`, etc.) that has more than one element. Defaults to 1 (for ``).
+ getTopLevel: function($scope) {
+ for (var i = 1; i <= 6; i++) {
+ var $headings = this.findOrFilter($scope, 'h' + i);
+ if ($headings.length > 1) {
+ return i;
+ }
+ }
+
+ return 1;
+ },
+
+ // returns the elements for the top level, and the next below it
+ getHeadings: function($scope, topLevel) {
+ var topSelector = 'h' + topLevel;
+
+ var secondaryLevel = topLevel + 1;
+ var secondarySelector = 'h' + secondaryLevel;
+
+ return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
+ },
+
+ getNavLevel: function(el) {
+ return parseInt(el.tagName.charAt(1), 10);
+ },
+
+ populateNav: function($topContext, topLevel, $headings) {
+ var $context = $topContext;
+ var $prevNav;
+
+ var helpers = this;
+ $headings.each(function(i, el) {
+ var $newNav = helpers.generateNavItem(el);
+ var navLevel = helpers.getNavLevel(el);
+
+ // determine the proper $context
+ if (navLevel === topLevel) {
+ // use top level
+ $context = $topContext;
+ } else if ($prevNav && $context === $topContext) {
+ // create a new level of the tree and switch to it
+ $context = helpers.createChildNavList($prevNav);
+ } // else use the current $context
+
+ $context.append($newNav);
+
+ $prevNav = $newNav;
+ });
+ },
+
+ parseOps: function(arg) {
+ var opts;
+ if (arg.jquery) {
+ opts = {
+ $nav: arg
+ };
+ } else {
+ opts = arg;
+ }
+ opts.$scope = opts.$scope || $(document.body);
+ return opts;
+ }
+ },
+
+ // accepts a jQuery object, or an options object
+ init: function(opts) {
+ opts = this.helpers.parseOps(opts);
+
+ // ensure that the data attribute is in place for styling
+ opts.$nav.attr('data-toggle', 'toc');
+
+ var $topContext = this.helpers.createChildNavList(opts.$nav);
+ var topLevel = this.helpers.getTopLevel(opts.$scope);
+ var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
+ this.helpers.populateNav($topContext, topLevel, $headings);
+ }
+ };
+
+ $(function() {
+ $('nav[data-toggle="toc"]').each(function(i, el) {
+ var $nav = $(el);
+ Toc.init($nav);
+ });
+ });
+})();
diff --git a/docsearch.css b/docsearch.css
new file mode 100644
index 0000000..e5f1fe1
--- /dev/null
+++ b/docsearch.css
@@ -0,0 +1,148 @@
+/* Docsearch -------------------------------------------------------------- */
+/*
+ Source: https://github.com/algolia/docsearch/
+ License: MIT
+*/
+
+.algolia-autocomplete {
+ display: block;
+ -webkit-box-flex: 1;
+ -ms-flex: 1;
+ flex: 1
+}
+
+.algolia-autocomplete .ds-dropdown-menu {
+ width: 100%;
+ min-width: none;
+ max-width: none;
+ padding: .75rem 0;
+ background-color: #fff;
+ background-clip: padding-box;
+ border: 1px solid rgba(0, 0, 0, .1);
+ box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+}
+
+@media (min-width:768px) {
+ .algolia-autocomplete .ds-dropdown-menu {
+ width: 175%
+ }
+}
+
+.algolia-autocomplete .ds-dropdown-menu::before {
+ display: none
+}
+
+.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+ padding: 0;
+ background-color: rgb(255,255,255);
+ border: 0;
+ max-height: 80vh;
+}
+
+.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
+ margin-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion {
+ padding: 0;
+ overflow: visible
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--category-header {
+ padding: .125rem 1rem;
+ margin-top: 0;
+ font-size: 1.3em;
+ font-weight: 500;
+ color: #00008B;
+ border-bottom: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
+ float: none;
+ padding-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
+ float: none;
+ width: auto;
+ padding: 0;
+ text-align: left
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content {
+ float: none;
+ width: auto;
+ padding: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content::before {
+ display: none
+}
+
+.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
+ padding-top: .75rem;
+ margin-top: .75rem;
+ border-top: 1px solid rgba(0, 0, 0, .1)
+}
+
+.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+ display: block;
