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Markdown_for_Manuscripts_ms.doc
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Markdown_for_Manuscripts_ms.doc
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta http-equiv="Content-Style-Type" content="text/css" />
<meta name="generator" content="pandoc" />
<title></title>
<style type="text/css">code{white-space: pre;}</style>
\usepackage[vmargin=1in,hmargin=1in]{geometry}
</head>
<body>
<h1 id="catchy-title-that-reviewers-will-love">Catchy Title that Reviewers will Love</h1>
<h3 id="daniel-j.-hocking-and-names-of-awesome-coauthors">Daniel J. Hocking and Names of Awesome Coauthors</h3>
<p><em>Daniel J. Hocking (<script type="text/javascript">
<!--
h='usgs.gov';a='@';n='dhocking';e=n+a+h;
document.write('<a h'+'ref'+'="ma'+'ilto'+':'+e+'" clas'+'s="em' + 'ail">'+e+'<\/'+'a'+'>');
// -->
</script><noscript>dhocking at usgs dot gov</noscript>), US Geological Survey, Conte Anadromous Fish Research Center, Turners Falls, MA, USA</em></p>
<h2 id="abstract">Abstract</h2>
<p>Set up the problem. Explain how you solve it. Tell what you find. Explain why it's the best thing ever.</p>
<h2 id="introduction">Introduction</h2>
<p>Background and problem setup <span class="citation">(Hocking and Babbitt 2014a, 2014b)</span></p>
<p>Relevant literature <span class="citation">(Hocking 2013, Hocking et al. 2013)</span></p>
<p>Objectives/hypotheses</p>
<h2 id="methods">Methods</h2>
<p>Describe what you did so it can actually be repeated. I don't want to see everything in the supplementary materials. Here's an example of using LaTeX to add equations:</p>
<p><br /><span class="math">$$
T_s = \mu + \frac{\alpha - \mu}{1 + e^{\gamma(\beta - T_a)}}
$$</span><br /></p>
<h2 id="results">Results</h2>
<p>Explain what you found. Avoid blind <em>P-values</em> (or avoid <em>P-values</em> altogether)</p>
<h2 id="discussion">Discussion</h2>
<p>Give context to what you found. Relate it to previous work. Describe why it's the most important scientific finding of the decade, yet avoid hyperbole. Easy, right?</p>
<h2 id="acknowledgements">Acknowledgements</h2>
<p>Thanks to Ethan White, Karthik Ram, Carl Boettiger, Ben Morris, and <a href="http://software-carpentry.org/">Software Carpentry</a> for getting me started with the skills needed to <a href="http://inundata.org/2012/12/04/how-to-ditch-word/">ditch MS Word</a> and produce more reproducible research.</p>
<h2 id="tables">Tables</h2>
<p>Table 1: Example Markdown table</p>
<table>
<colgroup>
<col width="20%" />
<col width="11%" />
<col width="8%" />
<col width="13%" />
<col width="12%" />
<col width="18%" />
</colgroup>
<thead>
<tr class="header">
<th align="left">Name</th>
<th align="left">col2</th>
<th align="left">col3</th>
<th align="left">col4</th>
<th align="left">col5</th>
<th align="left">Comments</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left"><p>Brook Trout</p></td>
<td align="left"><p>1</p></td>
<td align="left"><p>big</p></td>
<td align="left"><p>few</p></td>
<td align="left"><p>2.2</p></td>
<td align="left"><p>Ecology & life history data associated with trout</p></td>
</tr>
<tr class="even">
<td align="left"><p><em>Desmognathus</em> <em>fuscus</em></p></td>
<td align="left"><p>100</p></td>
<td align="left"><p>small</p></td>
<td align="left"><p>many</p></td>
<td align="left"><p>0.3</p></td>
<td align="left"><p>Widespread salamander species</p></td>
</tr>
</tbody>
</table>
<h2 id="figures">Figures</h2>
<p>Figure 1. Example of adding a figure.</p>
<div class="figure">
<img src="Figures/MADEP_W2033_T1.png" alt="Figure1" /><p class="caption">Figure1</p>
</div>
<div class="references">
<h2>Literature Cited</h2>
<p>Hocking, D. J. 2013. Comparing the influence of ecology journals using citation-based indices: making sense of a multitude of metrics. Ideas in Ecology and Evolution 6:55–65.</p>
<p>Hocking, D. J., and K. J. Babbitt. 2014a. Amphibian contributions to ecosystem services. Herpetological Conservation and Biology 9:1–17.</p>
<p>Hocking, D. J., and K. J. Babbitt. 2014b. Effects of red-backed salamanders on ecosystem functions. PloS one 9:e86854.</p>
<p>Hocking, D. J., K. J. Babbitt, and M. Yamasaki. 2013. Comparison of silvicultural and natural disturbance effects on terrestrial salamanders in northern hardwood forests. Biological Conservation 167:194–202.</p>
</div>
</body>
</html>