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.