+ padding: .1rem 1rem;
+ margin-bottom: 0.1;
+ font-size: 1.0em;
+ font-weight: 400
+ /* display: none */
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--title {
+ display: block;
+ padding: .25rem 1rem;
+ margin-bottom: 0;
+ font-size: 0.9em;
+ font-weight: 400
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text {
+ padding: 0 1rem .5rem;
+ margin-top: -.25rem;
+ font-size: 0.8em;
+ font-weight: 400;
+ line-height: 1.25
+}
+
+.algolia-autocomplete .algolia-docsearch-footer {
+ width: 110px;
+ height: 20px;
+ z-index: 3;
+ margin-top: 10.66667px;
+ float: right;
+ font-size: 0;
+ line-height: 0;
+}
+
+.algolia-autocomplete .algolia-docsearch-footer--logo {
+ background-image: url("data:image/svg+xml;utf8,");
+ background-repeat: no-repeat;
+ background-position: 50%;
+ background-size: 100%;
+ overflow: hidden;
+ text-indent: -9000px;
+ width: 100%;
+ height: 100%;
+ display: block;
+ transform: translate(-8px);
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--highlight {
+ color: #FF8C00;
+ background: rgba(232, 189, 54, 0.1)
+}
+
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
+ box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+}
+
+.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
+ background-color: rgba(192, 192, 192, .15)
+}
diff --git a/docsearch.js b/docsearch.js
new file mode 100644
index 0000000..b35504c
--- /dev/null
+++ b/docsearch.js
@@ -0,0 +1,85 @@
+$(function() {
+
+ // register a handler to move the focus to the search bar
+ // upon pressing shift + "/" (i.e. "?")
+ $(document).on('keydown', function(e) {
+ if (e.shiftKey && e.keyCode == 191) {
+ e.preventDefault();
+ $("#search-input").focus();
+ }
+ });
+
+ $(document).ready(function() {
+ // do keyword highlighting
+ /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
+ var mark = function() {
+
+ var referrer = document.URL ;
+ var paramKey = "q" ;
+
+ if (referrer.indexOf("?") !== -1) {
+ var qs = referrer.substr(referrer.indexOf('?') + 1);
+ var qs_noanchor = qs.split('#')[0];
+ var qsa = qs_noanchor.split('&');
+ var keyword = "";
+
+ for (var i = 0; i < qsa.length; i++) {
+ var currentParam = qsa[i].split('=');
+
+ if (currentParam.length !== 2) {
+ continue;
+ }
+
+ if (currentParam[0] == paramKey) {
+ keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
+ }
+ }
+
+ if (keyword !== "") {
+ $(".contents").unmark({
+ done: function() {
+ $(".contents").mark(keyword);
+ }
+ });
+ }
+ }
+ };
+
+ mark();
+ });
+});
+
+/* Search term highlighting ------------------------------*/
+
+function matchedWords(hit) {
+ var words = [];
+
+ var hierarchy = hit._highlightResult.hierarchy;
+ // loop to fetch from lvl0, lvl1, etc.
+ for (var idx in hierarchy) {
+ words = words.concat(hierarchy[idx].matchedWords);
+ }
+
+ var content = hit._highlightResult.content;
+ if (content) {
+ words = words.concat(content.matchedWords);
+ }
+
+ // return unique words
+ var words_uniq = [...new Set(words)];
+ return words_uniq;
+}
+
+function updateHitURL(hit) {
+
+ var words = matchedWords(hit);
+ var url = "";
+
+ if (hit.anchor) {
+ url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+ } else {
+ url = hit.url + '?q=' + escape(words.join(" "));
+ }
+
+ return url;
+}
diff --git a/index.html b/index.html
new file mode 100644
index 0000000..224b042
--- /dev/null
+++ b/index.html
@@ -0,0 +1,162 @@
+
+
+
+
+
+
+
+Generate Standard NWFSC Assessment Diagnostics • nwfscDiag
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+The package provides the functionality to conduct model diagnostics for Stock Synthesis (SS3) models. The standard diagnostic included in this package are standard required analysis for U.S. West Coast Groundfish stock assessments managed by the Pacific Fisheries Management Council. The package was designed to perform model diagnostics and create plots and tables in a standardized format. The standardized approach will facilitate the use of these outputs in the assessment template approach sa4ss.
