r4atlantis.github.io/index.html at master · r4atlantis/r4atlantis.github.io · GitHub

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
<!doctype html>
<html>
  <head>
    <meta charset="utf-8">
    <meta http-equiv="X-UA-Compatible" content="chrome=1">
    <title>r4atlantis by r4atlantis</title>

    <link rel="stylesheet" href="stylesheets/styles.css">
    <link rel="stylesheet" href="stylesheets/github-light.css">
    <meta name="viewport" content="width=device-width">
    <!--[if lt IE 9]>
    <script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
    <![endif]-->
  </head>
  <body>
    <div class="wrapper">
      <header>
        <h1>r4atlantis</h1>
        <p></p>


        <p class="view"><a href="https://github.com/r4atlantis">View My GitHub Profile</a></p>

      </header>
      <section>
        <h3>
<a id="welcome-to-r4atlantis-home-for-r-code-developed-by-the-atlantis-community" class="anchor" href="#welcome-to-r4atlantis-home-for-r-code-developed-by-the-atlantis-community" aria-hidden="true"><span class="octicon octicon-link"></span></a>Welcome to r4atlantis, home for R code developed by the Atlantis community</h3>

<p>r4atlantis is meant to be your link to code for developing, executing, and comparing Atlantis models in R. We will provide forked copies of existing projects that are regularly updated and also host code directly.  We hope this space can also serve both as a launching spot for finding all the code others have written and as a common development area where new packages can be designed.  </p>

<h3>
<a id="general-organization-set-up" class="anchor" href="#general-organization-set-up" aria-hidden="true"><span class="octicon octicon-link"></span></a>General organization set-up</h3>

<p>If you have code you'd like to contribute or would like to join the group or a specific team, please contact <a href="https://github.com/jsgosnell" class="user-mention">@jsgosnell</a> or <a href="https://github.com/thefaylab" class="user-mention">@thefaylab</a></p>

<h3>
<a id="current-packages-and-relation-to-atlantis-workflow" class="anchor" href="#current-packages-and-relation-to-atlantis-workflow" aria-hidden="true"><span class="octicon octicon-link"></span></a>Current packages and relation to Atlantis workflow</h3>

<h4>
<a id="developing-input-files" class="anchor" href="#developing-input-files" aria-hidden="true"><span class="octicon octicon-link"></span></a>Developing input files</h4>

<p><strong>ratlantis</strong>- functions to generate bgm file and run Atlantis from R console, gather data on species trait, interactions, and distribution from the cloud, suggest functional groupings, and generate the bio.prm file</p>

<h4>
<a id="tuning-and-visualization" class="anchor" href="#tuning-and-visualization" aria-hidden="true"><span class="octicon octicon-link"></span></a>Tuning and visualization</h4>

<p><strong>vat</strong> - code for shiny application to visualize Atlantis output</p>

<h4>
<a id="data-processing" class="anchor" href="#data-processing" aria-hidden="true"><span class="octicon octicon-link"></span></a>Data processing</h4>

<p><strong>atlantisom</strong> - functions to generate data sets from atlantis scenarios</p>
      </section>
      <footer>
        <p><small>Hosted on GitHub Pages &mdash; Theme by <a href="https://github.com/orderedlist">orderedlist</a></small></p>
      </footer>
    </div>
    <script src="javascripts/scale.fix.js"></script>

  </body>
</html>