }) + } + + function update_search_box() { + querystring = searchbox.val() + update_search(querystring) + } + + searchbox.keyup(_.debounce(update_search_box, 250)) + searchbox.change(update_search_box) + + // Disable enter-key form submission for the searchbox on the search page + // and just re-run search rather than refresh the whole page. + searchform.keypress( + function(event){ + if (event.which == '13') { + if (sidebar.hasClass('visible')) { + sidebar.removeClass('visible'); + } + update_search_box(); + event.preventDefault(); + } + } + ); + + search_query_uri = parseUri(window.location).queryKey["q"] + if(search_query_uri !== undefined) { + search_query = decodeURIComponent(search_query_uri.replace(/\+/g, '%20')) + searchbox.val(search_query) + } + update_search_box(); + }) +}) + +}) diff --git a/v0.13.16/assets/themes/documenter-dark.css b/v0.13.16/assets/themes/documenter-dark.css new file mode 100644 index 00000000..c94a294d --- /dev/null +++ b/v0.13.16/assets/themes/documenter-dark.css @@ -0,0 +1,7 @@ +@keyframes spinAround{from{transform:rotate(0deg)}to{transform:rotate(359deg)}}html.theme--documenter-dark .tabs,html.theme--documenter-dark .pagination-previous,html.theme--documenter-dark .pagination-next,html.theme--documenter-dark .pagination-link,html.theme--documenter-dark .pagination-ellipsis,html.theme--documenter-dark .breadcrumb,html.theme--documenter-dark .file,html.theme--documenter-dark .button,.is-unselectable,html.theme--documenter-dark .modal-close,html.theme--documenter-dark .delete{-webkit-touch-callout:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;user-select:none}html.theme--documenter-dark .navbar-link:not(.is-arrowless)::after,html.theme--documenter-dark .select:not(.is-multiple):not(.is-loading)::after{border:3px solid rgba(0,0,0,0);border-radius:2px;border-right:0;border-top:0;content:" 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kbd.button.is-outlined.is-loading.is-hovered::after,html.theme--documenter-dark .button.is-dark.is-outlined.is-loading:focus::after,html.theme--documenter-dark .content kbd.button.is-outlined.is-loading:focus::after,html.theme--documenter-dark .button.is-dark.is-outlined.is-loading.is-focused::after,html.theme--documenter-dark .content kbd.button.is-outlined.is-loading.is-focused::after{border-color:transparent transparent #ecf0f1 #ecf0f1 !important}html.theme--documenter-dark .button.is-dark.is-outlined[disabled],html.theme--documenter-dark .content kbd.button.is-outlined[disabled],fieldset[disabled] html.theme--documenter-dark .button.is-dark.is-outlined,fieldset[disabled] html.theme--documenter-dark .content kbd.button.is-outlined{background-color:transparent;border-color:#282f2f;box-shadow:none;color:#282f2f}html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined,html.theme--documenter-dark .content 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.button.is-dark.is-inverted.is-outlined.is-loading.is-hovered::after,html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined.is-loading.is-hovered::after,html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined.is-loading:focus::after,html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined.is-loading:focus::after,html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined.is-loading.is-focused::after,html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined.is-loading.is-focused::after{border-color:transparent transparent #282f2f #282f2f !important}html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined[disabled],html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined[disabled],fieldset[disabled] html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined,fieldset[disabled] html.theme--documenter-dark .content 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1055px){html.theme--documenter-dark .navbar>.container{display:block}html.theme--documenter-dark .navbar-brand .navbar-item,html.theme--documenter-dark .navbar-tabs .navbar-item{align-items:center;display:flex}html.theme--documenter-dark .navbar-link::after{display:none}html.theme--documenter-dark .navbar-menu{background-color:#375a7f;box-shadow:0 8px 16px rgba(10,10,10,0.1);padding:0.5rem 0}html.theme--documenter-dark .navbar-menu.is-active{display:block}html.theme--documenter-dark .navbar.is-fixed-bottom-touch,html.theme--documenter-dark .navbar.is-fixed-top-touch{left:0;position:fixed;right:0;z-index:30}html.theme--documenter-dark .navbar.is-fixed-bottom-touch{bottom:0}html.theme--documenter-dark .navbar.is-fixed-bottom-touch.has-shadow{box-shadow:0 -2px 3px rgba(10,10,10,0.1)}html.theme--documenter-dark .navbar.is-fixed-top-touch{top:0}html.theme--documenter-dark .navbar.is-fixed-top .navbar-menu,html.theme--documenter-dark .navbar.is-fixed-top-touch 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a.navbar-item:hover{background-color:rgba(0,0,0,0);color:#dbdee0}html.theme--documenter-dark .navbar-dropdown a.navbar-item.is-active{background-color:rgba(0,0,0,0);color:#1abc9c}.navbar.is-spaced html.theme--documenter-dark .navbar-dropdown,html.theme--documenter-dark .navbar-dropdown.is-boxed{border-radius:8px;border-top:none;box-shadow:0 8px 8px rgba(10,10,10,0.1), 0 0 0 1px rgba(10,10,10,0.1);display:block;opacity:0;pointer-events:none;top:calc(100% + (-4px));transform:translateY(-5px);transition-duration:86ms;transition-property:opacity, transform}html.theme--documenter-dark .navbar-dropdown.is-right{left:auto;right:0}html.theme--documenter-dark .navbar-divider{display:block}html.theme--documenter-dark .navbar>.container .navbar-brand,html.theme--documenter-dark .container>.navbar .navbar-brand{margin-left:-.75rem}html.theme--documenter-dark .navbar>.container .navbar-menu,html.theme--documenter-dark .container>.navbar .navbar-menu{margin-right:-.75rem}html.theme--documenter-dark .navbar.is-fixed-bottom-desktop,html.theme--documenter-dark .navbar.is-fixed-top-desktop{left:0;position:fixed;right:0;z-index:30}html.theme--documenter-dark .navbar.is-fixed-bottom-desktop{bottom:0}html.theme--documenter-dark .navbar.is-fixed-bottom-desktop.has-shadow{box-shadow:0 -2px 3px rgba(10,10,10,0.1)}html.theme--documenter-dark .navbar.is-fixed-top-desktop{top:0}html.theme--documenter-dark html.has-navbar-fixed-top-desktop,html.theme--documenter-dark body.has-navbar-fixed-top-desktop{padding-top:4rem}html.theme--documenter-dark html.has-navbar-fixed-bottom-desktop,html.theme--documenter-dark body.has-navbar-fixed-bottom-desktop{padding-bottom:4rem}html.theme--documenter-dark html.has-spaced-navbar-fixed-top,html.theme--documenter-dark body.has-spaced-navbar-fixed-top{padding-top:6rem}html.theme--documenter-dark html.has-spaced-navbar-fixed-bottom,html.theme--documenter-dark body.has-spaced-navbar-fixed-bottom{padding-bottom:6rem}html.theme--documenter-dark a.navbar-item.is-active,html.theme--documenter-dark .navbar-link.is-active{color:#1abc9c}html.theme--documenter-dark a.navbar-item.is-active:not(:focus):not(:hover),html.theme--documenter-dark .navbar-link.is-active:not(:focus):not(:hover){background-color:rgba(0,0,0,0)}html.theme--documenter-dark .navbar-item.has-dropdown:focus .navbar-link,html.theme--documenter-dark .navbar-item.has-dropdown:hover .navbar-link,html.theme--documenter-dark .navbar-item.has-dropdown.is-active .navbar-link{background-color:rgba(0,0,0,0)}}html.theme--documenter-dark .hero.is-fullheight-with-navbar{min-height:calc(100vh - 4rem)}html.theme--documenter-dark .pagination{font-size:15px;margin:-.25rem}html.theme--documenter-dark .pagination.is-small,html.theme--documenter-dark #documenter .docs-sidebar form.docs-search>input.pagination{font-size:.85em}html.theme--documenter-dark .pagination.is-medium{font-size:1.25rem}html.theme--documenter-dark .pagination.is-large{font-size:1.5rem}html.theme--documenter-dark .pagination.is-rounded .pagination-previous,html.theme--documenter-dark #documenter .docs-sidebar form.docs-search>input.pagination .pagination-previous,html.theme--documenter-dark .pagination.is-rounded .pagination-next,html.theme--documenter-dark #documenter .docs-sidebar form.docs-search>input.pagination .pagination-next{padding-left:1em;padding-right:1em;border-radius:290486px}html.theme--documenter-dark .pagination.is-rounded .pagination-link,html.theme--documenter-dark #documenter .docs-sidebar form.docs-search>input.pagination .pagination-link{border-radius:290486px}html.theme--documenter-dark .pagination,html.theme--documenter-dark .pagination-list{align-items:center;display:flex;justify-content:center;text-align:center}html.theme--documenter-dark .pagination-previous,html.theme--documenter-dark .pagination-next,html.theme--documenter-dark .pagination-link,html.theme--documenter-dark .pagination-ellipsis{font-size:1em;justify-content:center;margin:.25rem;padding-left:.5em;padding-right:.5em;text-align:center}html.theme--documenter-dark .pagination-previous,html.theme--documenter-dark .pagination-next,html.theme--documenter-dark .pagination-link{border-color:#5e6d6f;color:#1abc9c;min-width:2.25em}html.theme--documenter-dark .pagination-previous:hover,html.theme--documenter-dark .pagination-next:hover,html.theme--documenter-dark .pagination-link:hover{border-color:#8c9b9d;color:#1dd2af}html.theme--documenter-dark .pagination-previous:focus,html.theme--documenter-dark .pagination-next:focus,html.theme--documenter-dark .pagination-link:focus{border-color:#8c9b9d}html.theme--documenter-dark .pagination-previous:active,html.theme--documenter-dark .pagination-next:active,html.theme--documenter-dark .pagination-link:active{box-shadow:inset 0 1px 2px rgba(10,10,10,0.2)}html.theme--documenter-dark .pagination-previous[disabled],html.theme--documenter-dark 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ul.is-center{flex:none;justify-content:center;padding-left:0.75em;padding-right:0.75em}html.theme--documenter-dark .tabs ul.is-right{justify-content:flex-end;padding-left:0.75em}html.theme--documenter-dark .tabs .icon:first-child{margin-right:0.5em}html.theme--documenter-dark .tabs .icon:last-child{margin-left:0.5em}html.theme--documenter-dark .tabs.is-centered ul{justify-content:center}html.theme--documenter-dark .tabs.is-right ul{justify-content:flex-end}html.theme--documenter-dark .tabs.is-boxed a{border:1px solid transparent;border-radius:.4em .4em 0 0}html.theme--documenter-dark .tabs.is-boxed a:hover{background-color:#282f2f;border-bottom-color:#5e6d6f}html.theme--documenter-dark .tabs.is-boxed li.is-active a{background-color:#fff;border-color:#5e6d6f;border-bottom-color:rgba(0,0,0,0) !important}html.theme--documenter-dark .tabs.is-fullwidth li{flex-grow:1;flex-shrink:0}html.theme--documenter-dark .tabs.is-toggle a{border-color:#5e6d6f;border-style:solid;border-width:1px;margin-bottom:0;position:relative}html.theme--documenter-dark .tabs.is-toggle a:hover{background-color:#282f2f;border-color:#8c9b9d;z-index:2}html.theme--documenter-dark .tabs.is-toggle li+li{margin-left:-1px}html.theme--documenter-dark .tabs.is-toggle li:first-child a{border-radius:.4em 0 0 .4em}html.theme--documenter-dark .tabs.is-toggle li:last-child a{border-radius:0 .4em .4em 0}html.theme--documenter-dark .tabs.is-toggle li.is-active a{background-color:#1abc9c;border-color:#1abc9c;color:#fff;z-index:1}html.theme--documenter-dark .tabs.is-toggle ul{border-bottom:none}html.theme--documenter-dark .tabs.is-toggle.is-toggle-rounded li:first-child a{border-bottom-left-radius:290486px;border-top-left-radius:290486px;padding-left:1.25em}html.theme--documenter-dark .tabs.is-toggle.is-toggle-rounded li:last-child a{border-bottom-right-radius:290486px;border-top-right-radius:290486px;padding-right:1.25em}html.theme--documenter-dark 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span.sgr102{background-color:#0e8300}.ansi span.sgr103{background-color:#a98800}.ansi span.sgr104{background-color:#3c5dcd}.ansi span.sgr105{background-color:#9256af}.ansi span.sgr106{background-color:#008fa3}.ansi span.sgr107{background-color:#f5f5f5}code.language-julia-repl>span.hljs-meta{color:#066f00;font-weight:bolder}/*! + Theme: Default + Description: Original highlight.js style + Author: (c) Ivan Sagalaev + Maintainer: @highlightjs/core-team + Website: https://highlightjs.org/ + License: see project LICENSE + Touched: 2021 +*/pre code.hljs{display:block;overflow-x:auto}code.hljs{padding:3px 5px}.hljs{background:#F0F0F0;color:#444}.hljs-comment{color:#888888}.hljs-tag,.hljs-punctuation{color:#444a}.hljs-tag .hljs-name,.hljs-tag .hljs-attr{color:#444}.hljs-keyword,.hljs-attribute,.hljs-selector-tag,.hljs-meta .hljs-keyword,.hljs-doctag,.hljs-name{font-weight:bold}.hljs-type,.hljs-string,.hljs-number,.hljs-selector-id,.hljs-selector-class,.hljs-quote,.hljs-template-tag,.hljs-deletion{color:#880000}.hljs-title,.hljs-section{color:#880000;font-weight:bold}.hljs-regexp,.hljs-symbol,.hljs-variable,.hljs-template-variable,.hljs-link,.hljs-selector-attr,.hljs-operator,.hljs-selector-pseudo{color:#BC6060}.hljs-literal{color:#78A960}.hljs-built_in,.hljs-bullet,.hljs-code,.hljs-addition{color:#397300}.hljs-meta{color:#1f7199}.hljs-meta .hljs-string{color:#4d99bf}.hljs-emphasis{font-style:italic}.hljs-strong{font-weight:bold} diff --git a/v0.13.16/assets/themeswap.js b/v0.13.16/assets/themeswap.js new file mode 100644 index 00000000..c58e993e --- /dev/null +++ b/v0.13.16/assets/themeswap.js @@ -0,0 +1,66 @@ +// Small function to quickly swap out themes. Gets put into the tag.. +function set_theme_from_local_storage() { + // Intialize the theme to null, which means default + var theme = null; + // If the browser supports the localstorage and is not disabled then try to get the + // documenter theme + if(window.localStorage != null) { + // Get the user-picked theme from localStorage. May be `null`, which means the default + // theme. + theme = window.localStorage.getItem("documenter-theme"); + } + // Check if the browser supports user color preference + var darkPreference = false; + // Check if the users preference is for dark color scheme + if(window.matchMedia('(prefers-color-scheme: dark)').matches === true) { + darkPreference = true; + } + // Initialize a few variables for the loop: + // + // - active: will contain the index of the theme that should be active. Note that there + // is no guarantee that localStorage contains sane values. If `active` stays `null` + // we either could not find the theme or it is the default (primary) theme anyway. + // Either way, we then need to stick to the primary theme. + // + // - disabled: style sheets that should be disabled (i.e. all the theme style sheets + // that are not the currently active theme) + var active = null; var disabled = []; var darkTheme = null; + for (var i = 0; i < document.styleSheets.length; i++) { + var ss = document.styleSheets[i]; + // The tag of each style sheet is expected to have a data-theme-name attribute + // which must contain the name of the theme. The names in localStorage much match this. + var themename = ss.ownerNode.getAttribute("data-theme-name"); + // attribute not set => non-theme stylesheet => ignore + if(themename === null) continue; + // To distinguish the default (primary) theme, it needs to have the data-theme-primary + // attribute set. + var isprimary = (ss.ownerNode.getAttribute("data-theme-primary") !== null); + // Check if the theme is primary dark theme + var isDarkTheme = (ss.ownerNode.getAttribute("data-theme-primary-dark") !== null); + // If ss is for dark theme then set the value of darkTheme to the name of the theme + if(isDarkTheme) darkTheme = themename; + // If we find a matching theme (and it's not the default), we'll set active to non-null + if(themename === theme) active = i; + // Store the style sheets of inactive themes so that we could disable them + if(themename !== theme) disabled.push(ss); + } + if(active !== null) { + // If we did find an active theme, we'll (1) add the theme--$(theme) class to + document.getElementsByTagName('html')[0].className = "theme--" + theme; + // and (2) disable all the other theme stylesheets + disabled.forEach(function(ss){ + ss.disabled = true; + }); + } + else if(darkTheme !== null && darkPreference === true) { + // If we did find an active theme, we'll (1) add the theme--$(theme) class to + document.getElementsByTagName('html')[0].className = "theme--" + darkTheme; + // and (2) disable all the other theme stylesheets + disabled.forEach(function(ss){ + if (ss.ownerNode.getAttribute("data-theme-name") !== darkTheme) { + ss.disabled = true; + } + }); + } +} +set_theme_from_local_storage(); diff --git a/v0.13.16/assets/warner.js b/v0.13.16/assets/warner.js new file mode 100644 index 00000000..5531c885 --- /dev/null +++ b/v0.13.16/assets/warner.js @@ -0,0 +1,49 @@ +function maybeAddWarning () { + // DOCUMENTER_NEWEST is defined in versions.js, DOCUMENTER_CURRENT_VERSION and DOCUMENTER_STABLE + // in siteinfo.js. + // If either of these are undefined something went horribly wrong, so we abort. + if ( + window.DOCUMENTER_NEWEST === undefined || + window.DOCUMENTER_CURRENT_VERSION === undefined || + window.DOCUMENTER_STABLE === undefined + ) { + return + }; + + // Current version is not a version number, so we can't tell if it's the newest version. Abort. + if (!/v(\d+\.)*\d+/.test(window.DOCUMENTER_CURRENT_VERSION)) { + return + }; + + // Current version is newest version, so no need to add a warning. + if (window.DOCUMENTER_NEWEST === window.DOCUMENTER_CURRENT_VERSION) { + return + }; + + // Add a noindex meta tag (unless one exists) so that search engines don't index this version of the docs. + if (document.body.querySelector('meta[name="robots"]') === null) { + const meta = document.createElement('meta'); + meta.name = 'robots'; + meta.content = 'noindex'; + + document.getElementsByTagName('head')[0].appendChild(meta); + }; + + const div = document.createElement('div'); + div.classList.add('outdated-warning-overlay'); + const closer = document.createElement('button'); + closer.classList.add('outdated-warning-closer', 'delete'); + closer.addEventListener('click', function () { + document.body.removeChild(div); + }); + const href = window.documenterBaseURL + '/../' + window.DOCUMENTER_STABLE; + div.innerHTML = 'This documentation is not for the latest stable release, but for either the development version or an older release.
    Click here to go to the documentation for the latest stable release.'; + div.appendChild(closer); + document.body.appendChild(div); +}; + +if (document.readyState === 'loading') { + document.addEventListener('DOMContentLoaded', maybeAddWarning); +} else { + maybeAddWarning(); +}; diff --git a/v0.13.16/conversions/index.html b/v0.13.16/conversions/index.html new file mode 100644 index 00000000..613f6885 --- /dev/null +++ b/v0.13.16/conversions/index.html @@ -0,0 +1,54 @@ + +Supported Conversions · RCall.jl
    Edit on GitHub