+The diagnostics created by the package are: - jitter runs to ensure model convergence at the MLE, - retrospective runs to examine model sensitivity to recent data, and
+- likelihood profiles across parameters.
+This package does not maintain backward compatibility with previous versions of Stock Synthesis. However, if needed user can download older package versions that may work with older versions (3.30.+) of Stock Synthesis.
+
+Installation
+
+nwfscDiag can be installed via github:
+install.packages("remotes")
+remotes::install_github("pfmc-assessments/nwfscDiag")
+
+
+Running the code
+
+The package depends upon a few other packages and they should be installed upon installation of the package. The dependent packages are:
+install.packages('dplyr')
+remotes::install_github('r4ss/r4ss')
+A new version of r4ss package was released on July 29, 2022. This release included some significant changes that included changes to function names and function inputs. The current version of the nwfscDiag 1.1.2 package is designed to work with the latest release of r4ss. Please see release version 1.0.1 to use earlier versions of r4ss.
+
+
+Reporting problems
+
+Please report any issues with this package by posting a new github issue at https://github.com/pfmc-assessments/nwfscDiag/issues.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/link.svg b/link.svg
new file mode 100644
index 0000000..88ad827
--- /dev/null
+++ b/link.svg
@@ -0,0 +1,12 @@
+
+
+
diff --git a/pkgdown.css b/pkgdown.css
new file mode 100644
index 0000000..80ea5b8
--- /dev/null
+++ b/pkgdown.css
@@ -0,0 +1,384 @@
+/* Sticky footer */
+
+/**
+ * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
+ * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
+ *
+ * .Site -> body > .container
+ * .Site-content -> body > .container .row
+ * .footer -> footer
+ *
+ * Key idea seems to be to ensure that .container and __all its parents__
+ * have height set to 100%
+ *
+ */
+
+html, body {
+ height: 100%;
+}
+
+body {
+ position: relative;
+}
+
+body > .container {
+ display: flex;
+ height: 100%;
+ flex-direction: column;
+}
+
+body > .container .row {
+ flex: 1 0 auto;
+}
+
+footer {
+ margin-top: 45px;
+ padding: 35px 0 36px;
+ border-top: 1px solid #e5e5e5;
+ color: #666;
+ display: flex;
+ flex-shrink: 0;
+}
+footer p {
+ margin-bottom: 0;
+}
+footer div {
+ flex: 1;
+}
+footer .pkgdown {
+ text-align: right;
+}
+footer p {
+ margin-bottom: 0;
+}
+
+img.icon {
+ float: right;
+}
+
+/* Ensure in-page images don't run outside their container */
+.contents img {
+ max-width: 100%;
+ height: auto;
+}
+
+/* Fix bug in bootstrap (only seen in firefox) */
+summary {
+ display: list-item;
+}
+
+/* Typographic tweaking ---------------------------------*/
+
+.contents .page-header {
+ margin-top: calc(-60px + 1em);
+}
+
+dd {
+ margin-left: 3em;
+}
+
+/* Section anchors ---------------------------------*/
+
+a.anchor {
+ display: none;
+ margin-left: 5px;
+ width: 20px;
+ height: 20px;
+
+ background-image: url(./link.svg);
+ background-repeat: no-repeat;
+ background-size: 20px 20px;
+ background-position: center center;
+}
+
+h1:hover .anchor,
+h2:hover .anchor,
+h3:hover .anchor,
+h4:hover .anchor,
+h5:hover .anchor,
+h6:hover .anchor {
+ display: inline-block;
+}
+
+/* Fixes for fixed navbar --------------------------*/
+
+.contents h1, .contents h2, .contents h3, .contents h4 {
+ padding-top: 60px;
