Merge pull request #86 from nmfs-fish-tools/add_wiki_doc

documentation, small fixes

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SSMSE
 Type: Package
 Title: Management Strategy Evaluation (MSE) using Stock Synthesis (SS)
-Version: 0.2.0
+Version: 0.2.1
 Authors@R: c(
     person("Kathryn", "Doering", email = "[email protected]",
       role = c("aut", "cre")),
@@ -19,7 +19,7 @@ URL: https://github.com/nmfs-fish-tools/SSMSE
 BugReports: https://github.com/nmfs-fish-tools/SSMSE/issues
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Imports:
     stats,
     utils,

NAMESPACE

@@ -1,14 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
 export(SSMSE_summary_all)
-export(SSMSE_summary_iter)
-export(SSMSE_summary_scen)
 export(create_future_om_list)
 export(create_sample_struct)
 export(create_scen_list)
 export(develop_OMs)
 export(get_bin)
-export(get_input_value)
+export(parse_MS)
 export(plot_comp_sampling)
 export(plot_index_sampling)
 export(run_EM)

R/initOM.R

@@ -92,6 +92,9 @@ create_OM <- function(OM_out_dir,
     datsource = dat, ctlsource = ctl,
     verbose = FALSE
   )
+  if(ctl[["EmpiricalWAA"]] == 1) {
+    stop("OM is an empirical weight at age model, which is not yet possible to use.")
+  }
   # model checks ----
   if (ctl[["F_Method"]] == 1) {
     stop(

R/parse_MS.R

@@ -504,6 +504,11 @@ parse_MS <- function(MS, EM_out_dir = NULL, EM_init_dir = NULL,
         do_checks = TRUE,
         verbose = verbose
       )
+      ctl <- SS_readctl(file.path(EM_out_dir, start[["ctlfile"]]),
+                        datlist = new_EM_dat)
+      if(ctl[["EmpiricalWAA"]] == 1) {
+        stop("EM uses empirical weight at age, which is not yet possible to use.")
+      }
     } else {
       if (!is.null(sample_struct)) {
         sample_struct_sub <- lapply(sample_struct,

R/runSSMSE.R

@@ -176,6 +176,11 @@ run_SSMSE <- function(scen_name_vec,
       )
     }
   }
+
+
+  # make sure the output directories exist
+  result <- lapply(out_dir_scen_vec, function(x) if(!dir.exists(x)) dir.create(x, showWarnings = FALSE))
+
   # check and add implicit inputs to the future_om_list
   future_om_list <- check_future_om_list_str(future_om_list = future_om_list)
   # Note that all input checks are done in the check_scen_list function.

R/utils.R

@@ -66,6 +66,7 @@
 #'  expected value with the reference value identifying the lag in years for availability
 #'  of the index (Ref_years: vector length n indices).
 #' @author Kathryn Doering
+#' @export
 #' @examples
 #' scen_list <- create_scen_list(
 #'   scen_name_vec = c("scen 1", "scen_2"),
@@ -328,14 +329,14 @@ clean_init_mod_files <- function(OM_out_dir, EM_out_dir = NULL, MS = "EM",
 #'   "value" = c(2, 2, 2, 3, 3),
 #'   "se_log" = 0.2
 #' )
-#' get_input_value(
+#' SSMSE:::get_input_value(
 #'   data = dfr, method = "most_common_value", colname = "se_log",
 #'   group = "value"
 #' )
-#' get_input_value(data = dfr, method = "most_common_value", colname = "value")
-#' get_input_value(data = dfr, method = "only_value", colname = "se_log")
+#' SSMSE:::get_input_value(data = dfr, method = "most_common_value", colname = "value")
+#' SSMSE:::get_input_value(data = dfr, method = "only_value", colname = "se_log")
 #' # generates an error:
-#' # get_input_value(data = dfr, method = "only_value", colname = "value")
+#' # SSMSE:::get_input_value(data = dfr, method = "only_value", colname = "value")
 get_input_value <- function(data,
                             method = "most_common_value",
                             colname,
@@ -698,6 +699,7 @@ combine_cols <- function(dat_list, list_item, colnames) {
 #' Can be 1) NULL (default); 2) An integer vector of length 1, length 1+length(scen_name_vec), or length 1 + length(scen_name_vec)+sum(iter_vec); 3) A list with 3 components the same as teh output of set_MSE_seeds
 #' @param iter_vec The number of iterations per scenario. A vector of integers
 #'  in the same order as scen_name_vec.
+#' @export
 #' @returns A list of length 3 with 1) the global seed value; 2) the scenario seed values; and 3) the iteration seed values.
 #' @examples
 #' seeds <- set_MSE_seeds(seed = seq(10, 80, by = 10), iter_vec = c(2, 3))

docs/manual/libs/anchor-sections-1.0.1/anchor-sections.css

@@ -0,0 +1,5 @@
+/* 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;}
+ul > li > .anchor-section {display: none;}

docs/manual/libs/anchor-sections-1.0.1/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 === '' || x.matches(':empty')) {
+      return null;
+    }
+    let anchor = document.createElement('a');
+    anchor.href = '#' + id;
+    anchor.classList = ['anchor-section'];
+    x.classList.add('hasAnchor');
+    x.appendChild(anchor);
+  });
+});

