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ArboEpiSim is an arbovirus agent-based epidemiological simulator taking into account within-host dynamics in R.

This piece of code has been used in the following publication (please refer to it for more informations):

• Albin Fontaine, Sebastian Lequime, Isabelle Moltini-Conclois, Davy Jiolle, Isabelle Leparc-Goffart, Robert Charles Reiner, Louis Lambrechts (2018) Epidemiological significance of dengue virus genetic variation in mosquito infectiondynamics. PLoS Pathogens 14(7): e1007187.https://doi.org/10.1371/journal.ppat.1007187

The three different files can be found in the repository. They differ in the way "Mosquito to human" (or vertebrate host) transmission probability is computed:

• ArboEpiSim-3Parameter.R : the probability of transmission is depend on time according to a 3 parameter model (see above paper for more details). Each parameter set is uniquely drawn for each individual mosquito in the population.
• ArboEpiSim-Fixed_Threshold.R : the probability of transmission is constant (100%) once the EIP (fixed, same for every individual in the population) is reached.
• ArboEpiSim-Variable_Threshold.R : the probability of transmission is constant (100%) once the EIP (uniquely drawn from a distribution, according for measured parameters of the population, for each mosquito individual) is reached.

This code runs with the help of the following packages:

• foreach: Microsoft & Steve Weston (2017). foreach: Provides Foreach Looping Construct for R. R package version 1.4.4.https://CRAN.R-project.org/package=foreach
• doParallel: Microsoft & Steve Weston (2017). doParallel: Foreach Parallel Adaptor for the 'parallel' Package. R package version 1.0.11.https://CRAN.R-project.org/package=doParallel
• plyr: Hadley Wickham (2011) The Split=Apply=Combine Strategy for Data Analysis. Journal of Statistical Software 40(1):1=29
• dplyr: Hadley Wickham, Romain Francois, Lionel Henry, Kirill Müller (2017) dplyr: A Grammar of Data Manipulation. R package version 0.7.4.https://CRAN.R-project.org/package=dplyr
• reshape2: Hadley Wickham (2007) Reshaping Data with the reshape Package. Journal of Statistical Software 21(10):1=20
• data.table:Matt Dowle & Arun Srinivasan (2017) data.table: Extension of 'data.frame'. R package version 1.10.4=3.https://CRAN.R-project.org/package=data.table
• stringr:Hadley Wickham (2017) stringr: Simple, Consistant Wrappers for Common String Operations. R package version 1.2.0https://CRAN.R-project.org/package=stringr