+ margin-top: -40px;
+}
+
+/* Navbar submenu --------------------------*/
+
+.dropdown-submenu {
+ position: relative;
+}
+
+.dropdown-submenu>.dropdown-menu {
+ top: 0;
+ left: 100%;
+ margin-top: -6px;
+ margin-left: -1px;
+ border-radius: 0 6px 6px 6px;
+}
+
+.dropdown-submenu:hover>.dropdown-menu {
+ display: block;
+}
+
+.dropdown-submenu>a:after {
+ display: block;
+ content: " ";
+ float: right;
+ width: 0;
+ height: 0;
+ border-color: transparent;
+ border-style: solid;
+ border-width: 5px 0 5px 5px;
+ border-left-color: #cccccc;
+ margin-top: 5px;
+ margin-right: -10px;
+}
+
+.dropdown-submenu:hover>a:after {
+ border-left-color: #ffffff;
+}
+
+.dropdown-submenu.pull-left {
+ float: none;
+}
+
+.dropdown-submenu.pull-left>.dropdown-menu {
+ left: -100%;
+ margin-left: 10px;
+ border-radius: 6px 0 6px 6px;
+}
+
+/* Sidebar --------------------------*/
+
+#pkgdown-sidebar {
+ margin-top: 30px;
+ position: -webkit-sticky;
+ position: sticky;
+ top: 70px;
+}
+
+#pkgdown-sidebar h2 {
+ font-size: 1.5em;
+ margin-top: 1em;
+}
+
+#pkgdown-sidebar h2:first-child {
+ margin-top: 0;
+}
+
+#pkgdown-sidebar .list-unstyled li {
+ margin-bottom: 0.5em;
+}
+
+/* bootstrap-toc tweaks ------------------------------------------------------*/
+
+/* All levels of nav */
+
+nav[data-toggle='toc'] .nav > li > a {
+ padding: 4px 20px 4px 6px;
+ font-size: 1.5rem;
+ font-weight: 400;
+ color: inherit;
+}
+
+nav[data-toggle='toc'] .nav > li > a:hover,
+nav[data-toggle='toc'] .nav > li > a:focus {
+ padding-left: 5px;
+ color: inherit;
+ border-left: 1px solid #878787;
+}
+
+nav[data-toggle='toc'] .nav > .active > a,
+nav[data-toggle='toc'] .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav > .active:focus > a {
+ padding-left: 5px;
+ font-size: 1.5rem;
+ font-weight: 400;
+ color: inherit;
+ border-left: 2px solid #878787;
+}
+
+/* Nav: second level (shown on .active) */
+
+nav[data-toggle='toc'] .nav .nav {
+ display: none; /* Hide by default, but at >768px, show it */
+ padding-bottom: 10px;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a {
+ padding-left: 16px;
+ font-size: 1.35rem;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a:hover,
+nav[data-toggle='toc'] .nav .nav > li > a:focus {
+ padding-left: 15px;
+}
+
+nav[data-toggle='toc'] .nav .nav > .active > a,
+nav[data-toggle='toc'] .nav .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav .nav > .active:focus > a {
+ padding-left: 15px;
+ font-weight: 500;
+ font-size: 1.35rem;
+}
+
+/* orcid ------------------------------------------------------------------- */
+
+.orcid {
+ font-size: 16px;
+ color: #A6CE39;
+ /* margins are required by official ORCID trademark and display guidelines */
+ margin-left:4px;
+ margin-right:4px;
+ vertical-align: middle;
+}
+
+/* Reference index & topics ----------------------------------------------- */
+
+.ref-index th {font-weight: normal;}
+
+.ref-index td {vertical-align: top; min-width: 100px}
+.ref-index .icon {width: 40px;}
+.ref-index .alias {width: 40%;}
+.ref-index-icons .alias {width: calc(40% - 40px);}
+.ref-index .title {width: 60%;}
+
+.ref-arguments th {text-align: right; padding-right: 10px;}
+.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px}
+.ref-arguments .name {width: 20%;}
+.ref-arguments .desc {width: 80%;}
+
+/* Nice scrolling for wide elements --------------------------------------- */
+
+table {
+ display: block;
+ overflow: auto;
+}
