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		<h1>VizSearch: Visualizing NCEAS Research Projects and Publications</h1>
		<a href="https://www.nceas.ucsb.edu" target="_blank" class="intro-img"><img src="img/NCEAS-stacked-logo-200px.png" /></a>
		<p class="intro-text">
			In the past two decades, researchers at NCEAS have produced over 2200 peer-reviewed publications as part of nearly 500 projects. These products include groundbreaking innovations in synthesis science and encompass a broad range of topics, from the ecological effects of climate change to foundational concepts in evolution and community ecology.  Over time, the scope of research at NCEAS has continued to expand to encompass conservation and resource management challenges and critical issues at the nexus of nature conservation and human well-being. Given the volume and range of NCEAS research over the past 20 years, NCEAS has sought to create new tools to help understand and communicate both the scope and impact of our collective work. Through this process, sixteen themes have emerged that best describe NCEAS papers and projects.
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		<a href="#" class="expander title" data-target="intro-how-to-use"><i class="icon fa fa-caret-right"></i> How to use</a>
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			<p>The sixteen themes of NCEAS' research are represented as arcs on the outer circle. The colored circles and squares represent NCEAS projects and products and their relationships to the research themes.
				<ul class="four-col">
					<li class="cat-color" data-category="1">Informatics, Models, and Analytics</li>
					<li class="cat-color" data-category="2">Biodiversity Conservation</li>
					<li class="cat-color" data-category="3">Ecosystem Services</li>
					<li class="cat-color" data-category="4">Marine Ecology and Resources</li>
					<li class="cat-color" data-category="5">Community Ecology</li>
					<li class="cat-color" data-category="6">Ecological Effects of Climate Change</li>
					<li class="cat-color" data-category="7">Landscape Ecology</li>
					<li class="cat-color" data-category="8">Population Dynamics</li>
					<li class="cat-color" data-category="9">Biogeography</li>
					<li class="cat-color" data-category="10">Nutrient Cycling and Productivity</li>
					<li class="cat-color" data-category="11">Foodweb Ecology</li>
					<li class="cat-color" data-category="12">Paleoecology</li>
					<li class="cat-color" data-category="13">Evolution</li>
					<li class="cat-color" data-category="14">Forest Ecology</li>
					<li class="cat-color" data-category="15">Disturbances and Invasive Species</li>
					<li class="cat-color" data-category="16">Infectious Disease</li>
				</ul>
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				<ul>
					<li>Click on the <b>outer circle</b> to get a closer look at a theme and see which NCEAS projects and products most closely relate to it.</li>
					<li><b>Circles</b> represent NCEAS research projects or Working Groups.</li>
					<li><b>Squares</b> indicate individual NCEAS products (e.g. articles, reviews).</li>
					<li><b>Color</b> indicates the topic to which the circle or square is most closely related.</li>
					<li><b>Brightness:</b> when a theme is chosen, brightness shows how closely related the product or project is to that topic.</li>
					<li><b>Clusters</b> indicate projects and products that are most similar to each other at a finer scale.</li>
				</ul>
			</p>
		</div>
		<a href="#" class="expander title" data-target="intro-methodology"><i class="icon fa fa-caret-right"></i> Methodology</a>
		<div class="collapsed" id="intro-methodology">
			<p>Beginning in 2012, NCEAS Postdoctoral Associate (now Research Associate) Stacy Rebich Hespanha used Latent Dirichlet Allocation (LDA) topic modeling to identify these sixteen emergent subject areas that describe the main themes addressed in the titles, abstracts, and keywords of NCEAS papers and projects, as well as 87 finer-scale topics that define the clusters in this visualization. Latent Dirichlet Allocation, a probabilistic approach to discovering topics based on co-occurrence of terms, was first described in <a href="http://jmlr.csail.mit.edu/papers/v3/blei03a.html" target="_blank"> Blei, Ng &amp; Jordan, 2003</a>. A more general overview of topic modeling approaches by <a href="http://dx.doi.org/10.1145/2133806.2133826" target="_blank">David Blei (2012)</a> provides a good introduction. The location of the points was determined through the Hellinger distance and t-distributed stochastic neighbor embedding (t-SNE), which pulls each point together with its nearest neighbors in 2D space, but doesn't necessarily push dissimilar documents apart. t-SNE was described by <a href="http://jmlr.org/papers/volume9/vandermaaten08a/vandermaaten08a.pdf" target="_blank">van der Maarten and Hinton (2008)</a>.</p>
			<p>Based on these data, Stacy and NCEAS web developer and designer Lauren Walker sketched out a design for a web-based interactive visualization tool for browsing and exploring  the entire body of work at NCEAS. During the first <a href="http://nceas.github.io/open-science-codefest/" target="_blank">Open Science Codefest</a> in 2014, informatics experts contributed to the development of this visualization. Lauren has since continued development of the project, resulting in this interactive publication browser.</p>
