| EpiEstim | Estimate Time Varying Reproduction Numbers from Epidemic Curves Anne Cori , Simon Cauchemez , Neil M. Ferguson , Christophe Fraser , Elisabeth Dahlqwist , P. Alex Demarsh , Thibaut Jombart , Zhian N. Kamvar , Justin Lessler , Shikun Li , Jonathan A. Polonsky , Jake Stockwin , Robin Thompson , Rolina van Gaalen |
| ade4 | Analysis of Ecological Data Stéphane Dray , Anne-Béatrice Dufour , Jean Thioulouse , Thibaut Jombart , Sandrine Pavoine , Jean R. Lobry , Sébastien Ollier , Daniel Borcard , Pierre Legendre , Stéphanie Bougeard , Aurélie Siberchicot. Based on earlier work by Daniel Chessel. |
| adegenet | Exploratory Analysis of Genetic and Genomic Data Thibaut Jombart , Zhian N. Kamvar , Caitlin Collins , Roman Lustrik , Marie-Pauline Beugin , Brian J. Knaus , Peter Solymos , Vladimir Mikryukov , Klaus Schliep , Tiago Maié , Libor Morkovsky , Ismail Ahmed , Anne Cori , Federico Calboli , RJ Ewing , Frédéric Michaud , Rebecca DeCamp , Alexandre Courtiol , Lindsay V. Clark , Pavel Dimens |
| adephylo | Exploratory Analyses for the Phylogenetic Comparative Method Thibaut Jombart , Stéphane Dray , Anders Ellern Bilgrau |
| adespatial | Multivariate Multiscale Spatial Analysis Stéphane Dray , David Bauman , Guillaume Blanchet , Daniel Borcard , Sylvie Clappe , Guillaume Guenard , Thibaut Jombart , Guillaume Larocque , Pierre Legendre , Naima Madi , Hélène H Wagner , Aurélie Siberchicot |
| apex | Phylogenetic Methods for Multiple Gene Data Klaus Schliep , Thibaut Jombart , Zhian Namir Kamvar , Eric Archer , Rebecca Harris |
| distcrete | Discrete Distribution Approximations Steph Locke , Rich FitzJohn , Anne Cori , Thibaut Jombart |
| earlyR | Estimation of Transmissibility in the Early Stages of a Disease Outbreak Thibaut Jombart , Anne Cori , Pierre Nouvellet , Janetta Skarp , Zhian N. Kamvar , Tim Taylor |
| epicontacts | Handling, Visualisation and Analysis of Epidemiological Contacts Finlay Campbell , Thibaut Jombart , Nistara Randhawa , Bertr , Sudre , VP Nagraj , Thomas Crellen , Zhian N. Kamvar |
| epiflows | Predicting Disease Spread from Flow Data Pawel Piatkowski , Paula Moraga , Isobel Blake , Thibaut Jombart , VP Nagraj , Zhian N. Kamvar , Salla E. Toikkanen |
| epitrix | Small Helpers and Tricks for Epidemics Analysis Thibaut Jombart , Anne Cori , Zhian N. Kamvar , Dirk Schumacher , Flavio Finger , Charlie Whittaker |
| finalsize | Calculate the Final Size of an Epidemic Pratik Gupte , Edwin Van Leeuwen , Adam Kucharski , Rosalind Eggo , Hugo Gruson , Thibaut Jombart , Andree Valle-Campos , Joshua W. Lambert |
| hierfstat | Estimation and Tests of Hierarchical F-Statistics Jerome Goudet , Thibaut Jombart , Zhian N. Kamvar , Eric Archer , Olivier Hardy |
| i2extras | Functions to Work with 'incidence2' Objects Tim Taylor , Thibaut Jombart |
| incidence | Compute, Handle, Plot and Model Incidence of Dated Events Thibaut Jombart , Zhian N. Kamvar , Rich FitzJohn , Tim Taylor , Jun Cai , Sangeeta Bhatia , Jakob Schumacher , Juliet R.C. Pulliam |
| incidence2 | Compute, Handle and Plot Incidence of Dated Events Tim Taylor , Thibaut Jombart |
| linelist | Tagging and Validating Epidemiological Data Hugo Gruson , Thibaut Jombart , Tim Taylor , Chris Hartgerink |
| matchmaker | Flexible Dictionary-Based Cleaning Zhian N. Kamvar , Thibaut Jombart , Patrick Barks |
| o2geosocial | Reconstruction of Transmission Chains from Surveillance Data Alexis Robert , Sebastian Funk , Adam J Kucharski , Thibaut Jombart |
| odin | ODE Generation and Integration Rich FitzJohn , Thibaut Jombart , Imperial College of Science , Technology , Medicine |
| outbreaker2 | Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data Thibaut Jombart , Finlay Campbell , Rich Fitzjohn , Gerry Tonkin-Hill , Kristjan Eldjarn , Alexis Robert |
| outbreaks | A Collection of Disease Outbreak Data Thibaut Jombart , Simon Frost , Pierre Nouvellet , Finlay Campbell , Bertr , Sudre , Sang Woo Park , Juliet R.C. Pulliam , Jakob Schumacher , Eric Brown |
| pegas | Population and Evolutionary Genetics Analysis System Emmanuel Paradis , Thibaut Jombart , Zhian N. Kamvar , Brian Knaus , Klaus Schliep , Alastair Potts , David Winter |
| projections | Project Future Case Incidence Thibaut Jombart , Pierre Nouvellet , Sangeeta Bhatia , Zhian N. Kamvar , Tim Taylor , Stephane Ghozzi |
| reportfactory | Lightweight Infrastructure for Handling Multiple R Markdown Documents Thibaut Jombart , Amy Gimma , Tim Taylor |
| treespace | Statistical Exploration of Landscapes of Phylogenetic Trees Thibaut Jombart , Michelle Kendall , Jacob Almagro-Garcia , Caroline Colijn |
| trendeval | Evaluate Trending Models Dirk Schumacher , Thibaut Jombart , Tim Taylor |
| trending | Model Temporal Trends Tim Taylor , Dirk Schumacher , Thibaut Jombart |