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A Simulation Study Comparing Epidemic Dynamics on Exponential Random Graph and Edge-Triangle Configuration Type Contact Network Models

Identifieur interne : 000568 ( Ncbi/Merge ); précédent : 000567; suivant : 000569

A Simulation Study Comparing Epidemic Dynamics on Exponential Random Graph and Edge-Triangle Configuration Type Contact Network Models

Auteurs : David A. Rolls [Australie] ; Peng Wang [Australie] ; Emma Mcbryde [Australie] ; Philippa Pattison [Australie] ; Garry Robins [Australie]

Source :

RBID : PMC:4640514

Abstract

We compare two broad types of empirically grounded random network models in terms of their abilities to capture both network features and simulated Susceptible-Infected-Recovered (SIR) epidemic dynamics. The types of network models are exponential random graph models (ERGMs) and extensions of the configuration model. We use three kinds of empirical contact networks, chosen to provide both variety and realistic patterns of human contact: a highly clustered network, a bipartite network and a snowball sampled network of a “hidden population”. In the case of the snowball sampled network we present a novel method for fitting an edge-triangle model. In our results, ERGMs consistently capture clustering as well or better than configuration-type models, but the latter models better capture the node degree distribution. Despite the additional computational requirements to fit ERGMs to empirical networks, the use of ERGMs provides only a slight improvement in the ability of the models to recreate epidemic features of the empirical network in simulated SIR epidemics. Generally, SIR epidemic results from using configuration-type models fall between those from a random network model (i.e., an Erdős-Rényi model) and an ERGM. The addition of subgraphs of size four to edge-triangle type models does improve agreement with the empirical network for smaller densities in clustered networks. Additional subgraphs do not make a noticeable difference in our example, although we would expect the ability to model cliques to be helpful for contact networks exhibiting household structure.


