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R scripts and data for “Model-based assessment of Chikungunya and O’nyong-nyong virus circulation in Mali in a serological cross-reactivity context”

Data

The following data is available in a format that maintains anonymity of survey participants. For each individual: age group (10-year classes), ONNV VNT, CHIKV VNT, region (North or South), sex.

Code

The code was written in R (version 3.6.1) and requires the package rstan. It was tested on a Windows computer with rstan version 2.19.2. To use rstan, Windows users must previously install Rtools.

The R scripts allow to load the data, plot the data (figure 1), run the MCMC algorithm, and display the parameter estimates.

All the scripts can be run sequentially using the script main.R