    Supported Conversions

    RCall supports conversions to and from most base Julia types and popular Statistics packages, e.g., DataFrames, CategoricalArrays and AxisArrays.

    Base Julia Types

    # Julia -> R
+a = robject(1)
    RObject{IntSxp}
+[1] 1
+
    # R -> Julia
+rcopy(a)
    1
    # Julia -> R
+a = robject([1.0, 2.0])
    RObject{RealSxp}
+[1] 1 2
+
    # R -> Julia
+rcopy(a)
    2-element Vector{Float64}:
+ 1.0
+ 2.0

    Dictionaries

    # Julia -> R
+d = Dict(:a => 1, :b => [4, 5, 3])
+r = robject(d)
    RObject{VecSxp}
+$a
+[1] 1
+
+$b
+[1] 4 5 3
+
+
    # R -> Julia
+rcopy(r)
    OrderedCollections.OrderedDict{Symbol, Any} with 2 entries:
+  :a => 1
+  :b => [4, 5, 3]

    Date

    # Julia -> R
+d = Date(2012, 12, 12)
+r = robject(d)
    RObject{RealSxp}
+[1] "2012-12-12"
+
    # R -> Julia
+rcopy(r)
    2012-12-12

    DateTime

    # julia -> R
+d = DateTime(2012, 12, 12, 12, 12, 12)
+r = robject(d)
    RObject{RealSxp}
+[1] "2012-12-12 12:12:12 UTC"
+
    # R -> Julia
+rcopy(r)
    2012-12-12T12:12:12

    DataFrames

    d = DataFrame([[1.0, 4.5, 7.0]], [:x])
+# Julia -> R
+r = robject(d)
    RObject{VecSxp}
+    x
+1 1.0
+2 4.5
+3 7.0
+
    # R -> Julia
+rcopy(r)
    3×1 DataFrame
    Rowx
    Float64
    11.0
    24.5
    37.0

    In default, the column names of R data frames are normalized such that foo.bar would be replaced by foo_bar.

    rcopy(R"data.frame(a.b = 1:3)")
    3×1 DataFrame
    Rowa_b
    Int64
    11
    22
    33

    To avoid the normalization, use normalizenames option.

    rcopy(R"data.frame(a.b = 1:10)"; normalizenames = false)
    10×1 DataFrame
    Rowa.b
    Int64
    11
    22
    33
    44
    55
    66
    77
    88
    99
    1010

    AxisArrays

    # Julia -> R
+aa = AxisArray([1,2,3], Axis{:id}(["a", "b", "c"]))
+r = robject(aa)
    RObject{IntSxp}
+id
+a b c 
+1 2 3 
+
    # R -> Julia
+rcopy(AxisArray, r)
    1-dimensional AxisArray{Int64,1,...} with axes:
+    :id, ["a", "b", "c"]
+And data, a 3-element Vector{Int64}:
+ 1
+ 2
+ 3
    diff --git a/v0.13.16/custom/index.html b/v0.13.16/custom/index.html new file mode 100644 index 00000000..c62e8876 --- /dev/null +++ b/v0.13.16/custom/index.html @@ -0,0 +1,65 @@ + +Custom Conversion · RCall.jl
    Edit on GitHub

    Custom Conversion

    RCall supports an API for implicitly converting between R and Julia objects by means of rcopy and robject.