+
+/* Syntax highlighting ---------------------------------------------------- */
+
+pre, code, pre code {
+ background-color: #f8f8f8;
+ color: #333;
+}
+pre, pre code {
+ white-space: pre-wrap;
+ word-break: break-all;
+ overflow-wrap: break-word;
+}
+
+pre {
+ border: 1px solid #eee;
+}
+
+pre .img, pre .r-plt {
+ margin: 5px 0;
+}
+
+pre .img img, pre .r-plt img {
+ background-color: #fff;
+}
+
+code a, pre a {
+ color: #375f84;
+}
+
+a.sourceLine:hover {
+ text-decoration: none;
+}
+
+.fl {color: #1514b5;}
+.fu {color: #000000;} /* function */
+.ch,.st {color: #036a07;} /* string */
+.kw {color: #264D66;} /* keyword */
+.co {color: #888888;} /* comment */
+
+.error {font-weight: bolder;}
+.warning {font-weight: bolder;}
+
+/* Clipboard --------------------------*/
+
+.hasCopyButton {
+ position: relative;
+}
+
+.btn-copy-ex {
+ position: absolute;
+ right: 0;
+ top: 0;
+ visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+ visibility: visible;
+}
+
+/* headroom.js ------------------------ */
+
+.headroom {
+ will-change: transform;
+ transition: transform 200ms linear;
+}
+.headroom--pinned {
+ transform: translateY(0%);
+}
+.headroom--unpinned {
+ transform: translateY(-100%);
+}
+
+/* mark.js ----------------------------*/
+
+mark {
+ background-color: rgba(255, 255, 51, 0.5);
+ border-bottom: 2px solid rgba(255, 153, 51, 0.3);
+ padding: 1px;
+}
+
+/* vertical spacing after htmlwidgets */
+.html-widget {
+ margin-bottom: 10px;
+}
+
+/* fontawesome ------------------------ */
+
+.fab {
+ font-family: "Font Awesome 5 Brands" !important;
+}
+
+/* don't display links in code chunks when printing */
+/* source: https://stackoverflow.com/a/10781533 */
+@media print {
+ code a:link:after, code a:visited:after {
+ content: "";
+ }
+}
+
+/* Section anchors ---------------------------------
+ Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71
+*/
+
+div.csl-bib-body { }
+div.csl-entry {
+ clear: both;
+}
+.hanging-indent div.csl-entry {
+ margin-left:2em;
+ text-indent:-2em;
+}
+div.csl-left-margin {
+ min-width:2em;
+ float:left;
+}
+div.csl-right-inline {
+ margin-left:2em;
+ padding-left:1em;
+}
+div.csl-indent {
+ margin-left: 2em;
+}
diff --git a/pkgdown.js b/pkgdown.js
new file mode 100644
index 0000000..6f0eee4
--- /dev/null
+++ b/pkgdown.js
@@ -0,0 +1,108 @@
+/* http://gregfranko.com/blog/jquery-best-practices/ */
+(function($) {
+ $(function() {
+
+ $('.navbar-fixed-top').headroom();
+
+ $('body').css('padding-top', $('.navbar').height() + 10);
+ $(window).resize(function(){
+ $('body').css('padding-top', $('.navbar').height() + 10);
+ });
+
+ $('[data-toggle="tooltip"]').tooltip();
+
+ var cur_path = paths(location.pathname);
+ var links = $("#navbar ul li a");
+ var max_length = -1;
+ var pos = -1;
+ for (var i = 0; i < links.length; i++) {
+ if (links[i].getAttribute("href") === "#")
+ continue;
+ // Ignore external links
+ if (links[i].host !== location.host)
+ continue;
+
+ var nav_path = paths(links[i].pathname);
+
+ var length = prefix_length(nav_path, cur_path);
+ if (length > max_length) {
+ max_length = length;
+ pos = i;
+ }
+ }
+
+ // Add class to parent
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/link.svg b/link.svg
new file mode 100644
index 0000000..88ad827
--- /dev/null
+++ b/link.svg
@@ -0,0 +1,12 @@
+
+
+
diff --git a/pkgdown.css b/pkgdown.css
new file mode 100644
index 0000000..80ea5b8
--- /dev/null
+++ b/pkgdown.css