Url:
DOI: 10.1371/journal.pone.0142181
PubMed: 26555701
PubMed Central: 4640514

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PMC:4640514

Le document en format XML

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<pmc article-type="research-article">
<pmc-dir>properties open_access</pmc-dir>
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group>
<journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher>
<publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, CA USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="pmid">26555701</article-id>
<article-id pub-id-type="pmc">4640514</article-id>
<article-id pub-id-type="publisher-id">PONE-D-14-27406</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0142181</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>A Simulation Study Comparing Epidemic Dynamics on Exponential Random Graph and Edge-Triangle Configuration Type Contact Network Models</article-title>
<alt-title alt-title-type="running-head">Comparing Epidemics on ERGMs and Configuration Type Network Models</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Rolls</surname>
<given-names>David A.</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="currentaff001">
<sup>¤</sup>
</xref>
<xref ref-type="corresp" rid="cor001">*</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Wang</surname>
<given-names>Peng</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>McBryde</surname>
<given-names>Emma</given-names>
</name>
<xref ref-type="aff" rid="aff002">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Pattison</surname>
<given-names>Philippa</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Robins</surname>
<given-names>Garry</given-names>
</name>
<xref ref-type="aff" rid="aff001">
<sup>1</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff001">
<label>1</label>
<addr-line>Melbourne School of Psychological Sciences, University of Melbourne, Melbourne, VIC 3010, Australia</addr-line>
</aff>
<aff id="aff002">
<label>2</label>
<addr-line>Department of Medicine-RMH, University of Melbourne, Melbourne, VIC 3010, Australia</addr-line>
</aff>
<contrib-group>
<contrib contrib-type="editor">
<name>
<surname>Moreno</surname>
<given-names>Yamir</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">
<addr-line>University of Zaragoza, SPAIN</addr-line>
</aff>
<author-notes>
<fn fn-type="COI-statement" id="coi001">
<p>
<bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="con" id="contrib001">
<p>Conceived and designed the experiments: DAR PW EM PP GR. Performed the experiments: DAR. Analyzed the data: DAR. Contributed reagents/materials/analysis tools: DAR PW. Wrote the paper: DAR EM GR.</p>
</fn>
<fn fn-type="current-aff" id="currentaff001">
<label>¤</label>
<p>Current address: Melbourne School of Psychological Sciences, University of Melbourne, Melbourne, VIC 3010, Australia</p>
</fn>
<corresp id="cor001">* E-mail:
<email>drolls@unimelb.edu.au</email>
</corresp>
</author-notes>
<pub-date pub-type="collection">
<year>2015</year>
</pub-date>
<pub-date pub-type="epub">
<day>10</day>
<month>11</month>
<year>2015</year>
</pub-date>
<volume>10</volume>
<issue>11</issue>
<elocation-id>e0142181</elocation-id>
<history>
<date date-type="received">
<day>24</day>
<month>6</month>
<year>2014</year>
</date>
<date date-type="accepted">
<day>19</day>
<month>10</month>
<year>2015</year>
</date>
</history>
<permissions>
<copyright-statement>© 2015 Rolls et al</copyright-statement>
<copyright-year>2015</copyright-year>
<copyright-holder>Rolls et al</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p>
</license>
</permissions>
<self-uri content-type="pdf" xlink:type="simple" xlink:href="pone.0142181.pdf"></self-uri>
<abstract>
<p>We compare two broad types of empirically grounded random network models in terms of their abilities to capture both network features and simulated Susceptible-Infected-Recovered (SIR) epidemic dynamics. The types of network models are exponential random graph models (ERGMs) and extensions of the configuration model. We use three kinds of empirical contact networks, chosen to provide both variety and realistic patterns of human contact: a highly clustered network, a bipartite network and a snowball sampled network of a “hidden population”. In the case of the snowball sampled network we present a novel method for fitting an edge-triangle model. In our results, ERGMs consistently capture clustering as well or better than configuration-type models, but the latter models better capture the node degree distribution. Despite the additional computational requirements to fit ERGMs to empirical networks, the use of ERGMs provides only a slight improvement in the ability of the models to recreate epidemic features of the empirical network in simulated SIR epidemics. Generally, SIR epidemic results from using configuration-type models fall between those from a random network model (i.e., an Erdős-Rényi model) and an ERGM. The addition of subgraphs of size four to edge-triangle type models does improve agreement with the empirical network for smaller densities in clustered networks. Additional subgraphs do not make a noticeable difference in our example, although we would expect the ability to model cliques to be helpful for contact networks exhibiting household structure.</p>
</abstract>
<funding-group>
<funding-statement>DAR was partly funded by the Australian Research Council (Discovery project grant 0987730,
<ext-link ext-link-type="uri" xlink:href="http://www.arc.gov.au/ncgp/dp/dp_default.htm">http://www.arc.gov.au/ncgp/dp/dp_default.htm</ext-link>
) and partly by the University of Melbourne. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
<counts>
<fig-count count="14"></fig-count>
<table-count count="7"></table-count>
<page-count count="36"></page-count>
</counts>
<custom-meta-group>
<custom-meta id="data-availability">
<meta-name>Data Availability</meta-name>
<meta-value>The Supporting Information files contain MATLAB datasets with the node degrees, graph statistics, and SIR simulation results from this study along with the node degrees of snowball sampled empirical and simulated networks using estimators one to six. All empirical networks are held by third parties. Data for the high school contact network is publicly available with that paper. Our depiction of the relationships network is new, based on manually recoding the network depiction in Bearman et al. For the original network data, interested parties should contact the authors of that paper or the AddHealth study team. Data for the PWID network is held by the Burnet Institute. Researchers with serious enquiries should contact Dr. Margaret Hellard (
<email>hellard@burnet.edu.au</email>
).</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
<notes>
<title>Data Availability</title>
<p>The Supporting Information files contain MATLAB datasets with the node degrees, graph statistics, and SIR simulation results from this study along with the node degrees of snowball sampled empirical and simulated networks using estimators one to six. All empirical networks are held by third parties. Data for the high school contact network is publicly available with that paper. Our depiction of the relationships network is new, based on manually recoding the network depiction in Bearman et al. For the original network data, interested parties should contact the authors of that paper or the AddHealth study team. Data for the PWID network is held by the Burnet Institute. Researchers with serious enquiries should contact Dr. Margaret Hellard (
<email>hellard@burnet.edu.au</email>
).</p>
</notes>
</front>
</pmc>
<affiliations>
<list>
<country>
<li>Australie</li>
</country>
<region>
<li>Victoria (État)</li>
</region>
<settlement>
<li>Melbourne</li>
</settlement>
<orgName>
<li>Université de Melbourne</li>
</orgName>
</list>
<tree>
<country name="Australie">
<region name="Victoria (État)">
<name sortKey="Rolls, David A" sort="Rolls, David A" uniqKey="Rolls D" first="David A." last="Rolls">David A. Rolls</name>
</region>
<name sortKey="Mcbryde, Emma" sort="Mcbryde, Emma" uniqKey="Mcbryde E" first="Emma" last="Mcbryde">Emma Mcbryde</name>
<name sortKey="Pattison, Philippa" sort="Pattison, Philippa" uniqKey="Pattison P" first="Philippa" last="Pattison">Philippa Pattison</name>
<name sortKey="Robins, Garry" sort="Robins, Garry" uniqKey="Robins G" first="Garry" last="Robins">Garry Robins</name>
<name sortKey="Wang, Peng" sort="Wang, Peng" uniqKey="Wang P" first="Peng" last="Wang">Peng Wang</name>
</country>
</tree>
</affiliations>
</record>

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