    To illustrate the idea, we consider the following Julia type

    mutable struct Foo
+    x::Float64
+    y::String
+end
    foo = Foo(1.0, "hello")
+bar = R"""
+    bar <- list(x = 1, y = "hello")
+    class(bar) <- "Bar"
+    bar
+"""

    R to Julia direction

    The function rcopy and rcopytype are responsible for conversions of this direction. First we define an explicit converter for VecSxp (SEXP for list)

    import RCall.rcopy
+
+function rcopy(::Type{Foo}, s::Ptr{VecSxp})
+    Foo(rcopy(Float64, s[:x]), rcopy(String, s[:y]))
+end
    rcopy (generic function with 95 methods)

    The convert function will dispatch the corresponding rcopy function when it is found.

    rcopy(Foo, bar)
+convert(Foo, bar) # calls `rcopy`

    To allow the automatic conversion via rcopy(bar), the R class Bar has to be registered.

    import RCall: RClass, rcopytype
+
+rcopytype(::Type{RClass{:Bar}}, s::Ptr{VecSxp}) = Foo
+foo2 = rcopy(bar)

    Julia to R direction

    The function RCall.sexp has to be overwritten to allow Julia to R conversion. sexp function takes a julia object and returns an SEXP object (pointer to [Sxp]).

    First we define an explicit converter from Julia type Foo to R class Bar

    import RCall: sexp, protect, unprotect, setclass!, RClass
+
+function sexp(::Type{RClass{:Bar}}, f::Foo)
+    r = protect(sexp(Dict(:x => f.x, :y => f.y)))
+    setclass!(r, sexp("Bar"))
+    unprotect(1)
+    r
+end
+
+bar = robject(:Bar, foo)

    Remark: RCall.protect and RCall.unprotect should be used to protect SEXP from being garbage collected.

    To register the default conversion via robject(foo), we need to define sexpclass

    import RCall.sexpclass
+
+sexpclass(f::Foo) = RClass{:Bar}
+bar = robject(foo)

    Using @rput and @rget is seamless

    foo2.x = 2.0
+@rput foo2
+R"""
+foo2["x"]
+"""
    RObject{VecSxp}
+$x
+[1] 2
+
+
    R"""
+foo2["x"] = 3.0
+"""
+@rget foo2
+foo2.x
    3.0

    Nested conversion

    l = R"list(foo2 = foo2, bar = $bar)"
    RObject{VecSxp}
+$foo2
+$y
+[1] "hello"
+
+$x
+[1] 3
+
+attr(,"class")
+[1] "Bar"
+
+$bar
+$y
+[1] "hello"
+
+$x
+[1] 1
+
+attr(,"class")
+[1] "Bar"
+
+
    rcopy(l)
    OrderedCollections.OrderedDict{Symbol, Any} with 2 entries:
+  :foo2 => Foo(3.0, "hello")
+  :bar  => Foo(1.0, "hello")
    diff --git a/v0.13.16/eventloop/index.html b/v0.13.16/eventloop/index.html new file mode 100644 index 00000000..b3d4aa36 --- /dev/null +++ b/v0.13.16/eventloop/index.html @@ -0,0 +1,2 @@ + +Eventloop · RCall.jl
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    Eventloop

    In a non-IJulia interactive session, by R will by default open a new window to display the plot. In order to enable interactive features, such as plot-resizing, the R eventlopp will be started automatically.

    You could start manually the R event loop via

    RCall.rgui_start()

    This runs frequent calls to R to check if the plot has changed, and redraw if necessary. It can be stopped with

    RCall.rgui_stop()
    diff --git a/v0.13.16/gettingstarted/index.html b/v0.13.16/gettingstarted/index.html new file mode 100644 index 00000000..e2a58f4c --- /dev/null +++ b/v0.13.16/gettingstarted/index.html @@ -0,0 +1,123 @@ + +Getting Started · RCall.jl
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    Getting started

    The RCall package is loaded via

    julia> using RCall

    This will initialize the R process in the background.

    Several Ways to use RCall

    RCall provides multiple ways to allow R interacting with Julia.

    R REPL mode

    The R REPL mode allows real time switching between the Julia prompt and R prompt. Press $ to activate the R REPL mode and the R prompt will be shown. (Press backspace to leave R REPL mode in case you did not know.)

    julia> foo = 1
+1
+
+R> x <- $foo
+
+R> x
+[1] 1

    The R REPL mode supports variable substitution of Julia objects via the $ symbol. It is also possible to pass Julia expressions in the REPL mode.

    R> x = $(rand(10))
+
+R> sum(x)
+[1] 5.097083

    @rput and @rget macros

    These macros transfer variables between R and Julia environments. The copied variable will have the same name as the original.

    julia> z = 1
+1
+
+julia> @rput z
+1
+
+R> z
+[1] 1
+
+R> r = 2
+
+julia> @rget r
+2.0
+
+julia> r
+2.0

    It is also possible to put and get multiple variables in one line.

    julia> foo = 2
+2
+
+julia> bar = 4
+4
+
+julia> @rput foo bar
+4
+
+R> foo + bar
+[1] 6

    @R_str string macro

    Another way to use RCall is the R"" string macro, it is especially useful in script files.

    julia> R"rnorm(10)"RObject{RealSxp}
+ [1]  0.81959517  0.12656226 -0.29111505 -0.05826287  1.30574756  1.14403063
+ [7] -0.91370141 -0.10778344 -0.28455636  1.17228815

    This evaluates the expression inside the string in R, and returns the result as an RObject, which is a Julia wrapper type around an R object.

    The R"" string macro supports variable substitution of Julia objects via the $ symbol, whenever it is not valid R syntax (i.e. when not directly following a symbol or completed expression such as aa$bb):

    julia> x = randn(10)10-element Vector{Float64}:
+  0.5436265117729131
+  0.2981541432897502
+ -0.2103823372221778
+ -0.7039729157117988
+  0.04981239564919098
+  1.5523373794522117
+ -0.18737692130116654
+ -0.8454093831342282
+  0.7293055268151365
+  0.7245233988353085
    julia> R"t.test($x)"RObject{VecSxp}
+
+	One Sample t-test
+
+data:  `#JL`$x
+t = 0.84795, df = 9, p-value = 0.4184
+alternative hypothesis: true mean is not equal to 0
+95 percent confidence interval:
+ -0.3253247  0.7154483
+sample estimates:
+mean of x
+0.1950618

    It is also possible to pass Julia expressions which are evaluated before being passed to R: these should be included in parentheses

    julia> R"optim(0, $(x -> x-cos(x)), method='BFGS')"RObject{VecSxp}
+$par
+[1] -1.56343
+
+$value
+[1] -1.570796
+
+$counts
+function gradient
+      14       13
+
+$convergence
+[1] 0
+
+$message
+NULL

    A large chunk of code could be quoted between triple string quotations

    julia> y = 11
    julia> R"""
+       f <- function(x, y) x + y
+       ret <- f(1, $y)
+       """RObject{RealSxp}
+[1] 2

    RCall API

    The reval function evaluates any given input string as R code in the R environment. The returned result is an RObject object.

    julia> jmtcars = reval("mtcars");
    julia> names(jmtcars)11-element Vector{Symbol}:
+ :mpg
+ :cyl
+ :disp
+ :hp
+ :drat
+ :wt
+ :qsec
+ :vs
+ :am
+ :gear
+ :carb
    julia> jmtcars[:mpg]Ptr{RealSxp} @0x00000000083b4750
    julia> typeof(jmtcars)RObject{VecSxp}

    The rcall function is used to construct function calls.

    julia> rcall(:dim, jmtcars)RObject{IntSxp}
+[1] 32 11

    The arguments will be implicitly converted to RObject upon evaluation.

    julia> rcall(:sum, Float64[1.0, 4.0, 6.0])RObject{RealSxp}
+[1] 11

    The rcopy function converts RObjects to Julia objects. It uses a variety of heuristics to pick the most appropriate Julia type:

    julia> rcopy(R"c(1)")1.0
    julia> rcopy(R"c(1, 2)")2-element Vector{Float64}:
+ 1.0
+ 2.0
    julia> rcopy(R"list(1, 'zz')")2-element Vector{Any}:
+ 1.0
+  "zz"
    julia> rcopy(R"list(a = 1, b= 'zz')")OrderedCollections.OrderedDict{Symbol, Any} with 2 entries:
+  :a => 1.0
+  :b => "zz"

    It is possible to force a specific conversion by passing the output type as the first argument:

    julia> rcopy(Array{Int}, R"c(1, 2)")2-element Vector{Int64}:
+ 1
+ 2

    Converter could also be used specifically to yield the desired type.

    julia> convert(Array{Float64}, R"c(1, 2)")2-element Vector{Float64}:
+ 1.0
+ 2.0

    The robject function converts any julia object to an RObject.

    julia> robject(1)RObject{IntSxp}
+[1] 1
    julia> robject(Dict(:a => 1, :b = 2))ERROR: syntax: invalid keyword argument name ":b" around REPL[2]:1

    @rlibrary and @rimport macros

    This macro loads all exported functions/objects of an R package to the current module.

    julia> @rlibrary boot
    julia> city = rcopy(R"boot::city")  # get some data10×2 DataFrame
+ Row │ u        x
+     │ Float64  Float64
+─────┼──────────────────
+   1 │   138.0    143.0
+   2 │    93.0    104.0
+   3 │    61.0     69.0
+   4 │   179.0    260.0
+   5 │    48.0     75.0
+   6 │    37.0     63.0
+   7 │    29.0     50.0
+   8 │    23.0     48.0
+   9 │    30.0    111.0
+  10 │     2.0     50.0
    julia> ratio(d, w) = sum(d[!, :x] .* w)/sum(d[!, :u] .* w)ratio (generic function with 1 method)
    julia> b = boot(city, ratio, R = 100, stype = "w");
    julia> rcall(:summary, b[:t])RObject{StrSxp}
+       V1
+ Min.   :1.228
+ 1st Qu.:1.348
+ Median :1.470
+ Mean   :1.511
+ 3rd Qu.:1.616
+ Max.   :2.264

    Of course, it is highly inefficient, because the data are copying multiple times between R and Julia. The R"" string macro is more recommended for efficiency.

    Some R functions may have keyword arguments which contain dots. RCall provides a string macro to escape those keywords, e.g,

    julia> @rimport base as rbase
    julia> rbase.sum([1, 2, 3], var"rm.na" = true)RObject{IntSxp}
+[1] 7
    diff --git a/v0.13.16/index.html b/v0.13.16/index.html new file mode 100644 index 00000000..7a4f6bf2 --- /dev/null +++ b/v0.13.16/index.html @@ -0,0 +1,2 @@ + +Introduction · RCall.jl
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    RCall.jl

    R is a language for statistical computing and graphics that has been around for couple of decades and it has one of the most impressive collections of scientific and statistical packages of any environment. Recently, the Julia language has become an attractive alternative because it provides the remarkable performance of a low-level language without sacrificing the readability and ease-of-use of high-level languages. However, Julia still lacks the depth and scale of the R package environment.

