Update website pages

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dsmextra
 Title: A Toolkit for Extrapolation Assessments in Density Surface Models
-Version: 1.1.3
+Version: 1.1.4
 Authors@R: c(person("Phil", "Bouchet", email = "pjbouchet@gmail.com", role = c("aut", "cre")), person("David", "Miller", email = "dlm22@st-andrews.ac.uk", role = c("aut")), person("Laura", "Mannocci", email = "laura.mannocci@duke.edu", role = c("aut")), person("Jason", "Roberts", email = "jason.roberts@duke.edu", role = c("aut")), person("Catriona", "Harris", email = "Catriona.Harris@st-andrews.ac.uk", role = c("aut")), person("Len", "Thomas", email = "len.thomas@st-andrews.ac.uk", role = c("aut")))
 Description: User-friendly tools for the detection and assessment of extrapolation in multivariate environmental space (Bouchet et al. 2019), with applications to density surface models of line transect data. Provides convenience functions for summarising and visualising extrapolation in prediction areas.
 License: GPL-3 + file LICENSE

R/zzz.R

@@ -1,6 +1,6 @@
 .onAttach <- function(libname, pkgname) {
   packageStartupMessage("-----------------------------------------------\n",
-                        "dsmextra: version 1.1.3:\n",
+                        "dsmextra: version 1.1.4:\n",
                         "-----------------------------------------------\n",
                         "* Please cite as:\nBouchet PJ, Miller DL, Roberts JJ, Mannocci L, Harris CM, Thomas L (2020). dsmextra: Extrapolation assessment tools for density surface models. Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.13469\n",
                         "\n* Quick start guide:\nA vignette is available at:\nhttps://densitymodelling.github.io/dsmextra/\n",

docs/articles/dsmextra-bigdata_files/anchor-sections-1.0/anchor-sections.css

@@ -0,0 +1,4 @@
+/* Styles for section anchors */
+a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
+a.anchor-section::before {content: '#';}
+.hasAnchor:hover a.anchor-section {visibility: visible;}

docs/articles/dsmextra-bigdata_files/anchor-sections-1.0/anchor-sections.js

@@ -0,0 +1,33 @@
+// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
+document.addEventListener('DOMContentLoaded', function() {
+  // Do nothing if AnchorJS is used
+  if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
+    return;
+  }
+
+  const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
+
+  // Do nothing if sections are already anchored
+  if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
+    return null;
+  }
+
+  // Use section id when pandoc runs with --section-divs
+  const section_id = function(x) {
+    return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
+            ? x.id : '');
+  };
+
+  // Add anchors
+  h.forEach(function(x) {
+    const id = x.id || section_id(x.parentElement);
+    if (id === '') {
+      return null;
+    }
+    let anchor = document.createElement('a');
+    anchor.href = '#' + id;
+    anchor.classList = ['anchor-section'];
+    x.classList.add('hasAnchor');
+    x.appendChild(anchor);
+  });
+});

docs/articles/dsmextra-bigdata_files/header-attrs-2.5/header-attrs.js

@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});

docs/articles/dsmextra-covariateselection_files/anchor-sections-1.0/anchor-sections.css

@@ -0,0 +1,4 @@
+/* Styles for section anchors */
+a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
+a.anchor-section::before {content: '#';}
+.hasAnchor:hover a.anchor-section {visibility: visible;}

docs/articles/dsmextra-covariateselection_files/anchor-sections-1.0/anchor-sections.js

@@ -0,0 +1,33 @@
+// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
+document.addEventListener('DOMContentLoaded', function() {
+  // Do nothing if AnchorJS is used
+  if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
+    return;
+  }
+
+  const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
+
+  // Do nothing if sections are already anchored
+  if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
+    return null;
+  }
+
+  // Use section id when pandoc runs with --section-divs
+  const section_id = function(x) {
+    return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
+            ? x.id : '');
+  };
+
+  // Add anchors
+  h.forEach(function(x) {
+    const id = x.id || section_id(x.parentElement);
+    if (id === '') {
+      return null;
+    }
+    let anchor = document.createElement('a');
+    anchor.href = '#' + id;
+    anchor.classList = ['anchor-section'];
+    x.classList.add('hasAnchor');
+    x.appendChild(anchor);
+  });
+});

docs/articles/dsmextra-covariateselection_files/header-attrs-2.5/header-attrs.js

@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});

docs/articles/dsmextra.css

@@ -96,3 +96,6 @@ ul{padding-left: 1.2em;}
 .figure{
   display: block;
   margin: 0 auto;}
+
+.csl-entry{
+  margin-bottom: 10px !important;}