outbreaker2: a modular platform for outbreak reconstruction.
outbreaker2: a modular platform for outbreak reconstruction.
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DOI：
10.1186/s12859-018-2330-z
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发表时间：
2018-10-22
影响因子：
3
通讯作者：
Jombart T
中科院分区：
文献类型：
--
作者：
Campbell F;Didelot X;Fitzjohn R;Ferguson N;Cori A;Jombart T
重建传染病暴发中的个体传播事件可以提供有价值的信息，并有助于制定感染控制政策。近年来，在利用流行病学和遗传数据重建传播链的方法发展方面取得了相当大的进展。然而，这些方法中只有少数已经在软件包中实现，并且很少考虑可定制性和互操作性。因此，用户被限制在少数可选的、具有固定功能的不兼容工具中，或者被迫花费大量个人精力开发自己的算法。在这里，我们提出了outbreaker2，这是一个用于爆发重建的灵活框架。这个R包重新实现并扩展了outbreaker引入的原始模型，但最重要的是，它还提供了一个模块化平台，允许用户在优化的推理框架内指定自定义模型。作为概念的证明，我们实现了由TransPhylo引入的宿主内进化模型，该模型与outbreaker中的原始遗传模型非常不同，并演示了如何以最小的努力成功地包含复杂的模型结果。Outbreaker2为未来的爆发重建工具提供了一个有价值的起点，并且代表了一个促进可定制性和互操作性的统一平台。在R软件中实现的outbreaker2加入了越来越多的爆发分析工具。
Reconstructing individual transmission events in an infectious disease outbreak can provide valuable information and help inform infection control policy. Recent years have seen considerable progress in the development of methodologies for reconstructing transmission chains using both epidemiological and genetic data. However, only a few of these methods have been implemented in software packages, and with little consideration for customisability and interoperability. Users are therefore limited to a small number of alternatives, incompatible tools with fixed functionality, or forced to develop their own algorithms at considerable personal effort. Here we present outbreaker2, a flexible framework for outbreak reconstruction. This R package re-implements and extends the original model introduced with outbreaker, but most importantly also provides a modular platform allowing users to specify custom models within an optimised inferential framework. As a proof of concept, we implement the within-host evolutionary model introduced with TransPhylo, which is very distinct from the original genetic model in outbreaker, and demonstrate how even complex model results can be successfully included with minimal effort. outbreaker2 provides a valuable starting point for future outbreak reconstruction tools, and represents a unifying platform that promotes customisability and interoperability. Implemented in the R software, outbreaker2 joins a growing body of tools for outbreak analysis.
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影响因子：
4.3
作者：
Lau MS;Marion G;Streftaris G;Gibson G
通讯作者：
Gibson G
DOI：
10.1056/nejmoa1411100
发表时间：
2014-10-16
期刊：
The New England journal of medicine
影响因子：
--
作者：
WHO Ebola Response Team;Aylward B;Barboza P;Bawo L;Bertherat E;Bilivogui P;Blake I;Brennan R;Briand S;Chakauya JM;Chitala K;Conteh RM;Cori A;Croisier A;Dangou JM;Diallo B;Donnelly CA;Dye C;Eckmanns T;Ferguson NM;Formenty P;Fuhrer C;Fukuda K;Garske T;Gasasira A;Gbanyan S;Graaff P;Heleze E;Jambai A;Jombart T;Kasolo F;Kadiobo AM;Keita S;Kertesz D;Koné M;Lane C;Markoff J;Massaquoi M;Mills H;Mulba JM;Musa E;Myhre J;Nasidi A;Nilles E;Nouvellet P;Nshimirimana D;Nuttall I;Nyenswah T;Olu O;Pendergast S;Perea W;Polonsky J;Riley S;Ronveaux O;Sakoba K;Santhana Gopala Krishnan R;Senga M;Shuaib F;Van Kerkhove MD;Vaz R;Wijekoon Kannangarage N;Yoti Z
通讯作者：
Yoti Z
影响因子：
3.8
作者：
Jombart, T.;Eggo, R. M.;Dodd, P. J.;Balloux, F.
通讯作者：
Balloux, F.
DOI：
10.1126/science.1259657
发表时间：
2014-09-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gire SK;Goba A;Andersen KG;Sealfon RS;Park DJ;Kanneh L;Jalloh S;Momoh M;Fullah M;Dudas G;Wohl S;Moses LM;Yozwiak NL;Winnicki S;Matranga CB;Malboeuf CM;Qu J;Gladden AD;Schaffner SF;Yang X;Jiang PP;Nekoui M;Colubri A;Coomber MR;Fonnie M;Moigboi A;Gbakie M;Kamara FK;Tucker V;Konuwa E;Saffa S;Sellu J;Jalloh AA;Kovoma A;Koninga J;Mustapha I;Kargbo K;Foday M;Yillah M;Kanneh F;Robert W;Massally JL;Chapman SB;Bochicchio J;Murphy C;Nusbaum C;Young S;Birren BW;Grant DS;Scheiffelin JS;Lander ES;Happi C;Gevao SM;Gnirke A;Rambaut A;Garry RF;Khan SH;Sabeti PC
通讯作者：
Sabeti PC
影响因子：
64.8
作者：
Lloyd-Smith JO;Schreiber SJ;Kopp PE;Getz WM
通讯作者：
Getz WM