-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathmodels.html
387 lines (318 loc) · 13.2 KB
/
models.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>models.utf8</title>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<script src="site_libs/accessible-code-block-0.0.1/empty-anchor.js"></script>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<!DOCTYPE html>
<head>
<!-- Favicon for various operating systems -->
<link rel="apple-touch-icon" sizes="180x180" href="./favicon/apple-touch-icon.png">
<link rel="icon" type="image/png" sizes="32x32" href="./favicon/favicon-32x32.png">
<link rel="icon" type="image/png" sizes="16x16" href="./favicon/favicon-16x16.png">
<!-- <link rel="manifest" href="./favicon/site.webmanifest"> -->
<link rel="mask-icon" href="./favicon/safari-pinned-tab.svg" color="#603cba">
<link rel="shortcut icon" href="./favicon/favicon.ico">
<meta name="msapplication-TileColor" content="#603cba">
<meta name="msapplication-config" content="./favicon/browserconfig.xml">
<meta name="theme-color" content="#382121">
</head>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
<link rel="stylesheet" href="styles.css" type="text/css" />
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 51px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 56px;
margin-top: -56px;
}
.section h2 {
padding-top: 56px;
margin-top: -56px;
}
.section h3 {
padding-top: 56px;
margin-top: -56px;
}
.section h4 {
padding-top: 56px;
margin-top: -56px;
}
.section h5 {
padding-top: 56px;
margin-top: -56px;
}
.section h6 {
padding-top: 56px;
margin-top: -56px;
}
.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;
}
</style>
<script>
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
</head>
<body>
<div class="container-fluid main-container">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">shadia</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fa fa-home"></span>
</a>
</li>
<li>
<a href="gettingstarted.html">Getting started</a>
</li>
<li>
<a href="models.html">Models</a>
</li>
<li>
<a href="examples.html">Examples</a>
</li>
<li>
<a href="version_history.html">Version history</a>
</li>
<li>
<a href="contact.html">Contact</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/danStich/shadia">
<span class="fa fa-github"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
</div>
<h2 id="multi">
<b>The models </b>
</h2>
<p><img id="multi" src="images/roboshad.png" alt="logo"></p>
<p><code>shadia</code> contains life-history based simulation models of American shad and blueback herring population dynamics. Each model uses simulated fish populations to predict responses to user-specified fish passage scenarios at dams. The user can change settings for upstream and downstream passage standards, in addition to commercial, sustenance, and recreational fishing mortality rates. Model outputs include reach-specific and whole-basin abundances, percent repeat spawners, and other metrics as they are added.</p>
<p>A description of the status and versioning for each model is provided below, and detailed descriptions of each can be found at corresponding links. Briefly, these models rely on best available information to parameterize a combination of cohort- and individual-based models to simulate annual population dynamics and spawning migrations. The majority of the functions and parameters included in the models are the same (e.g., behavioral parameters). The balance are derived from river-specific information about habitat, environmental conditions, and biological characteristics. For a detailed explanation of model inputs and outputs, please see <a href="https://danstich.github.io/stich/pubs/Stich_etal_CJFAS_shadia.pdf">Stich et al. (2019)</a>, who used the <code>penobscotRiverModel()</code> as a case study for application. Please see the links below for overviews of river-specific data.</p>
<p>The models provided through <code>shadia</code> can be used for a variety of purposes, from management strategy evaluation to quantifying scope of single-project or catchment-wide dam impacts, to exploring life-history uncertainty and sensitivities. Because these models are continually evolving and new models are still being added, it is <strong>strongly recommended</strong> that users contact the package maintainer, Dan Stich (daniel.stich at oneonta.edu), before using them for research or management. For examples of how the models can be used, please see the <a href="examples.html">this page</a>.</p>
<p>Models that are currently implemented in <code>shadia</code> (with current status) include :</p>
<p><b><a href="about_androscoggin.html"><code>androscogginRiverModel</code></a></b> This model is currently undergoing review with fishery and habitat scientists and managers at the Maine Deparment of Marine Resources.</p>
<p><b><a href="about_connecticut.html"><code>connecticutRiverModel</code></a></b> This model has been vetted with cooperators and fishery managers during the course of several years. Version 2.0 is currently in preparation for submission for peer-review as part of a cross-sectional analysis with the Merrimack, Penobscot, and Susquehanna rivers. Version (1.8.0) is described in Gilligan (2020). This model was used previously to inform federal hydropower relicensing (v 1.3.0).</p>
<p><b><a href="about_kennebec.html"><code>kennebecRiverModel</code></a></b> This model has undergone review with fishery and habitat managers at Maine Department of Marine Resources and the National Oceanic and Atmospheric administration Habitat Division. System-specific blueback herring data are used in this model.</p>
<p><b><a href="about_merrimack.html"><code>merrimackRiverModel</code></a></b>This model has undergone preliminary review with fishery scientists and managers with United States Fish and Wildlife Service and the National Oceanic and Atmospheric administration Habitat Division. Version 1.8.0 is described in Gilligan (2020). Version 2.0 is currently in preparation for submission for peer-review as part of a cross-sectional analysis with the Connecticut, Penobscot, and Susquehanna rivers.</p>
<p><b><a href="about_mohawkHudson.html"><code>mohawkHudsonRiverModel</code></a></b> This model has undergone review with agency collaborators at the New York State Department of Environmental Conservation and the Cornell Cooperative Extension. System-specific blueback herring data are used in this model. Version 2.0 is currently in preparation for submission for peer-review as an applied fishery management article.</p>
<p><b><a href="about_penobscot.html"><code>penobscotRiverModel</code></a></b> This model, which forms the basis for all others, is peer-reviewed <a href="https://danstich.github.io/stich/pubs/Stich_etal_CJFAS_shadia.pdf">Stich et al. (2019)</a>. This model has been used previously to inform federal hydropower relisencing (v 1.3.0). Version 2.0 is currently in preparation for submission for peer-review as part of a cross-sectional analysis with the Connecticut, Merrimack, and Susquehanna rivers.</p>
<p><b><a href="about_saco.html"><code>sacoRiverModel</code></a></b> This model has undergone preliminary review with fishery and habitat managers at Maine Department of Marine Resources and the National Oceanic and Atmospheric administration Habitat Division.</p>
<p><b><a href="about_susquehanna.html"><code>susquehannaRiverModel</code></a></b> This model has undergone preliminary review with fishery scientists and managers with United States Fish and Wildlife Service and US Geological Survey. Version 1.8.0 is detailed in Gilligan (2020). Version 2.0 is currently in preparation for submission for peer-review as part of a cross-sectional analysis with the Connecticut, Merrimack, and Susquehanna rivers.</p>
<p><br></p>
<!DOCTYPE html>
<br>
<hr>
<p style="color:gray; text-align:center">This work is licensed under a <a href= "https://github.com/shadia-ui/shadia-ui.github.io/blob/master/LICENSE"> Creative Commons 4.0 International License</a>.</p>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
});
});
</script>
<!-- code folding -->
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>