		</div>	
		<a href="#" class="expander title" data-target="intro-acknowledgements"><i class="icon fa fa-caret-right"></i> Acknowledgments</a>
		<div class="collapsed" id="intro-acknowledgements">
			<p>
				<cite >Rebich-Hespanha S, Walker L, Donahue D, Fine L, French L, Hampton SE, Harris DJ and Visalli M. (2015) VizSearch: Visualizing NCEAS Research Projects and Publications. <a href="https://www.nceas.ucsb.edu//VizSearch">https://www.nceas.ucsb.edu/VizSearch</a></cite>
			</p>
			<p>The open source code for this visualization <a href="https://github.com/lauren-walker/TopicViz" target="_blank">is on GitHub</a> and is free to use.</p>
			<p class="smaller">
				Thanks to <a href="https://github.com/jmaccuish" target="_blank">John MacCuish</a> and <a href="https://github.com/parkerabercrombie" target="_blank">Parker Abercrombie</a> 
				for their contributions to the development of this visualization. The topic modeling and visualization was conducted using the <a href="http://www.ece.ucsb.edu/~hespanha/software/textvistools.html" target="_blank">Text Visualization Toolbox</a>, 
				the <a href="http://d3js.org/" target="_blank">D3 JavaScript Library</a>, the <a href="http://cran.r-project.org/web/packages/tsne/index.html" target="_blank">tsne</a> R package, 
				and <a href="http://shiny.rstudio.com/" target="_blank">Shiny</a>.
			</p>
		</div>
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	<div class="replacement-text container" id="cat-info-1">
		<span class="pretitle">Theme</span>
		<h1 class="project" data-category="1">Informatics, Modeling &amp; Analytics</h1>
		<p class="project">The NCEAS projects and products most closely related to Informatics, Modeling &amp; Analytics describe innovative models and data analysis methods for ecological synthesis.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> models, data, methods, uncertainty, analysis</p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div  class="replacement-text container" id="cat-info-2">
		<span class="pretitle">Theme</span>
		<h1 class="project" data-category="2">Biodiversity Conservation &amp; Management</h1>
		<p class="project">These papers and projects address critical questions about how to protect biodiversity and manage scarce resources in the face of uncertainty.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> conservation, biodiversity, species, threats</p>
		<p class="project"><a href="https://www.nceas.ucsb.edu/science-highlights?id=conservation-highlights" class="more-link" target="_blank">NCEAS Science Highlights<i class="icon fa fa-external-link-square"></i></a></p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div  class="replacement-text container" id="cat-info-3">
		<span class="pretitle">Theme</span>
		<h1 class="project" data-category="3">Ecosystem Services</h1>
		<p class="project">NCEAS research has developed quantitative approaches and tools to evaluate the benefits people obtain from ecosystems.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> ecosystem services, restoration, land, management</p>
		<p class="project"><a href="https://www.nceas.ucsb.edu/science-highlights?id=services-highlights" class="more-link" target="_blank">NCEAS Science Highlights<i class="icon fa fa-external-link-square"></i></a></p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div  class="replacement-text container" id="cat-info-4">
		<span class="pretitle">Theme</span>
		<h1 class="project"  data-category="4">Marine Ecology and Resources Management</h1>
		<p class="project">These papers and projects focus on interdisciplinary marine ecosystem science, and many of them have informed effective policy and management.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> fisheries, marine reserves, ocean, management</p>
		<p class="project"><a href="https://www.nceas.ucsb.edu/science-highlights?id=marine-highlights" class="more-link" target="_blank">NCEAS Science Highlights<i class="icon fa fa-external-link-square"></i></a></p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div class="replacement-text container" id="cat-info-5">
		<span class="pretitle">Theme</span>
		<h1 class="project"  data-category="5">Community Ecology</h1>
		<p class="project">Papers and projects most closely related to Community Ecology focus on community-scale determinants of species richness, diversity, and coexistence.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> species, communities, diversity, productivity, species richness</p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div class="replacement-text container" id="cat-info-6">
		<span class="pretitle">Theme</span>
		<h1 class="project"  data-category="6">Ecological Effects of Climate Change</h1>
		<p class="project">Over 100 NCEAS projects have focused on climate change feedbacks and the effects of climate change on organisms and ecosystems.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> climate change, temperature, vegetation, responses, precipitation</p>