    This package, RCall, facilitates communication between these two languages and allows the user to call R packages from within Julia, providing the best of both worlds. Additionally, this is a pure Julia package so it is portable and easy to use.

    diff --git a/v0.13.16/installation/index.html b/v0.13.16/installation/index.html new file mode 100644 index 00000000..4f376db5 --- /dev/null +++ b/v0.13.16/installation/index.html @@ -0,0 +1,10 @@ + +Installation · RCall.jl
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    Installing RCall.jl

    RCall.jl can simply be installed with

    Pkg.add("RCall")

    Customizing the R installation

    The RCall build script (run by Pkg.add) will check for an existing R installation by looking in the following locations, in order.

    • The R_HOME environment variable, if set, should be the location of the R home directory. You could run R.home() in R to determine its location.
    • Otherwise, it runs the R RHOME command, assuming R is located in your PATH.
    • Otherwise, on Windows, it looks in the Windows registry.

    To change which R installation is used for RCall, set the R_HOME environment variable and run Pkg.build("RCall"). Once this is configured, RCall remembers the location of R in future updates, so you don't need to set R_HOME permanently.

    ENV["R_HOME"] = "....directory of R home...."
+Pkg.build("RCall")

    When R_HOME is set to "*", RCall.jl will automatically install R for you using Conda.

    Should you experience problems with any of these methods, please open an issue.

    Standard installations

    If you want to install R yourself, rather than relying on the automatic Conda installation, you can use one of the following options:

    Windows

    The current Windows binary from CRAN.

    OS X

    The CRAN .pkg or the homebrew/science tap.

    Linux

    Most Linux distributions allow installation of R from their package manager, however these are often out of date, and may not work with RCall.jl. We recommend that you use the updated repositories from CRAN.

    Ubuntu

    The following will update R on recent versions of Ubuntu:

    sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
+sudo add-apt-repository -y "deb http://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -s -c)-cran40/"
+sudo apt-get update -y
+sudo apt-get install -y r-base r-base-dev

    See also the official documentation on CRAN: Ubuntu Packages For R.

    Julia ≤ 1.5: Failure on recent Linux distributions

    The version of libstdc++ shipped by Julia might be outdated if you are using a recent Linux distribution (e.g. Ubuntu 19.10) and make use of certain R packages (e.g. Rcpp). In this case RCall will fail with an error message looking similar to this:

    Error: package or namespace load failed for ‘package’ in dyn.load(file, DLLpath = DLLpath, ...):
+unable to load shared object '/home/user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/libs/Rcpp.so':
+/home/user/julia-1.3.1/bin/../lib/julia/libstdc++.so.6: version `GLIBCXX_3.4.26' not found 
+(required by /home/user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/libs/Rcpp.so)

    Until this issue is fixed in Julia (see https://github.com/JuliaLang/julia/issues/34276) a workaround is to replace Julias libstdc++ with the one of your OS:

    # works for Ubuntu 19.10 64bit - match your locations accordingly!
+cp /usr/lib/x86_64-linux-gnu/libstdc++.so.6 $JULIA_HOME/lib/julia/

    This problem doesn't affect Julia ≥ 1.6!

    Other methods

    If you have installed R by some other method (e.g. building from scratch, or files copied but not installed in the usual manner), which often happens on cluster installations, then you may need to set R_HOME or your PATH as described above before running Pkg.build("RCall") in order for the build script to find your R installation. RCall requires R to be installed with its shared library. It could be done with the flag --enable-R-shlib, consult your server administrator to see if it was the case.

    For some environments, you might also need to specify LD_LIBRARY_PATH

    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:`R RHOME`/lib"

    Updating R

    If you have updated your R installation, you may need to re-run Pkg.build("RCall") as described above, possibly changing the R_HOME environment variable first.

    diff --git a/v0.13.16/internal/index.html b/v0.13.16/internal/index.html new file mode 100644 index 00000000..97ab88f7 --- /dev/null +++ b/v0.13.16/internal/index.html @@ -0,0 +1,14 @@ + +Internal · RCall.jl
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    Internal API

    Types

    RCall.RObject — Type

    An RObject is a Julia wrapper for an R object (known as an "S-expression" or "SEXP"). It is stored as a pointer which is protected from the R garbage collector, until the RObject itself is finalized by Julia. The parameter is the type of the S-expression.

    When called with a Julia object as an argument, a corresponding R object is constructed.

    julia> RObject(1)
+RObject{IntSxp}
+[1] 1
+
+julia> RObject(1:3)
+RObject{IntSxp}
+[1] 1 2 3
+
+julia> RObject(1.0:3.0)
+RObject{RealSxp}
+[1] 1 2 3
    source
    RCall.Sxp — Type

    RCall.jl's type Sxp mirrors the R symbolic expression record SEXPREC in R API. These are represented by a pointer Ptr{S<:Sxp} (which is called SEXP in R API).

    source

    Methods

    Base.isascii — Method

    Determines the encoding of the CharSxp. This is determined by the 'gp' part of the sxpinfo (this is the middle 16 bits).

    • 0x00000200 (bit 1): set of bytes (no known encoding)
    • 0x00000400 (bit 2): Latin-1
    • 0x00000800 (bit 3): UTF-8
    • 0x00004000 (bit 6): ASCII

    We only support ASCII and UTF-8.

    source
    Base.length — Method

    Sxp methods for length return the R length.

    Rf_xlength handles Sxps that are not vector-like and R's "long vectors", which have a negative value for the length member.

    source
    Base.names — Method

    Returns the names of an R vector, the result is converted to a Julia symbol array.

    source
    RCall.bound — Method

    The R NAMED property, represented by 2 bits in the info field. This can take values 0,1 or 2, corresponding to whether it is bound to 0,1 or 2 or more symbols. See http://cran.r-project.org/doc/manuals/r-patched/R-exts.html#Named-objects-and-copying

    source
    RCall.getNamespace — Method

    get namespace by name of the namespace. It is safer to be used than findNamespace as it checks bound.

    source
    RCall.ijulia_setdevice — Method

    Set options for R plotting with IJulia.

    The first argument should be a MIME object: currently supported are

    • MIME("image/png") [default]
    • MIME("image/svg+xml")

    The remaining arguments (keyword only) are passed to the appropriate R graphics device: see the relevant R help for details.

    source
    RCall.initEmbeddedR — Method
    initEmbeddedR()

    This initializes an embedded R session. It should only be called when R is not already running (e.g. if Julia is running inside an R session)

    source
    RCall.isNA — Method

    Check if a value corresponds to R's sentinel NA values. These function should not be exported.

    source
    RCall.isna — Method

    Check if the ith member of s correspond to R's NA values.

    source
    RCall.isna — Method

    Check if the members of a vector are NA values. Always return a BitArray.

    source
    RCall.julia_extptr_callback — Method

    The function called by R .External for Julia callbacks.

    It receives a Ptr{ListSxp} containing

    • a pointer to the function itself (Ptr{ExtPtrSxp})
    • a pointer to the Julia function (Ptr{ExtPtrSxp})
    • any arguments (as Ptr{S<:Sxp})
    source
    RCall.makeNativeSymbolRef — Method

    Register a function pointer as an R NativeSymbol. We technically are supposed to use RregisterRoutines. Starting from R 3.4, `RMakeExternalPtrFn` is a part of R API in R 3.4. It is probably safe to such to make the external pointer.

    source
    RCall.newEnvironment — Method
    newEnvironment([env])

    Create a new environment which extends environment env (globalEnv by default).

    source
    RCall.preserve — Method

    Prevent garbage collection of an R object. Object can be released via release.

    This is slower than protect, as it requires searching an internal list, but more flexible.

    source
    RCall.protect — Method

    Stack-based protection of garbage collection of R objects. Objects are released via unprotect. Returns the same pointer, allowing inline use.

    This is faster than preserve, but more restrictive. Really only useful inside functions.

    source
    RCall.rcall — Method

    Evaluate a function in the global environment. The first argument corresponds to the function to be called. It can be either a FunctionSxp type, a SymSxp or a Symbol.

    source
    RCall.rcall_p — Method

    Evaluate a function in the global environment. The first argument corresponds to the function to be called. It can be either a FunctionSxp type, a SymSxp or a Symbol.

    source
    RCall.rcopy — Method

    rcopy(r) copies the contents of an R object into a corresponding canonical Julia type.

    source
    RCall.render — Method

    Render an inline R script, substituting invalid "$(Expr(:incomplete, "incomplete: invalid string syntax"))

    source
    RCall.reval — Function

    Evaluate an R symbol or language object (i.e. a function call) in an R try/catch block, returning an RObject.

    source
    RCall.reval_p — Method

    Evaluate an R expression array iteratively. If throw_error is false, the error message and warning will be thrown to stderr.

    source
    RCall.reval_p — Method

    Evaluate an R symbol or language object (i.e. a function call) in an R try/catch block, returning a Sxp pointer.

    source
    RCall.rimport — Function

    Import an R package as a julia module. Sanitizes the imported symbols by default, because otherwise certain symbols cannot be used.

    E.g.: PerformanceAnalytics::charts.Bar in R becomes PerformanceAnalytics.charts_Bar in Julia

    gg = rimport("ggplot2")
    source
    RCall.rlang — Method

    Create a function call from a function pointer and a list of arguments and return it as an RObject, which can then be evaluated

    source
    RCall.robject — Method

    robject(x) converts a Julia object x to a corresponding RObject implicitly. Explicit conversions could be called with robject(<R Class>, x).

    source
    RCall.sexp — Method

    sexp(x) converts a Julia object x to a pointer to a corresponding Sxp Object.

    source
    RCall.sexp — Method

    Convert a Ptr{UnknownSxp} to an appropriate Ptr{S<:Sxp}.

    source
    RCall.sexp — Method

    Wrap a Julia object an a R Ptr{ExtPtrSxp}.

    We store the pointer and the object in a const Dict to prevent it being removed by the Julia GC.

    source
    RCall.sexp — Method

    Wrap a callable Julia object f an a R ClosSxpPtr.

    Constructs the following R code

    function(...) .External(juliaCallback, fExPtr, ...)
    source
    RCall.sexpnum — Method

    The SEXPTYPE number of a Sxp

    Determined from the trailing 5 bits of the first 32-bit word. Is a 0-based index into the info field of a SxpHead.

    source
    RCall.unsafe_vec — Method

    Represent the contents of a VectorSxp type as a Vector.

    This does not copy the contents. If the argument is not named (in R) or otherwise protected from R's garbage collection (e.g. by keeping the containing RObject in scope) the contents of this vector can be modified or could cause a memory error when accessed.

    The contents are as stored in R. Missing values (NA's) are represented in R by sentinels. Missing data values in RealSxp and CplxSxp show up as NaN and NaN + NaNim, respectively. Missing data in IntSxp show up as -2147483648, the minimum 32-bit integer value. Internally a LglSxp is represented as Vector{Int32}. The convention is that 0 is false, -2147483648 is NA and all other values represent true.

    source
    RCall.validate_libR — Method
    validate_libR(libR)

    Checks that the R library libR can be loaded and is satisfies version requirements.

    source

    Macros

    RCall.@R_str — Macro
    R"..."

    An inline R expression, the result of which is evaluated and returned as an RObject.