docs/manual/libs/gitbook-2.6.7/css/plugin-bookdown.css

@@ -97,3 +97,9 @@ div.proof>*:last-child:after {
 .header-section-number {
   padding-right: .5em;
 }
+#header .multi-author {
+  margin: 0.5em 0 -0.5em 0;
+}
+#header .date {
+  margin-top: 1.5em;
+}

docs/manual/libs/gitbook-2.6.7/css/plugin-fontsettings.css

@@ -44,13 +44,24 @@
   line-height: 30px;
   font-size: 1em;
 }
+
+/* sidebar transition background */
+div.book.color-theme-1 {
+  background: #f3eacb;
+}
 .book.color-theme-1 .book-body {
   color: #704214;
   background: #f3eacb;
 }
 .book.color-theme-1 .book-body .page-wrapper .page-inner section {
   background: #f3eacb;
 }
+
+/* sidebar transition background */
+div.book.color-theme-2 {
+  background: #1c1f2b;
+}
+
 .book.color-theme-2 .book-body {
   color: #bdcadb;
   background: #1c1f2b;

docs/manual/libs/gitbook-2.6.7/js/plugin-search.js

@@ -1,9 +1,24 @@
 gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
     var index = null;
+    var fuse = null;
+    var _search = {engine: 'lunr', opts: {}};
     var $searchInput, $searchLabel, $searchForm;
     var $highlighted = [], hi, hiOpts = { className: 'search-highlight' };
     var collapse = false, toc_visible = [];
 
+    function init(config) {
+        // Instantiate search settings
+        _search = gitbook.storage.get("search", {
+            engine: config.search.engine || 'lunr',
+            opts: config.search.options || {},
+        });
+    };
+
+    // Save current search settings
+    function saveSearchSettings() {
+        gitbook.storage.set("search", _search);
+    }
+
     // Use a specific index
     function loadIndex(data) {
         // [Yihui] In bookdown, I use a character matrix to store the chapter
@@ -14,18 +29,36 @@ gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
         // lunr cannot handle non-English text very well, e.g. the default
         // tokenizer cannot deal with Chinese text, so we may want to replace
         // lunr with a dumb simple text matching approach.
-        index = lunr(function () {
-          this.ref('url');
-          this.field('title', { boost: 10 });
-          this.field('body');
-        });
-        data.map(function(item) {
-          index.add({
-            url: item[0],
-            title: item[1],
-            body: item[2]
+        if (_search.engine === 'lunr') {
+          index = lunr(function () {
+            this.ref('url');
+            this.field('title', { boost: 10 });
+            this.field('body');
           });
-        });
+          data.map(function(item) {
+            index.add({
+              url: item[0],
+              title: item[1],
+              body: item[2]
+            });
+          });
+          return;
+        }
+        fuse = new Fuse(data.map((_data => {
+            return {
+                url: _data[0],
+                title: _data[1],
+                body: _data[2]
+            };
+        })), Object.assign(
+            {
+                includeScore: true,
+                threshold: 0.1,
+                ignoreLocation: true,
+                keys: ["title", "body"]
+            },
+            _search.opts
+        ));
     }
 
     // Fetch the search index
@@ -36,20 +69,33 @@ gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
 
     // Search for a term and return results
     function search(q) {
-        if (!index) return;
-
-        var results = _.chain(index.search(q))
-        .map(function(result) {
-            var parts = result.ref.split("#");
-            return {
-                path: parts[0],
-                hash: parts[1]
-            };
-        })
-        .value();
+        let results = [];
+        switch (_search.engine) {
+            case 'fuse':
+                if (!fuse) return;
+                results = fuse.search(q).map(function(result) {
+                    var parts = result.item.url.split('#');
+                    return {
+                        path: parts[0],
+                        hash: parts[1]
+                    };
+                });
+                break;
+            case 'lunr':
+            default:
+                if (!index) return;
+                results = _.chain(index.search(q)).map(function(result) {
+                    var parts = result.ref.split("#");
+                    return {
+                        path: parts[0],
+                        hash: parts[1]
+                    };
+                })
+                .value();
+        }
 
         // [Yihui] Highlight the search keyword on current page
-        $highlighted = results.length === 0 ? [] : $('.page-inner')
+        $highlighted = $('.page-inner')
           .unhighlight(hiOpts).highlight(q, hiOpts).find('span.search-highlight');
         scrollToHighlighted(0);
 
@@ -172,6 +218,7 @@ gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
     gitbook.events.bind("start", function(e, config) {
         // [Yihui] disable search
         if (config.search === false) return;
+        init(config);
         collapse = !config.toc || config.toc.collapse === 'section' ||
           config.toc.collapse === 'subsection';
 

docs/manual/libs/gitbook-2.6.7/js/plugin-sharing.js

@@ -57,10 +57,21 @@ gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
                 e.preventDefault();
                 window.open("http://vkontakte.ru/share.php?url="+encodeURIComponent(location.href));
             }
-        }
+        },
+        'whatsapp': {
+            'label': 'Whatsapp',
+            'icon': 'fa fa-whatsapp',
+            'onClick': function(e) {
+                e.preventDefault();
+                var url = encodeURIComponent(location.href);
+                window.open((isMobile() ? "whatsapp://send" : "https://web.whatsapp.com/send") + "?text=" + url);
+            }
+        },
     };
 
-
+    function isMobile() {
+      return !!navigator.maxTouchPoints;
+    }
 
     gitbook.events.bind("start", function(e, config) {
         var opts = config.sharing;

docs/manual/libs/header-attrs-2.11/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);
+  }
+});