@@ -0,0 +1,384 @@
+/* Sticky footer */
+
+/**
+ * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
+ * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
+ *
+ * .Site -> body > .container
+ * .Site-content -> body > .container .row
+ * .footer -> footer
+ *
+ * Key idea seems to be to ensure that .container and __all its parents__
+ * have height set to 100%
+ *
+ */
+
+html, body {
+ height: 100%;
+}
+
+body {
+ position: relative;
+}
+
+body > .container {
+ display: flex;
+ height: 100%;
+ flex-direction: column;
+}
+
+body > .container .row {
+ flex: 1 0 auto;
+}
+
+footer {
+ margin-top: 45px;
+ padding: 35px 0 36px;
+ border-top: 1px solid #e5e5e5;
+ color: #666;
+ display: flex;
+ flex-shrink: 0;
+}
+footer p {
+ margin-bottom: 0;
+}
+footer div {
+ flex: 1;
+}
+footer .pkgdown {
+ text-align: right;
+}
+footer p {
+ margin-bottom: 0;
+}
+
+img.icon {
+ float: right;
+}
+
+/* Ensure in-page images don't run outside their container */
+.contents img {
+ max-width: 100%;
+ height: auto;
+}
+
+/* Fix bug in bootstrap (only seen in firefox) */
+summary {
+ display: list-item;
+}
+
+/* Typographic tweaking ---------------------------------*/
+
+.contents .page-header {
+ margin-top: calc(-60px + 1em);
+}
+
+dd {
+ margin-left: 3em;
+}
+
+/* Section anchors ---------------------------------*/
+
+a.anchor {
+ display: none;
+ margin-left: 5px;
+ width: 20px;
+ height: 20px;
+
+ background-image: url(./link.svg);
+ background-repeat: no-repeat;
+ background-size: 20px 20px;
+ background-position: center center;
+}
+
+h1:hover .anchor,
+h2:hover .anchor,
+h3:hover .anchor,
+h4:hover .anchor,
+h5:hover .anchor,
+h6:hover .anchor {
+ display: inline-block;
+}
+
+/* Fixes for fixed navbar --------------------------*/
+
+.contents h1, .contents h2, .contents h3, .contents h4 {
+ padding-top: 60px;
+ margin-top: -40px;
+}
+
+/* Navbar submenu --------------------------*/
+
+.dropdown-submenu {
+ position: relative;
+}
+
+.dropdown-submenu>.dropdown-menu {
+ top: 0;
+ left: 100%;
+ margin-top: -6px;
+ margin-left: -1px;
+ border-radius: 0 6px 6px 6px;
+}
+
+.dropdown-submenu:hover>.dropdown-menu {
+ display: block;
+}
+
+.dropdown-submenu>a:after {
+ display: block;
+ content: " ";
+ float: right;
+ width: 0;
+ height: 0;
+ border-color: transparent;
+ border-style: solid;
+ border-width: 5px 0 5px 5px;
+ border-left-color: #cccccc;
+ margin-top: 5px;
+ margin-right: -10px;
+}
+
+.dropdown-submenu:hover>a:after {
+ border-left-color: #ffffff;
+}
+
+.dropdown-submenu.pull-left {
+ float: none;
+}
+
+.dropdown-submenu.pull-left>.dropdown-menu {
+ left: -100%;
+ margin-left: 10px;
+ border-radius: 6px 0 6px 6px;
+}
+
+/* Sidebar --------------------------*/
+
+#pkgdown-sidebar {
+ margin-top: 30px;
+ position: -webkit-sticky;
+ position: sticky;
+ top: 70px;
+}
+
+#pkgdown-sidebar h2 {
+ font-size: 1.5em;
+ margin-top: 1em;
+}
+
+#pkgdown-sidebar h2:first-child {
+ margin-top: 0;
+}
+
+#pkgdown-sidebar .list-unstyled li {
+ margin-bottom: 0.5em;
+}
+
+/* bootstrap-toc tweaks ------------------------------------------------------*/
+
+/* All levels of nav */
+
+nav[data-toggle='toc'] .nav > li > a {
+ padding: 4px 20px 4px 6px;
+ font-size: 1.5rem;
+ font-weight: 400;
+ color: inherit;
+}
+
+nav[data-toggle='toc'] .nav > li > a:hover,
+nav[data-toggle='toc'] .nav > li > a:focus {
+ padding-left: 5px;
+ color: inherit;
+ border-left: 1px solid #878787;