    It supports substitution of Julia variables and expressions via prefix with $ whenever not valid R syntax (i.e. when not immediately following another completed R expression):

    R"glm(Sepal.Length ~ Sepal.Width, data=$iris)"

    It is also possible to pass Julia expressions:

    R"plot(#42)"

    All such Julia expressions are evaluated once, before the R expression is evaluated.

    The expression does not support assigning to Julia variables, so the only way retrieve values from R via the return value.

    source
    RCall.@rimport — Macro

    Import an R Package as a Julia module. For example,

    @rimport ggplot2

    is equivalent to ggplot2 = rimport("ggplot2") with error checking.

    You can also use classic Python syntax to make an alias: @rimport *package-name* as *shorthand*

    @rimport ggplot2 as gg

    which is equivalent to gg = rimport("ggplot2").

    source
    RCall.@rlibrary — Macro

    Load all exported functions/objects of an R package to the current module. Almost equivalent to

    __temp__ = rimport("ggplot2")
+using .__temp__
    source
    RCall.@var_str — Macro

    Returns a variable named "str". Useful for passing keyword arguments containing dots.

    source

    Constants

    RCall.jtypExtPtrs — Constant

    Julia types (typically functions) which are wrapped in Ptr{ExtPtrSxp} are stored here to prevent garbage collection by Julia.

    source
    diff --git a/v0.13.16/known-issues/index.html b/v0.13.16/known-issues/index.html new file mode 100644 index 00000000..114776f7 --- /dev/null +++ b/v0.13.16/known-issues/index.html @@ -0,0 +1,2 @@ + +Known issues · RCall.jl
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    Installing packages via Conda

    When using the Conda environment, installing packages via install.packages or devtools will result in installation failures such as "x86_64-conda-linux-gnu-cc: not found". Instead, use Conda to install packages. For example, Conda.add("r-ggplot2").

    diff --git a/v0.13.16/search/index.html b/v0.13.16/search/index.html new file mode 100644 index 00000000..534fce45 --- /dev/null +++ b/v0.13.16/search/index.html @@ -0,0 +1,2 @@ + +Search · RCall.jl

    Loading search...

