This package demonstrates use of the odin, dust and mcstate R packages for running stochastic SIR and SEIR models and fitting them to simulated data [1]. See also the SIR model odin.dust vignette and mcstate vignette.
The package requires the following versions of the eigen1, odin, dust, odin.dust and mcstate packages to be installed:
eigen1 0.1.3
odin 1.5.10
dust 0.15.1
odin.dust 0.3.10
mcstate 0.9.20
These can be installed in R with:
remotes::install_github(c(
"mrc-ide/[email protected]",
"mrc-ide/[email protected]",
"mrc-ide/[email protected]",
"mrc-ide/[email protected]",
"mrc-ide/[email protected]"))The vignettes use the coda package, which can be installed from CRAN with:
install.packages("coda")Install the package with:
remotes::install_github("LloydChapman/seir", upgrade = FALSE, build_vignettes = TRUE)- FitzJohn RG, Knock ES, Whittles LK, Perez-Guzman PN, Bhatia S, Guntoro F, Watson OJ, Whittaker C, Ferguson NM, Cori A, Baguelin M, and Lees JA. Reproducible parallel inference and simulation of stochastic state space models using odin, dust, and mcstate. Wellcome Open Research, 5:288, 12 2021. doi:10.12688/wellcomeopenres.16466.2