+}
+
+nav[data-toggle='toc'] .nav > .active > a,
+nav[data-toggle='toc'] .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav > .active:focus > a {
+ padding-left: 5px;
+ font-size: 1.5rem;
+ font-weight: 400;
+ color: inherit;
+ border-left: 2px solid #878787;
+}
+
+/* Nav: second level (shown on .active) */
+
+nav[data-toggle='toc'] .nav .nav {
+ display: none; /* Hide by default, but at >768px, show it */
+ padding-bottom: 10px;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a {
+ padding-left: 16px;
+ font-size: 1.35rem;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a:hover,
+nav[data-toggle='toc'] .nav .nav > li > a:focus {
+ padding-left: 15px;
+}
+
+nav[data-toggle='toc'] .nav .nav > .active > a,
+nav[data-toggle='toc'] .nav .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav .nav > .active:focus > a {
+ padding-left: 15px;
+ font-weight: 500;
+ font-size: 1.35rem;
+}
+
+/* orcid ------------------------------------------------------------------- */
+
+.orcid {
+ font-size: 16px;
+ color: #A6CE39;
+ /* margins are required by official ORCID trademark and display guidelines */
+ margin-left:4px;
+ margin-right:4px;
+ vertical-align: middle;
+}
+
+/* Reference index & topics ----------------------------------------------- */
+
+.ref-index th {font-weight: normal;}
+
+.ref-index td {vertical-align: top; min-width: 100px}
+.ref-index .icon {width: 40px;}
+.ref-index .alias {width: 40%;}
+.ref-index-icons .alias {width: calc(40% - 40px);}
+.ref-index .title {width: 60%;}
+
+.ref-arguments th {text-align: right; padding-right: 10px;}
+.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px}
+.ref-arguments .name {width: 20%;}
+.ref-arguments .desc {width: 80%;}
+
+/* Nice scrolling for wide elements --------------------------------------- */
+
+table {
+ display: block;
+ overflow: auto;
+}
+
+/* Syntax highlighting ---------------------------------------------------- */
+
+pre, code, pre code {
+ background-color: #f8f8f8;
+ color: #333;
+}
+pre, pre code {
+ white-space: pre-wrap;
+ word-break: break-all;
+ overflow-wrap: break-word;
+}
+
+pre {
+ border: 1px solid #eee;
+}
+
+pre .img, pre .r-plt {
+ margin: 5px 0;
+}
+
+pre .img img, pre .r-plt img {
+ background-color: #fff;
+}
+
+code a, pre a {
+ color: #375f84;
+}
+
+a.sourceLine:hover {
+ text-decoration: none;
+}
+
+.fl {color: #1514b5;}
+.fu {color: #000000;} /* function */
+.ch,.st {color: #036a07;} /* string */
+.kw {color: #264D66;} /* keyword */
+.co {color: #888888;} /* comment */
+
+.error {font-weight: bolder;}
+.warning {font-weight: bolder;}
+
+/* Clipboard --------------------------*/
+
+.hasCopyButton {
+ position: relative;
+}
+
+.btn-copy-ex {
+ position: absolute;
+ right: 0;
+ top: 0;
+ visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+ visibility: visible;
+}
+
+/* headroom.js ------------------------ */
+
+.headroom {
+ will-change: transform;
+ transition: transform 200ms linear;
+}
+.headroom--pinned {
+ transform: translateY(0%);
+}
+.headroom--unpinned {
+ transform: translateY(-100%);
+}
+
+/* mark.js ----------------------------*/
+
+mark {
+ background-color: rgba(255, 255, 51, 0.5);
+ border-bottom: 2px solid rgba(255, 153, 51, 0.3);
+ padding: 1px;
+}
+
+/* vertical spacing after htmlwidgets */
+.html-widget {
+ margin-bottom: 10px;
+}
+
+/* fontawesome ------------------------ */
+
+.fab {
+ font-family: "Font Awesome 5 Brands" !important;