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","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"R REPL mode\n@rput and @rget macros\nR\"\" string macro\nRCall API: reval, rcall, rcopy and robject etc.\n@rlibrary and @rimport macros","category":"page"},{"location":"gettingstarted/#R-REPL-mode","page":"Getting Started","title":"R REPL mode","text":"","category":"section"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"The R REPL mode allows real time switching between the Julia prompt and R prompt. Press $ to activate the R REPL mode and the R prompt will be shown. (Press backspace to leave R REPL mode in case you did not know.)","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"julia> foo = 1\n1\n\nR> x <- $foo\n\nR> x\n[1] 1","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"The R REPL mode supports variable substitution of Julia objects via the $ symbol. It is also possible to pass Julia expressions in the REPL mode.","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"R> x = $(rand(10))\n\nR> sum(x)\n[1] 5.097083","category":"page"},{"location":"gettingstarted/#@rput-and-@rget-macros","page":"Getting Started","title":"@rput and @rget macros","text":"","category":"section"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"These macros transfer variables between R and Julia environments. The copied variable will have the same name as the original.","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"julia> z = 1\n1\n\njulia> @rput z\n1\n\nR> z\n[1] 1\n\nR> r = 2\n\njulia> @rget r\n2.0\n\njulia> r\n2.0","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"It is also possible to put and get multiple variables in one line.","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"julia> foo = 2\n2\n\njulia> bar = 4\n4\n\njulia> @rput foo bar\n4\n\nR> foo + bar\n[1] 6","category":"page"},{"location":"gettingstarted/#@R_str-string-macro","page":"Getting Started","title":"@R_str string macro","text":"","category":"section"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"Another way to use RCall is the R\"\" string macro, it is especially useful in script files.","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"R\"rnorm(10)\"","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"This evaluates the expression inside the string in R, and returns the result as an RObject, which is a Julia wrapper type around an R object.","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"The R\"\" string macro supports variable substitution of Julia objects via the $ symbol, whenever it is not valid R syntax (i.e. when not directly following a symbol or completed expression such as aa$bb):","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"x = randn(10)\nR\"t.test($x)\"","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"It is also possible to pass Julia expressions which are evaluated before being passed to R: these should be included in parentheses","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"R\"optim(0, $(x -> x-cos(x)), method='BFGS')\"","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"A large chunk of code could be quoted between triple string quotations","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"y = 1\nR\"\"\"\nf <- function(x, y) x + y\nret <- f(1, $y)\n\"\"\"","category":"page"},{"location":"gettingstarted/#RCall-API","page":"Getting Started","title":"RCall API","text":"","category":"section"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"The reval function evaluates any given input string as R code in the R environment. The returned result is an RObject object.","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"jmtcars = reval(\"mtcars\");\nnames(jmtcars)\njmtcars[:mpg]\ntypeof(jmtcars)","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"The rcall function is used to construct function calls.","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"rcall(:dim, jmtcars)","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"The arguments will be implicitly converted to RObject upon evaluation.","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"rcall(:sum, Float64[1.0, 4.0, 6.0])","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"The rcopy function converts RObjects to Julia objects. It uses a variety of heuristics to pick the most appropriate Julia type:","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"rcopy(R\"c(1)\")\nrcopy(R\"c(1, 2)\")\nrcopy(R\"list(1, 'zz')\")\nrcopy(R\"list(a = 1, b= 'zz')\")","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"It is possible to force a specific conversion by passing the output type as the first argument:","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"rcopy(Array{Int}, R\"c(1, 2)\")","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"Converter could also be used specifically to yield the desired type.","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"convert(Array{Float64}, R\"c(1, 2)\")","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"The robject function converts any julia object to an RObject.","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"robject(1)\nrobject(Dict(:a => 1, :b = 2))","category":"page"},{"location":"gettingstarted/#@rlibrary-and-@rimport-macros","page":"Getting Started","title":"@rlibrary and @rimport macros","text":"","category":"section"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"This macro loads all exported functions/objects of an R package to the current module.","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"@rlibrary boot\ncity = rcopy(R\"boot::city\") # get some data\nratio(d, w) = sum(d[!, :x] .* w)/sum(d[!, :u] .* w)\nb = boot(city, ratio, R = 100, stype = \"w\");\nrcall(:summary, b[:t])","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"Of course, it is highly inefficient, because the data are copying multiple times between R and Julia. The R\"\" string macro is more recommended for efficiency.","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"Some R functions may have keyword arguments which contain dots. RCall provides a string macro to escape those keywords, e.g,","category":"page"},{"location":"gettingstarted/","page":"Getting Started","title":"Getting Started","text":"@rimport base as rbase\nrbase.sum([1, 2, 3], var\"rm.na\" = true)","category":"page"},{"location":"known-issues/#Installing-packages-via-Conda","page":"Known issues","title":"Installing packages via Conda","text":"","category":"section"},{"location":"known-issues/","page":"Known issues","title":"Known issues","text":"When using the Conda environment, installing packages via install.packages or devtools will result in installation failures such as \"x86_64-conda-linux-gnu-cc: not found\". Instead, use Conda to install packages. For example, Conda.add(\"r-ggplot2\").","category":"page"},{"location":"custom/#Custom-Conversion","page":"Custom Conversion","title":"Custom Conversion","text":"","category":"section"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"RCall supports an API for implicitly converting between R and Julia objects by means of rcopy and robject.","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"To illustrate the idea, we consider the following Julia type","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"using RCall","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"mutable struct Foo\n x::Float64\n y::String\nend","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"foo = Foo(1.0, \"hello\") \nbar = R\"\"\"\n bar <- list(x = 1, y = \"hello\")\n class(bar) <- \"Bar\"\n bar\n\"\"\"\nnothing # hide","category":"page"},{"location":"custom/#R-to-Julia-direction","page":"Custom Conversion","title":"R to Julia direction","text":"","category":"section"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"The function rcopy and rcopytype are responsible for conversions of this direction. First we define an explicit converter for VecSxp (SEXP for list)","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"import RCall.rcopy\n\nfunction rcopy(::Type{Foo}, s::Ptr{VecSxp})\n Foo(rcopy(Float64, s[:x]), rcopy(String, s[:y]))\nend","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"The convert function will dispatch the corresponding rcopy function when it is found.","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"rcopy(Foo, bar)\nconvert(Foo, bar) # calls `rcopy`\nnothing # hide","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"To allow the automatic conversion via rcopy(bar), the R class Bar has to be registered.","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"import RCall: RClass, rcopytype\n\nrcopytype(::Type{RClass{:Bar}}, s::Ptr{VecSxp}) = Foo\nfoo2 = rcopy(bar)\nnothing # hide","category":"page"},{"location":"custom/#Julia-to-R-direction","page":"Custom Conversion","title":"Julia to R direction","text":"","category":"section"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"The function RCall.sexp has to be overwritten to allow Julia to R conversion. sexp function takes a julia object and returns an SEXP object (pointer to [Sxp]).","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"First we define an explicit converter from Julia type Foo to R class Bar","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"import RCall: sexp, protect, unprotect, setclass!, RClass\n\nfunction sexp(::Type{RClass{:Bar}}, f::Foo)\n r = protect(sexp(Dict(:x => f.x, :y => f.y)))\n setclass!(r, sexp(\"Bar\"))\n unprotect(1)\n r\nend\n\nbar = robject(:Bar, foo)\nnothing # hide","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"Remark: RCall.protect and RCall.unprotect should be used to protect SEXP from being garbage collected.","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"To register the default conversion via robject(foo), we need to define sexpclass","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"import RCall.sexpclass\n\nsexpclass(f::Foo) = RClass{:Bar}\nbar = robject(foo)\nnothing # hide","category":"page"},{"location":"custom/#Using-@rput-and-@rget-is-seamless","page":"Custom Conversion","title":"Using @rput and @rget is seamless","text":"","category":"section"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"foo2.x = 2.0\n@rput foo2\nR\"\"\"\nfoo2[\"x\"]\n\"\"\"","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"R\"\"\"\nfoo2[\"x\"] = 3.0\n\"\"\"\n@rget foo2\nfoo2.x","category":"page"},{"location":"custom/#Nested-conversion","page":"Custom Conversion","title":"Nested conversion","text":"","category":"section"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"l = R\"list(foo2 = foo2, bar = $bar)\"","category":"page"},{"location":"custom/","page":"Custom Conversion","title":"Custom Conversion","text":"rcopy(l)","category":"page"},{"location":"eventloop/#Eventloop","page":"Eventloop","title":"Eventloop","text":"","category":"section"},{"location":"eventloop/","page":"Eventloop","title":"Eventloop","text":"In a non-IJulia interactive session, by R will by default open a new window to display the plot. In order to enable interactive features, such as plot-resizing, the R eventlopp will be started automatically.","category":"page"},{"location":"eventloop/","page":"Eventloop","title":"Eventloop","text":"You could start manually the R event loop via","category":"page"},{"location":"eventloop/","page":"Eventloop","title":"Eventloop","text":"RCall.rgui_start()","category":"page"},{"location":"eventloop/","page":"Eventloop","title":"Eventloop","text":"This runs frequent calls to R to check if the plot has changed, and redraw if necessary. It can be stopped with","category":"page"},{"location":"eventloop/","page":"Eventloop","title":"Eventloop","text":"RCall.rgui_stop()","category":"page"},{"location":"installation/#Installing-RCall.jl","page":"Installation","title":"Installing RCall.jl","text":"","category":"section"},{"location":"installation/","page":"Installation","title":"Installation","text":"RCall.jl can simply be installed with","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"Pkg.add(\"RCall\")","category":"page"},{"location":"installation/#Customizing-the-R-installation","page":"Installation","title":"Customizing the R installation","text":"","category":"section"},{"location":"installation/","page":"Installation","title":"Installation","text":"The RCall build script (run by Pkg.add) will check for an existing R installation by looking in the following locations, in order.","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"The R_HOME environment variable, if set, should be the location of the R home directory. You could run R.home() in R to determine its location.\nOtherwise, it runs the R RHOME command, assuming R is located in your PATH.\nOtherwise, on Windows, it looks in the Windows registry.","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"To change which R installation is used for RCall, set the R_HOME environment variable and run Pkg.build(\"RCall\"). Once this is configured, RCall remembers the location of R in future updates, so you don't need to set R_HOME permanently.","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"ENV[\"R_HOME\"] = \"....directory of R home....\"\nPkg.build(\"RCall\")","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"When R_HOME is set to \"*\", RCall.jl will automatically install R for you using Conda.","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"Should you experience problems with any of these methods, please open an issue.","category":"page"},{"location":"installation/#Standard-installations","page":"Installation","title":"Standard installations","text":"","category":"section"},{"location":"installation/","page":"Installation","title":"Installation","text":"If you want to install R yourself, rather than relying on the automatic Conda installation, you can use one of the following options:","category":"page"},{"location":"installation/#Windows","page":"Installation","title":"Windows","text":"","category":"section"},{"location":"installation/","page":"Installation","title":"Installation","text":"The current Windows binary from CRAN.","category":"page"},{"location":"installation/#OS-X","page":"Installation","title":"OS X","text":"","category":"section"},{"location":"installation/","page":"Installation","title":"Installation","text":"The CRAN .pkg or the homebrew/science tap.","category":"page"},{"location":"installation/#Linux","page":"Installation","title":"Linux","text":"","category":"section"},{"location":"installation/","page":"Installation","title":"Installation","text":"Most Linux distributions allow installation of R from their package manager, however these are often out of date, and may not work with RCall.jl. We recommend that you use the updated repositories from CRAN.","category":"page"},{"location":"installation/#Ubuntu","page":"Installation","title":"Ubuntu","text":"","category":"section"},{"location":"installation/","page":"Installation","title":"Installation","text":"The following will update R on recent versions of Ubuntu:","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9\nsudo add-apt-repository -y \"deb http://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -s -c)-cran40/\"\nsudo apt-get update -y\nsudo apt-get install -y r-base r-base-dev","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"See also the official documentation on CRAN: Ubuntu Packages For R.","category":"page"},{"location":"installation/#Julia-1.5:-Failure-on-recent-Linux-distributions","page":"Installation","title":"Julia ≤ 1.5: Failure on recent Linux distributions","text":"","category":"section"},{"location":"installation/","page":"Installation","title":"Installation","text":"The version of libstdc++ shipped by Julia might be outdated if you are using a recent Linux distribution (e.g. Ubuntu 19.10) and make use of certain R packages (e.g. Rcpp). In this case RCall will fail with an error message looking similar to this:","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"Error: package or namespace load failed for ‘package’ in dyn.load(file, DLLpath = DLLpath, ...):\nunable to load shared object '/home/user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/libs/Rcpp.so':\n/home/user/julia-1.3.1/bin/../lib/julia/libstdc++.so.6: version `GLIBCXX_3.4.26' not found \n(required by /home/user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/libs/Rcpp.so)","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"Until this issue is fixed in Julia (see https://github.com/JuliaLang/julia/issues/34276) a workaround is to replace Julias libstdc++ with the one of your OS:","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"# works for Ubuntu 19.10 64bit - match your locations accordingly!