Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: outbreaker2
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/outbreaker2
Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data
6 versions
Latest release: over 2 years ago
1 dependent package
322 downloads last month
Papers Mentioning outbreaker2 7
10.1111/2041-210X.13422
nosoi: A stochastic agent‐based transmission chain simulation framework in <scp>r</scp>Cited by: 19
Author(s): Sébastian Lequime, Paul Bastide, Simon Dellicour, Philippe Lemey, Guy Baele
Software Mentions: 8
Published: about 4 years ago
10.1186/s12859-018-2330-z
outbreaker2: a modular platform for outbreak reconstructionCited by: 50
Author(s): Finlay Campbell, Xavier Didelot, Richard G. FitzJohn, Neil Ferguson, Anne Cori, Thibaut Jombart
Software Mentions: 6
Published: almost 6 years ago
10.3390/v13071186
Retrospective Characterization of the 2006–2007 Swine Vesicular Disease Epidemic in Northern Italy by Whole Genome Sequence AnalysisCited by: 0
Author(s): Giulia Pezzoni, Arianna Bregoli, Chiara Chiapponi, Santina Grazioli, Antonello Di Nardo, Emiliana Brocchi
Software Mentions: 4
Published: about 3 years ago
10.1098/rsif.2020.0084
Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance dataCited by: 7
Author(s): Alexis Robert, Adam J. Kucharski, Paul A. Gastañaduy, Prabasaj Paul, Sebastian Funk
Software Mentions: 3
Published: about 4 years ago
10.1038/s41598-020-78900-3
Identifying likely transmissions in Mycobacterium bovis infected populations of cattle and badgers using the Kolmogorov Forward EquationsCited by: 2
Author(s): Gianluigi Rossi, Joseph Crispell, Daniel Balaz, Samantha Lycett, Clare H. Benton, Richard J. Delahay, Rowland R. Kao
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pcbi.1006930
Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact dataCited by: 56
Author(s): Finlay Campbell, Anne Cori, Neil M. Ferguson, Thibaut Jombart
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.ppat.1006885
When are pathogen genome sequences informative of transmission events?Cited by: 159
Author(s): Finlay Campbell, Camilla Strang, Neil Ferguson, Anne Cori, Thibaut Jombart
Software Mentions: 1
Published: over 6 years ago