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index.html
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<!DOCTYPE html>
<html lang="en-US" xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>Welcome to Pandora toolbox</title>
<style type="text/css">
body, html {
font-family: Helvetica, Arial, sans-serif;
background-color: #F5F5F5;
color: #114;
margin: 0;
padding: 0;
}
a {
text-decoration: none;
}
a:hover {
text-decoration: underline;
}
#titleBar {
height: 80px;
background-color: #3475b4;
overflow: hidden;
border-bottom: 1px solid #3475b3;
-moz-box-shadow: 0px 0px 10px 3px #BBC;
-webkit-box-shadow: 0px 0px 10px 3px #BBC;
box-shadow: 0px 0px 10px 3px #BBC;
}
#titleBar #container {
margin-top: 14px;
}
#titleBar h1 {
margin: 0 auto .5em auto;
padding: .2em;
color: #EEE;
text-align: center;
}
#intro {
background-color: #DDD;
margin: 1em 1em 0 1em;
padding: .75em;
text-align: center;
border: 1px solid #CCC;
font-size: 18px;
}
#intro p {
margin: .3em 0 .3em 0;
}
#outer-content {
max-width: 910px;
margin-left: auto;
margin-right: auto;
}
#content {
margin: 1em auto 1em auto;
float: left;
}
#main{
margin-left: auto;
margin-right: auto;
float: left;
line-height: 24px;
max-width: 910px;
text-align:justify;
}
<!--
#shiny{
float: left;
width: 305px;
margin-left: -330px;
padding-left: 20px;
border-left: 1px solid #AAA;
}
#shiny iframe {
margin-top: 30px;
}
-->
.caption{
font-size: 13px;
}
.button {
background-color: #3475b4;
border: none;
color: white;
padding: 15px 32px;
text-align: center;
text-decoration: none;
display: inline-block;
font-size: 24px;
margin: 4px 2px;
cursor: pointer;
border-radius: 8px;
box-shadow: 0 8px 16px 0 rgba(0,0,0,0.2), 0 6px 20px 0 rgba(0,0,0,0.19);
transition-duration: 0.4s;
}
.button:hover {
background-color: #3475b4; /* Blue */
color: white;
}
code {
background-color: #E5E5E5;
border: 1px solid #AAA;
-webkit-border-radius: 3px;
-khtml-border-radius: 3px;
-moz-border-radius: 3px;
border-radius: 3px;
padding: 0 .5em 0 .5em;
}
</style>
</head>
<body>
<div id="titleBar">
<div id="container">
<h1>Pandora Toolbox</h1>
</div>
</div>
<div id="outer-content">
<div id="intro">
<p> Stock assessment shiny apps <strong>Beta version</strong> </p>
</div>
<div id="content">
<div id="main">
<div style = "text-align: center">
<a href="./sample-apps/spict/" class="button" align = "left">SPiCT app</a>
<a href="./sample-apps/a4a/" class="button" align = "right">a4a app</a>
</div>
<h3> Overview </h3>
<p> Through this web application the user can implement two fisheries stock assessment models/approaches: </p>
<ul>
<li> the stochastic surplus production model in continuous time (SPiCT) [1] and </li>
<li> the statistical catch-at-age stock assessment model developed as part of the assessment for all (a4a) [2]. </li>
</ul>
<p> The SPiCT application includes the two time-variant productivity extensions, allowing for gradually varying productivity or regimes of productivity [3].
The a4a assessment is modified to include environmental variability on recruitment though an external environmental index provided by the user. </p>
<p> The application was developed in Shiny under the R language programming environment [4, 5].</p>
<h3> Documentation </h3>
<p><a href="https://flr-project.org/FLa4a/articles/sca.pdf">a4a manual</a></p>
<p><a href="https://github.com/DTUAqua/spict/raw/master/spict/inst/doc/spict_handbook.pdf ">SPiCT manual</a></p>
<h3> Help files </h3>
<p> Test files, source code and official manuals for both approaches can be found in
<a href="https://cloudfs.hcmr.gr/index.php/s/yRqWk0zTTOCWbZT ">HCMR's cloud</a> </p>
<h3> Acknowledgments </h3>
<p> This application is part of the PANDORA’s toolbox developed as part of the
<a href="https://www.pandora-fisheries-project.eu/"> PANDORA project</a> </p>
<h3> How to cite </h3>
<h3> Developers </h3>
<p> Contacts: Danai Mantopoulou-Palouka, Maria Kikeri, Vasiliki Sgardeli, Dimitrios Damalas [email protected], [email protected], [email protected] </p>
<h3> References </h3>
<ol>
<li> Pedersen, M.W., Berg, C.W. (2017). A stochastic surplus production model in continuous time.
<em>Fish and Fisheries</em>, 18: 226-243. </li>
<li> Jardim, E., Millar, C.P., Mosqueira, I., Scott, F., Osio, G.C., Ferretti, M., Alzorriz, N., Orio, A. (2015).
What if stock assessment is as simple as a linear model? The a4a initiative. <em>ICES Journal of Marine Science</em>, 72: 232-236</li>
<li> Mildenberger, T.K., Berg, C.W., Pedersen, M.W., Kokkalis, A., Nielsen, J.R. (2020).
Time-variant productivity in biomass dynamic models on seasonal and long-term scales, <em>ICES Journal of Marine Science</em>, 77(1): 174-187.</li>
<li> R Core Team (2020). R: A language and environment for statistical computing. R Foundation for
Statistical Computing, Vienna, Austria. URL <a href="https://www.R-project.org/"> https://www.R-project.org/ </a>.</li>
<li> Chang, W., Cheng, J., Allaire, J.J., Xie, Y., McPherson, J. (2020). shiny: Web Application
Framework for R. R package version 1.5.0. <a href="https://CRAN.R-project.org/package=shiny">https://CRAN.R-project.org/package=shiny </a> </li>
</ol>
<h3> Disclaimer </h3>
<p> This software is free to use for educational and demonstration purposes
only and comes with absolutely no warranty.
It is distributed under <a href="https://joinup.ec.europa.eu/collection/eupl/eupl-text-eupl-12">EUPL- 1.2 license</a>.</p>
</div>
</div>
</div>
</body>
</html>