\ncp /usr/lib/x86_64-linux-gnu/libstdc++.so.6 $JULIA_HOME/lib/julia/","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"This problem doesn't affect Julia ≥ 1.6!","category":"page"},{"location":"installation/#Other-methods","page":"Installation","title":"Other methods","text":"","category":"section"},{"location":"installation/","page":"Installation","title":"Installation","text":"If you have installed R by some other method (e.g. building from scratch, or files copied but not installed in the usual manner), which often happens on cluster installations, then you may need to set R_HOME or your PATH as described above before running Pkg.build(\"RCall\") in order for the build script to find your R installation. RCall requires R to be installed with its shared library. It could be done with the flag --enable-R-shlib, consult your server administrator to see if it was the case.","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"For some environments, you might also need to specify LD_LIBRARY_PATH","category":"page"},{"location":"installation/","page":"Installation","title":"Installation","text":"export LD_LIBRARY_PATH=\"$LD_LIBRARY_PATH:`R RHOME`/lib\"","category":"page"},{"location":"installation/#Updating-R","page":"Installation","title":"Updating R","text":"","category":"section"},{"location":"installation/","page":"Installation","title":"Installation","text":"If you have updated your R installation, you may need to re-run Pkg.build(\"RCall\") as described above, possibly changing the R_HOME environment variable first.","category":"page"},{"location":"conversions/#Supported-Conversions","page":"Supported Conversions","title":"Supported Conversions","text":"","category":"section"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"RCall supports conversions to and from most base Julia types and popular Statistics packages, e.g., DataFrames, CategoricalArrays and AxisArrays.","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"using Pkg\nPkg.add(\"DataFrames\")\nPkg.add(\"AxisArrays\")\n\nusing RCall\nusing Dates\nusing DataFrames\nusing AxisArrays","category":"page"},{"location":"conversions/#Base-Julia-Types","page":"Supported Conversions","title":"Base Julia Types","text":"","category":"section"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# Julia -> R\na = robject(1)","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# R -> Julia\nrcopy(a)","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# Julia -> R\na = robject([1.0, 2.0])","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# R -> Julia\nrcopy(a)","category":"page"},{"location":"conversions/#Dictionaries","page":"Supported Conversions","title":"Dictionaries","text":"","category":"section"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# Julia -> R\nd = Dict(:a => 1, :b => [4, 5, 3])\nr = robject(d)","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# R -> Julia\nrcopy(r)","category":"page"},{"location":"conversions/#Date","page":"Supported Conversions","title":"Date","text":"","category":"section"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# Julia -> R\nd = Date(2012, 12, 12)\nr = robject(d)","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# R -> Julia\nrcopy(r)","category":"page"},{"location":"conversions/#DateTime","page":"Supported Conversions","title":"DateTime","text":"","category":"section"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# julia -> R\nd = DateTime(2012, 12, 12, 12, 12, 12)\nr = robject(d)","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# R -> Julia\nrcopy(r)","category":"page"},{"location":"conversions/#DataFrames","page":"Supported Conversions","title":"DataFrames","text":"","category":"section"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"d = DataFrame([[1.0, 4.5, 7.0]], [:x])\n# Julia -> R\nr = robject(d)","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# R -> Julia\nrcopy(r)","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"In default, the column names of R data frames are normalized such that foo.bar would be replaced by foo_bar.","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"rcopy(R\"data.frame(a.b = 1:3)\")","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"To avoid the normalization, use normalizenames option.","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"rcopy(R\"data.frame(a.b = 1:10)\"; normalizenames = false)","category":"page"},{"location":"conversions/#AxisArrays","page":"Supported Conversions","title":"AxisArrays","text":"","category":"section"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# Julia -> R\naa = AxisArray([1,2,3], Axis{:id}([\"a\", \"b\", \"c\"]))\nr = robject(aa)","category":"page"},{"location":"conversions/","page":"Supported Conversions","title":"Supported Conversions","text":"# R -> Julia\nrcopy(AxisArray, r)","category":"page"},{"location":"#RCall.jl","page":"Introduction","title":"RCall.jl","text":"","category":"section"},{"location":"","page":"Introduction","title":"Introduction","text":"R is a language for statistical computing and graphics that has been around for couple of decades and it has one of the most impressive collections of scientific and statistical packages of any environment. Recently, the Julia language has become an attractive alternative because it provides the remarkable performance of a low-level language without sacrificing the readability and ease-of-use of high-level languages. However, Julia still lacks the depth and scale of the R package environment.","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"This package, RCall, facilitates communication between these two languages and allows the user to call R packages from within Julia, providing the best of both worlds. Additionally, this is a pure Julia package so it is portable and easy to use.","category":"page"},{"location":"internal/#Internal-API","page":"Internal","title":"Internal API","text":"","category":"section"},{"location":"internal/#Types","page":"Internal","title":"Types","text":"","category":"section"},{"location":"internal/","page":"Internal","title":"Internal","text":"Modules = [RCall]\nOrder = [:type]","category":"page"},{"location":"internal/#RCall.AnySxp","page":"Internal","title":"RCall.AnySxp","text":"R \"any\" object\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.BcodeSxp","page":"Internal","title":"RCall.BcodeSxp","text":"R byte code\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.BuiltinSxp","page":"Internal","title":"RCall.BuiltinSxp","text":"R built-in function\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.CharSxp","page":"Internal","title":"RCall.CharSxp","text":"R character string\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.ClosSxp","page":"Internal","title":"RCall.ClosSxp","text":"R function closure\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.CplxSxp","page":"Internal","title":"RCall.CplxSxp","text":"R complex vector\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.DotSxp","page":"Internal","title":"RCall.DotSxp","text":"R dot-dot-dot object\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.EnvSxp","page":"Internal","title":"RCall.EnvSxp","text":"R environment\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.ExprSxp","page":"Internal","title":"RCall.ExprSxp","text":"R expression vector\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.ExtPtrSxp","page":"Internal","title":"RCall.ExtPtrSxp","text":"R external pointer\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.IntSxp","page":"Internal","title":"RCall.IntSxp","text":"R integer vector\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.LangSxp","page":"Internal","title":"RCall.LangSxp","text":"R function call\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.LglSxp","page":"Internal","title":"RCall.LglSxp","text":"R logical vector\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.ListSxp","page":"Internal","title":"RCall.ListSxp","text":"R pairs (cons) list cell\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.NilSxp","page":"Internal","title":"RCall.NilSxp","text":"R NULL value\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.PromSxp","page":"Internal","title":"RCall.PromSxp","text":"R promise\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.RClass","page":"Internal","title":"RCall.RClass","text":"R Class\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.RObject","page":"Internal","title":"RCall.RObject","text":"An RObject is a Julia wrapper for an R object (known as an \"S-expression\" or \"SEXP\"). It is stored as a pointer which is protected from the R garbage collector, until the RObject itself is finalized by Julia. The parameter is the type of the S-expression.\n\nWhen called with a Julia object as an argument, a corresponding R object is constructed.\n\njulia> RObject(1)\nRObject{IntSxp}\n[1] 1\n\njulia> RObject(1:3)\nRObject{IntSxp}\n[1] 1 2 3\n\njulia> RObject(1.0:3.0)\nRObject{RealSxp}\n[1] 1 2 3\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.RawSxp","page":"Internal","title":"RCall.RawSxp","text":"R byte vector\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.RealSxp","page":"Internal","title":"RCall.RealSxp","text":"R real vector\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.S4Sxp","page":"Internal","title":"RCall.S4Sxp","text":"R S4 object\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.SpecialSxp","page":"Internal","title":"RCall.SpecialSxp","text":"R special function\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.StrSxp","page":"Internal","title":"RCall.StrSxp","text":"R vector of character strings\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.Sxp","page":"Internal","title":"RCall.Sxp","text":"RCall.jl's type Sxp mirrors the R symbolic expression record SEXPREC in R API. These are represented by a pointer Ptr{S<:Sxp} (which is called SEXP in R API).\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.SxpHead","page":"Internal","title":"RCall.SxpHead","text":"R Sxp header: a pointer to this is used for unknown types.\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.SymSxp","page":"Internal","title":"RCall.SymSxp","text":"R symbol\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.VecSxp","page":"Internal","title":"RCall.VecSxp","text":"R list (i.e. Array{Any,1})\n\n\n\n\n\n","category":"type"},{"location":"internal/#RCall.WeakRefSxp","page":"Internal","title":"RCall.WeakRefSxp","text":"R weak reference\n\n\n\n\n\n","category":"type"},{"location":"internal/#Methods","page":"Internal","title":"Methods","text":"","category":"section"},{"location":"internal/","page":"Internal","title":"Internal","text":"Modules = [RCall]\nOrder = [:function]","category":"page"},{"location":"internal/#Base.eltype-Tuple{Type{LglSxp}}","page":"Internal","title":"Base.eltype","text":"Element types of R vectors.\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.getindex-Tuple{Ptr{EnvSxp}, Ptr{RCall.SymSxp}}","page":"Internal","title":"Base.getindex","text":"extract the value of symbol s in the environment e\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.getindex-Tuple{Ptr{S4Sxp}, Ptr{RCall.SymSxp}}","page":"Internal","title":"Base.getindex","text":"extract an element from a S4Sxp by label\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.getindex-Union{Tuple{S}, Tuple{Ptr{S}, AbstractString}} where S<:RCall.PairListSxp","page":"Internal","title":"Base.getindex","text":"extract an element from a PairListSxp by label\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.getindex-Union{Tuple{S}, Tuple{Ptr{S}, AbstractString}} where S<:RCall.VectorSxp","page":"Internal","title":"Base.getindex","text":"Set element of a VectorSxp by a label.\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.getindex-Union{Tuple{S}, Tuple{Ptr{S}, Integer}} where S<:RCall.PairListSxp","page":"Internal","title":"Base.getindex","text":"extract the i-th element of a PairListSxp\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.isascii-Tuple{CharSxp}","page":"Internal","title":"Base.isascii","text":"Determines the encoding of the CharSxp. This is determined by the 'gp' part of the sxpinfo (this is the middle 16 bits).\n\n0x00000200 (bit 1): set of bytes (no known encoding)\n0x00000400 (bit 2): Latin-1\n0x00000800 (bit 3): UTF-8\n0x00004000 (bit 6): ASCII\n\nWe only support ASCII and UTF-8.\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.length-Union{Tuple{Ptr{S}}, Tuple{S}} where S<:Sxp","page":"Internal","title":"Base.length","text":"Sxp methods for length return the R length.\n\nRf_xlength handles Sxps that are not vector-like and R's \"long vectors\", which have a negative value for the length member.\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.names-Tuple{RObject}","page":"Internal","title":"Base.names","text":"Returns the names of an R vector, the result is converted to a Julia symbol array.\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.setindex!-Union{Tuple{S}, Tuple{Ptr{EnvSxp}, Ptr{S}, Ptr{StrSxp}}} where S<:Sxp","page":"Internal","title":"Base.setindex!","text":"assign value v to symbol s in the environment e\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.setindex!-Union{Tuple{T}, Tuple{Ptr{S4Sxp}, Ptr{T}, Ptr{RCall.SymSxp}}} where T<:Sxp","page":"Internal","title":"Base.setindex!","text":"extract an element from a S4Sxp by label\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.setindex!-Union{Tuple{T}, Tuple{S}, Tuple{Ptr{S}, Ptr{T}, AbstractString}} where {S<:RCall.PairListSxp, T<:Sxp}","page":"Internal","title":"Base.setindex!","text":"Set element of a PairListSxp by a label.\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.setindex!-Union{Tuple{T}, Tuple{S}, Tuple{Ptr{S}, Ptr{T}, AbstractString}} where {S<:RCall.VectorSxp, T<:Sxp}","page":"Internal","title":"Base.setindex!","text":"Set element of a VectorSxp by a label.\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.setindex!-Union{Tuple{T}, Tuple{S}, Tuple{Ptr{S}, Ptr{T}, Integer}} where {S<:RCall.PairListSxp, T<:Sxp}","page":"Internal","title":"Base.setindex!","text":"assign value v to the i-th element of a PairListSxp\n\n\n\n\n\n","category":"method"},{"location":"internal/#Base.size-Union{Tuple{Ptr{S}}, Tuple{S}} where S<:Sxp","page":"Internal","title":"Base.size","text":"Returns the size of an R object.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.anyna-Union{Tuple{RObject{S}}, Tuple{S}} where S<:RCall.VectorSxp","page":"Internal","title":"RCall.anyna","text":"Check if there are any NA values in the vector.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.bound-Union{Tuple{Ptr{S}}, Tuple{S}} where S<:Sxp","page":"Internal","title":"RCall.bound","text":"The R NAMED property, represented by 2 bits in the info field. This can take values 0,1 or 2, corresponding to whether it is bound to 0,1 or 2 or more symbols. See http://cran.r-project.org/doc/manuals/r-patched/R-exts.html#Named-objects-and-copying\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.decref_extptr-Tuple{Ptr{RCall.ExtPtrSxp}}","page":"Internal","title":"RCall.decref_extptr","text":"Called by the R finalizer.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.endEmbeddedR-Tuple{}","page":"Internal","title":"RCall.endEmbeddedR","text":"endEmbeddedR()\n\nClose embedded R session.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.findNamespace-Tuple{String}","page":"Internal","title":"RCall.findNamespace","text":"find namespace by name of the namespace, it is not error tolerant.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.getNamespace-Tuple{String}","page":"Internal","title":"RCall.getNamespace","text":"get namespace by name of the namespace. It is safer to be used than findNamespace as it checks bound.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.getParseErrorMsg-Tuple{}","page":"Internal","title":"RCall.getParseErrorMsg","text":"Get the R parser error msg for the previous parsing result.