		<p class="project"><a href="https://www.nceas.ucsb.edu/science-highlights?id=climate-highlights" class="more-link" target="_blank">NCEAS Science Highlights<i class="icon fa fa-external-link-square"></i></a></p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div class="replacement-text container" id="cat-info-7">
		<span class="pretitle">Theme</span>
		<h1 class="project"  data-category="7">Landscape Ecology</h1>
		<p class="project">NCEAS papers and projects on Landscape Ecology examine how species move through habitat patches and corridors.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> dispersal, habitat, populations, landscape, patches</p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div class="replacement-text container" id="cat-info-8">
		<span class="pretitle">Theme</span>
		<h1 class="project"  data-category="8">Population Dynamics</h1>
		<p class="project">These papers and projects have contributed foundation science analyzing survival, mortality, and how populations change over time.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> populations, individuals, dynamics, mortality, survival</p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div class="replacement-text container" id="cat-info-9">
		<span class="pretitle">Theme</span>
		<h1 class="project"  data-category="9">Biogeography</h1>
		<p class="project">Biogeography studies global patterns of species distribution, abundance, and biodiversity and their causes.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> patterns, species, range, distribution</p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div class="replacement-text container" id="cat-info-10">
		<span class="pretitle">Theme</span>
		<h1 class="project"  data-category="10">Nutrient Cycling and Productivity</h1>
		<p class="project">These papers and projects examine how carbon, nitrogen, and other nutrients move through ecosystems.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> global, npp, soil, decomposition</p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div class="replacement-text container" id="cat-info-11">
		<span class="pretitle">Theme</span>
		<h1 class="project"  data-category="11">Foodweb Ecology</h1>
		<p class="project">NCEAS research in this area has improved our understanding of interactions between predators, prey, and competitors.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> prey, predators, food webs, coexistence</p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div class="replacement-text container" id="cat-info-12">
		<span class="pretitle">Theme</span>
		<h1 class="project"  data-category="12">Paleoecology</h1>
		<p class="project">NCEAS researchers have developed new approaches to reconstructing the history of biodiversity on Earth.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> diversity, extinction, taxa, time, fossil record</p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div class="replacement-text container" id="cat-info-13">
		<span class="pretitle">Theme</span>
		<h1 class="project"  data-category="13">Evolution</h1>
		<p class="project">Papers and projects related to Evolution address foundational concepts in selection, speciation, adaptation, and phylogenetics.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> evolution, selection, traits, species</p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div class="replacement-text container" id="cat-info-14">
		<span class="pretitle">Theme</span>
		<h1 class="project"  data-category="14">Forest Ecology</h1>
		<p class="project">These papers and projects study how tropical and temperate forests grow and change.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> forest, plants, growth</p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div class="replacement-text container" id="cat-info-15">
		<span class="pretitle">Theme</span>
		<h1 class="project" data-category="15">Disturbances and Invasive Species</h1>
		<p class="project">Research in this area examines ecosystem responses to fire, invasions, and other disturbances.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> invasion, disturbance, establishment, success</p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
	</div>
	
	<div class="replacement-text container" id="cat-info-16">
		<span class="pretitle">Theme</span>
		<h1 class="project" data-category="16">Infectious Disease</h1>
		<p class="project">These papers and projects have contributed new knowledge about the drivers of the spread of disease in human and wild populations.</p>
		<p class="project terms"><span class="pretitle">Representative terms</span> disease, parasites, host, pathogens, transmission</p>
		<p class="project"><a href="https://www.nceas.ucsb.edu/science-highlights?id=disease-highlights" class="more-link" target="_blank">NCEAS Science Highlights <i class="icon fa fa-external-link-square"></i></a></p>
		<p class="footnote"><strong>Circles</strong> represent NCEAS research projects or Working Groups and <strong>squares</strong> represent individual NCEAS products, such as articles or reviews. The <strong>brightness</strong> of the circles and squares indicates how closely related the product or project is to the chosen topic.</p>
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