-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathgettingstarted.html
390 lines (321 loc) · 11.8 KB
/
gettingstarted.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
388
389
390
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>gettingstarted.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>Getting started with <code>shadia</code></b>
</h2>
<p>The purpose of this page is to get users set up to run American shad dam passage performance standards models. New users should follow instructions for installation and read notes related to use on this page before moving on to <a href="models.html">model overviews</a> and <a href="examples.html">examples</a>.</p>
<h3 id="multi">
<b>Installation</b>
</h3>
<p>This package can be installed with the <a href="https://www.rstudio.com/products/rpackages/devtools/"><code>devtools</code></a> package in R using the repository url: <code>devtools::install_github("danStich/shadia")</code>.</p>
<p>To install <code>shadia</code>, you will need to have <code>devtools</code> installed ahead of time in R, but that requires some special tools. To install on <strong>Windows</strong>, you will need to download and install the appropriate version of <a href="https://cran.r-project.org/bin/windows/Rtools/">Rtools</a>. To install on <strong>Mac</strong>, you will need to have the <a href="http://osxdaily.com/2014/02/12/install-command-line-tools-mac-os-x/">XCode command-line tools</a> installed. And, if running from <strong>Linux</strong>, you will need to install the developer version of R (<code>r-base-dev</code>) if you have not already.</p>
<h3 id="multi">
<b>Use</b>
</h3>
<p>The purpose of this package is to distribute code used to run the American shad dam passage performance standard model. Currently, the model is implemented for the <strong>Connecticut</strong>, <strong>Kennebec</strong>, <strong>Merrimack</strong>, <strong>Mohawk and Hudson</strong>, <strong>Penobscot</strong>, <strong>Saco</strong>, and <strong>Susquehanna</strong> rivers, USA, and we add new rivers as need arises. The main package functions include <code>connecticutRiverModel()</code>, <code>kennebecRiverModel()</code>, <code>merrimackRiverModel()</code>, <code>mohawkHudsonRiverModel()</code>, <code>penobscotRiverModel()</code>, <code>sacoRiverModel()</code>, and <code>susquehannaRiverModel()</code>.</p>
<p>These models can be run without any arguments to estimate population abundance in specific reaches or in whole rivers under ‘no dam’ passage scenarios. Alternatively, the user can specify upstream and downstream fish passage at dams to simulate populations under different hydropower management scenarios. Timing of upstream passage, fishery, and bycatch mortality can also be defined as deterministic management scenarios or stochastic inputs for all rivers. Outputs include population abundance of spawners in the watersheds, within specific production units of each river, and the proportion of repeat spawners in each age class.</p>
<p>The models each take several (10-30) seconds to run for one iteration on most standard workstations. For that reason, we strongly recommend using a parallel approach where multiple model runs are needed.</p>
<h3 id="multi">
<b>Parallel execution</b>
</h3>
<p>Management decisions should not be based on a single model run. The models rely on stochastic inputs for parameterization, as detailed in <a href="http://www.nrcresearchpress.com/doi/10.1139/cjfas-2018-0008#.W2SVohRKgeI">Stich et al. (2019)</a>. As such, any two model runs might result in substantially different predictions, even under the same management scenario. Thus, mutliple runs of a given scenario are needed to provide a minimal characterization of stochasticity, and an understanding of variability in the response(s) of interest. In these cases, we strongly recommend running the model using the <code>snowfall</code> package as demonstrated in the help file for each model, which can be accessed by typing <code>?...RiverModel</code> (where ‘<code>...</code>’ is the name of each river in lowercase) in the console and pressing <code>< Enter ></code>, or on the <a href="examples.html">examples page of this website</a>.</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>