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.getattrib-Union{Tuple{S}, Tuple{Ptr{S}, Ptr{RCall.SymSxp}}} where S<:Sxp","page":"Internal","title":"RCall.getattrib","text":"Return a particular attribute of an RObject\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.getclass-Union{Tuple{Ptr{S}}, Tuple{S}, Tuple{Ptr{S}, Bool}} where S<:Sxp","page":"Internal","title":"RCall.getclass","text":"Returns the class of an R object.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.getnames-Union{Tuple{Ptr{S}}, Tuple{S}} where S<:Sxp","page":"Internal","title":"RCall.getnames","text":"Returns the names of an R vector.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.ijulia_displayplots-Tuple{}","page":"Internal","title":"RCall.ijulia_displayplots","text":"Called after cell evaluation. Closes graphics device and displays files in notebook.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.ijulia_setdevice-Tuple{MIME}","page":"Internal","title":"RCall.ijulia_setdevice","text":"Set options for R plotting with IJulia.\n\nThe first argument should be a MIME object: currently supported are\n\nMIME(\"image/png\") [default]\nMIME(\"image/svg+xml\")\n\nThe remaining arguments (keyword only) are passed to the appropriate R graphics device: see the relevant R help for details.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.initEmbeddedR-Tuple{}","page":"Internal","title":"RCall.initEmbeddedR","text":"initEmbeddedR()\n\nThis initializes an embedded R session. It should only be called when R is not already running (e.g. if Julia is running inside an R session)\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.isNA-Tuple{ComplexF64}","page":"Internal","title":"RCall.isNA","text":"Check if a value corresponds to R's sentinel NA values. These function should not be exported.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.isna-Tuple{RObject, Integer}","page":"Internal","title":"RCall.isna","text":"Check if the ith member of s correspond to R's NA values.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.isna-Tuple{RObject}","page":"Internal","title":"RCall.isna","text":"Check if the members of a vector are NA values. Always return a BitArray.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.isnull-Tuple{RObject}","page":"Internal","title":"RCall.isnull","text":"Check if values correspond to R's NULL object.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.julia_extptr_callback-Tuple{Ptr{ListSxp}}","page":"Internal","title":"RCall.julia_extptr_callback","text":"The function called by R .External for Julia callbacks.\n\nIt receives a Ptr{ListSxp} containing\n\na pointer to the function itself (Ptr{ExtPtrSxp})\na pointer to the Julia function (Ptr{ExtPtrSxp})\nany arguments (as Ptr{S<:Sxp})\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.makeExternalPtr","page":"Internal","title":"RCall.makeExternalPtr","text":"Create an Ptr{ExtPtrSxp} object\n\n\n\n\n\n","category":"function"},{"location":"internal/#RCall.makeNativeSymbolRef-Tuple{Ptr{Nothing}}","page":"Internal","title":"RCall.makeNativeSymbolRef","text":"Register a function pointer as an R NativeSymbol. We technically are supposed to use RregisterRoutines. Starting from R 3.4, `RMakeExternalPtrFn` is a part of R API in R 3.4. It is probably safe to such to make the external pointer.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.naeltype-Tuple{Type{LglSxp}}","page":"Internal","title":"RCall.naeltype","text":"NA element for each R base class\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.newEnvironment-Tuple{Ptr{EnvSxp}}","page":"Internal","title":"RCall.newEnvironment","text":"newEnvironment([env])\n\nCreate a new environment which extends environment env (globalEnv by default).\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.parseVector-Union{Tuple{S}, Tuple{Ptr{StrSxp}, Ref{Int32}}, Tuple{Ptr{StrSxp}, Ref{Int32}, Ptr{S}}} where S<:Sxp","page":"Internal","title":"RCall.parseVector","text":"A pure julia wrapper of R_ParseVector\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.polled_events-Tuple{}","page":"Internal","title":"RCall.polled_events","text":"polled_events()::Cvoid\n\nEvent Callback: allows R to process Julia events when R is busy. For example, writing output to stdout while running an expensive R command.\n\nSee Writing R Extensions: Calling R.dll directly and Writing R Extensions: Meshing Event Loops\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.prepare_inline_julia_code","page":"Internal","title":"RCall.prepare_inline_julia_code","text":"Prepare code for evaluating the julia expressions. When the code is evaluated, the results are stored in the R environment #JL.\n\n\n\n\n\n","category":"function"},{"location":"internal/#RCall.preserve-Union{Tuple{Ptr{S}}, Tuple{S}} where S<:Sxp","page":"Internal","title":"RCall.preserve","text":"Prevent garbage collection of an R object. Object can be released via release.\n\nThis is slower than protect, as it requires searching an internal list, but more flexible.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.protect-Union{Tuple{Ptr{S}}, Tuple{S}} where S<:Sxp","page":"Internal","title":"RCall.protect","text":"Stack-based protection of garbage collection of R objects. Objects are released via unprotect. Returns the same pointer, allowing inline use.\n\nThis is faster than preserve, but more restrictive. Really only useful inside functions.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.rcall-Tuple{Any, Vararg{Any}}","page":"Internal","title":"RCall.rcall","text":"Evaluate a function in the global environment. The first argument corresponds to the function to be called. It can be either a FunctionSxp type, a SymSxp or a Symbol.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.rcall_p-Tuple{Any, Vararg{Any}}","page":"Internal","title":"RCall.rcall_p","text":"Evaluate a function in the global environment. The first argument corresponds to the function to be called. It can be either a FunctionSxp type, a SymSxp or a Symbol.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.rcopy-Union{Tuple{RObject{S}}, Tuple{S}} where S<:Sxp","page":"Internal","title":"RCall.rcopy","text":"rcopy(r) copies the contents of an R object into a corresponding canonical Julia type.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.read_console-Tuple{Cstring, Ptr{UInt8}, Int32, Int32}","page":"Internal","title":"RCall.read_console","text":"read_console\n\nR_ReadConsole API callback to read input.\n\nSee Writing R extensions: Setting R callbacks\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.registerCFinalizerEx-Tuple{Ptr{RCall.ExtPtrSxp}}","page":"Internal","title":"RCall.registerCFinalizerEx","text":"Register finalizer to be called by the R GC.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.release-Union{Tuple{Ptr{S}}, Tuple{S}} where S<:Sxp","page":"Internal","title":"RCall.release","text":"Release object that has been gc protected by preserve.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.render-Tuple{String}","page":"Internal","title":"RCall.render","text":"Render an inline R script, substituting invalid \"$(Expr(:incomplete, \"incomplete: invalid string syntax\"))\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.reval","page":"Internal","title":"RCall.reval","text":"Evaluate an R symbol or language object (i.e. a function call) in an R try/catch block, returning an RObject.\n\n\n\n\n\n","category":"function"},{"location":"internal/#RCall.reval_p-Tuple{Ptr{RCall.ExprSxp}, Ptr{EnvSxp}}","page":"Internal","title":"RCall.reval_p","text":"Evaluate an R expression array iteratively. If throw_error is false, the error message and warning will be thrown to stderr.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.reval_p-Union{Tuple{Ptr{S}}, Tuple{S}, Tuple{Ptr{S}, Ptr{EnvSxp}}} where S<:Sxp","page":"Internal","title":"RCall.reval_p","text":"Evaluate an R symbol or language object (i.e. a function call) in an R try/catch block, returning a Sxp pointer.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.rimport","page":"Internal","title":"RCall.rimport","text":"Import an R package as a julia module. Sanitizes the imported symbols by default, because otherwise certain symbols cannot be used.\n\nE.g.: PerformanceAnalytics::charts.Bar in R becomes PerformanceAnalytics.charts_Bar in Julia\n\ngg = rimport(\"ggplot2\")\n\n\n\n\n\n","category":"function"},{"location":"internal/#RCall.rlang-Tuple{Any, Vararg{Any}}","page":"Internal","title":"RCall.rlang","text":"Create a function call from a function pointer and a list of arguments and return it as an RObject, which can then be evaluated\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.rlang_p-Tuple{Any, Vararg{Any}}","page":"Internal","title":"RCall.rlang_p","text":"Create a function call from a list of arguments\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.robject-Tuple{Any}","page":"Internal","title":"RCall.robject","text":"robject(x) converts a Julia object x to a corresponding RObject implicitly. Explicit conversions could be called with robject(, x).\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.rparse-Tuple{AbstractString}","page":"Internal","title":"RCall.rparse","text":"Parse a string as an R expression, returning an RObject.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.rparse_p-Union{Tuple{Ptr{StrSxp}}, Tuple{S}, Tuple{Ptr{StrSxp}, Ptr{S}}} where S<:Sxp","page":"Internal","title":"RCall.rparse_p","text":"Parse a string as an R expression, returning a Sxp pointer.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.rprint-Union{Tuple{S}, Tuple{IO, Ptr{S}}} where S<:Sxp","page":"Internal","title":"RCall.rprint","text":"Print the value of an Sxp using R's printing mechanism\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.safe_parseVector-Union{Tuple{S}, Tuple{Ptr{StrSxp}, Ref{Int32}}, Tuple{Ptr{StrSxp}, Ref{Int32}, Ptr{S}}} where S<:Sxp","page":"Internal","title":"RCall.safe_parseVector","text":"RParseVector wrapped by RtryCatchError. It catches possible R's stop calls which may cause longjmp in C.\n\nSee Writing R Extensions: Condition handling and cleanup code\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.set_last_value-Union{Tuple{Ptr{S}}, Tuple{S}} where S<:Sxp","page":"Internal","title":"RCall.set_last_value","text":"Set the variable .Last.value to a given value\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.setattrib!-Union{Tuple{T}, Tuple{S}, Tuple{Ptr{S}, Ptr{RCall.SymSxp}, Ptr{T}}} where {S<:Sxp, T<:Sxp}","page":"Internal","title":"RCall.setattrib!","text":"Set a particular attribute of an RObject\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.setclass!-Union{Tuple{S}, Tuple{Ptr{S}, Ptr{StrSxp}}} where S<:Sxp","page":"Internal","title":"RCall.setclass!","text":"Set the class of an R object.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.setnames!-Union{Tuple{S}, Tuple{Ptr{S}, Ptr{StrSxp}}} where S<:Sxp","page":"Internal","title":"RCall.setnames!","text":"Set the names of an R vector.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.sexp-Tuple{Any}","page":"Internal","title":"RCall.sexp","text":"sexp(x) converts a Julia object x to a pointer to a corresponding Sxp Object.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.sexp-Tuple{Ptr{RCall.SxpHead}}","page":"Internal","title":"RCall.sexp","text":"Convert a Ptr{UnknownSxp} to an appropriate Ptr{S<:Sxp}.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.sexp-Tuple{Type{RCall.RClass{:externalptr}}, Any}","page":"Internal","title":"RCall.sexp","text":"Wrap a Julia object an a R Ptr{ExtPtrSxp}.\n\nWe store the pointer and the object in a const Dict to prevent it being removed by the Julia GC.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.sexp-Tuple{Type{RCall.RClass{:function}}, Any}","page":"Internal","title":"RCall.sexp","text":"Wrap a callable Julia object f an a R ClosSxpPtr.\n\nConstructs the following R code\n\nfunction(...) .External(juliaCallback, fExPtr, ...)\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.sexp_arglist_dots-Tuple","page":"Internal","title":"RCall.sexp_arglist_dots","text":"Create an argument list for an R function call, with a varargs \"dots\" at the end.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.sexpnum-Tuple{RCall.SxpHead}","page":"Internal","title":"RCall.sexpnum","text":"The SEXPTYPE number of a Sxp\n\nDetermined from the trailing 5 bits of the first 32-bit word. Is a 0-based index into the info field of a SxpHead.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.tryEval-Union{Tuple{Ptr{S}}, Tuple{S}, Tuple{Ptr{S}, Ptr{EnvSxp}}, Tuple{Ptr{S}, Ptr{EnvSxp}, Ref{Int32}}} where S<:Sxp","page":"Internal","title":"RCall.tryEval","text":"A pure julia wrapper of R_tryEval.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.unprotect-Tuple{Integer}","page":"Internal","title":"RCall.unprotect","text":"Release last n objects gc-protected by protect.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.unsafe_array-Union{Tuple{Ptr{S}}, Tuple{S}} where S<:RCall.VectorSxp","page":"Internal","title":"RCall.unsafe_array","text":"The same as unsafe_vec, except returns an appropriately sized array.\n\n\n\n\n\n","category":"method"},{"location":"internal/#RCall.unsafe_vec-Union{Tuple{Ptr{S}}, Tuple{S}} where S<:RCall.VectorSxp","page":"Internal","title":"RCall.unsafe_vec","text":"Represent the contents of a VectorSxp type as a Vector.\n\nThis does not copy the contents. If the argument is not named (in R) or otherwise protected from R's garbage collection (e.g. by keeping the containing RObject in scope) the contents of this vector can be modified or could cause a memory error when accessed.\n\nThe contents are as stored in R. Missing values (NA's) are represented in R by sentinels. Missing data values in RealSxp and CplxSxp show up as NaN and NaN + NaNim, respectively. Missing data in IntSxp show up as -2147483648, the minimum 32-bit integer value. Internally a LglSxp is represented as Vector{Int32}. 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For example,\n\n@rimport ggplot2\n\nis equivalent to ggplot2 = rimport(\"ggplot2\") with error checking.\n\nYou can also use classic Python syntax to make an alias: @rimport *package-name* as *shorthand*\n\n@rimport ggplot2 as gg\n\nwhich is equivalent to gg = rimport(\"ggplot2\").\n\n\n\n\n\n","category":"macro"},{"location":"internal/#RCall.@rlibrary-Tuple{Any}","page":"Internal","title":"RCall.@rlibrary","text":"Load all exported functions/objects of an R package to the current module. Almost equivalent to\n\n__temp__ = rimport(\"ggplot2\")\nusing .__temp__\n\n\n\n\n\n","category":"macro"},{"location":"internal/#RCall.@rput-Tuple","page":"Internal","title":"RCall.@rput","text":"Copies variables from Julia to R using the same name.\n\n\n\n\n\n","category":"macro"},{"location":"internal/#RCall.@var_str-Tuple{Any}","page":"Internal","title":"RCall.@var_str","text":"Returns a variable named \"str\". Useful for passing keyword arguments containing dots.\n\n\n\n\n\n","category":"macro"},{"location":"internal/#Constants","page":"Internal","title":"Constants","text":"","category":"section"},{"location":"internal/","page":"Internal","title":"Internal","text":"Modules = [RCall]\nOrder = [:constant]","category":"page"},{"location":"internal/#RCall.globalEnv","page":"Internal","title":"RCall.globalEnv","text":"R global Environment.\n\nglobalEnv[:x] = 1\nglobalEnv[:x]\n\n\n\n\n\n","category":"constant"},{"location":"internal/#RCall.jtypExtPtrs","page":"Internal","title":"RCall.jtypExtPtrs","text":"Julia types (typically functions) which are wrapped in Ptr{ExtPtrSxp} are stored here to prevent garbage collection by Julia.\n\n\n\n\n\n","category":"constant"},{"location":"internal/#RCall.typs","page":"Internal","title":"RCall.typs","text":"vector of R Sxp types\n\n\n\n\n\n","category":"constant"}] +} diff --git a/v0.13.16/siteinfo.js b/v0.13.16/siteinfo.js new file mode 100644 index 00000000..69479035 --- /dev/null +++ b/v0.13.16/siteinfo.js @@ -0,0 +1 @@ +var DOCUMENTER_CURRENT_VERSION = "v0.13.16"; diff --git a/versions.js b/versions.js index 9f4b4f1c..b4176cb2 100644 --- a/versions.js +++ b/versions.js @@ -12,5 +12,5 @@ var DOC_VERSIONS = [ "v0.4", "dev", ]; -var DOCUMENTER_NEWEST = "v0.13.15"; +var DOCUMENTER_NEWEST = "v0.13.16"; var DOCUMENTER_STABLE = "stable";