ZamCovid is a mechanistic model of SARS-CoV-2 transmission (COVID-19) designed to be used with Zambian epidemiological surveillance data. It is implemented as stochastic compartmental models in odin and dust, and it uses mcstate to perfom parsimonious Bayesian evidence synthesis, requiring at a minimum seroprevalence and all deaths data. It is flexiblo to incorporate PCR-positive/LFT-positive cases data and COVID-19 confirmed deaths, when official public health guidelines match model space variable definitions (see ?ZamCovid::zamcovid_data() for details).
Contact ZamCovid developer if you require access to the package. After access is given, you can install the development version of ZamCovid using:
devtools::install_github("pabloperguz/ZamCovid")Please note this package has been designed for very specific purposes, using selected datasets. Contact the developer before attempting to use ZamCovid for other projects or analyses.
ZamCovid has been developed with the use of dust, mcstate, odin, odin.dust. All these packages are under constant development and ZamCovid might not compile with versions other than the ones specified in DESCRIPTION.
For further information on the above packages and practical examples of their functionality see FitzJohn et al., 2021. Reproducible parallel inference and simulation of stochastic state space models using odin, dust, and mcstate.