+}
+
+/* don't display links in code chunks when printing */
+/* source: https://stackoverflow.com/a/10781533 */
+@media print {
+ code a:link:after, code a:visited:after {
+ content: "";
+ }
+}
+
+/* Section anchors ---------------------------------
+ Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71
+*/
+
+div.csl-bib-body { }
+div.csl-entry {
+ clear: both;
+}
+.hanging-indent div.csl-entry {
+ margin-left:2em;
+ text-indent:-2em;
+}
+div.csl-left-margin {
+ min-width:2em;
+ float:left;
+}
+div.csl-right-inline {
+ margin-left:2em;
+ padding-left:1em;
+}
+div.csl-indent {
+ margin-left: 2em;
+}
diff --git a/pkgdown.js b/pkgdown.js
new file mode 100644
index 0000000..6f0eee4
--- /dev/null
+++ b/pkgdown.js
@@ -0,0 +1,108 @@
+/* http://gregfranko.com/blog/jquery-best-practices/ */
+(function($) {
+ $(function() {
+
+ $('.navbar-fixed-top').headroom();
+
+ $('body').css('padding-top', $('.navbar').height() + 10);
+ $(window).resize(function(){
+ $('body').css('padding-top', $('.navbar').height() + 10);
+ });
+
+ $('[data-toggle="tooltip"]').tooltip();
+
+ var cur_path = paths(location.pathname);
+ var links = $("#navbar ul li a");
+ var max_length = -1;
+ var pos = -1;
+ for (var i = 0; i < links.length; i++) {
+ if (links[i].getAttribute("href") === "#")
+ continue;
+ // Ignore external links
+ if (links[i].host !== location.host)
+ continue;
+
+ var nav_path = paths(links[i].pathname);
+
+ var length = prefix_length(nav_path, cur_path);
+ if (length > max_length) {
+ max_length = length;
+ pos = i;
+ }
+ }
+
+ // Add class to parent
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ The package provides the functionality to conduct model diagnostics for Stock Synthesis (SS3) models. The standard diagnostic included in this package are standard required analysis for U.S. West Coast Groundfish stock assessments managed by the Pacific Fisheries Management Council. The package was designed to perform model diagnostics and create plots and tables in a standardized format. The standardized approach will facilitate the use of these outputs in the assessment template approach sa4ss.
+The diagnostics created by the package are: - jitter runs to ensure model convergence at the MLE, - retrospective runs to examine model sensitivity to recent data, and
+- likelihood profiles across parameters.
This package does not maintain backward compatibility with previous versions of Stock Synthesis. However, if needed user can download older package versions that may work with older versions (3.30.+) of Stock Synthesis.
+
+
+Installation +
+nwfscDiag can be installed via github:
+install.packages("remotes")
+remotes::install_github("pfmc-assessments/nwfscDiag")
+
+Running the code +
+The package depends upon a few other packages and they should be installed upon installation of the package. The dependent packages are:
+install.packages('dplyr')
+remotes::install_github('r4ss/r4ss')A new version of r4ss package was released on July 29, 2022. This release included some significant changes that included changes to function names and function inputs. The current version of the nwfscDiag 1.1.2 package is designed to work with the latest release of r4ss. Please see release version 1.0.1 to use earlier versions of r4ss.
+
+
+Reporting problems +
+Please report any issues with this package by posting a new github issue at https://github.com/pfmc-assessments/nwfscDiag/issues.
+