This package has implementations of epidemiologic compartmental models, [Wk1, HH1],
modified to fit better simulations of propagation of COVID-19, [Wk2].
The models implemented in this package deal with one, two, or all three of the rectangles in this diagram:
The content of the package corresponds to the Mathematica packages and notebooks referenced below.
(But there are some significant differences.)
Here is an installation command using "devtools":
devtools::install_github(repo = "antononcube/ECMMon-R")
Remark: The simulations done by the package functions rely on the R package
"deSolve",
which in turn relies on FORTRAN code. For example, on Mac OS X the installation of gfortran
is needed.
Here is a notebook that demonstrates usage of the provided objects and functions:
"Basic experiments workflow for simple epidemiological models",
(HTML).
The package repository has flexdashboard interfaces for the more important models.
Here are the core (single-site) models
SIR
“Susceptible, Infected, Recovered” populations
SEIR
“Susceptible, Exposed, Infected, Recovered” populations
SEI2R
“Susceptible, Exposed, Infected two, Recovered” populations
SEI2HR
“Susceptible, Exposed, Infected two, Hospitalized, Recovered” populations
SEI2HREcon
“Susceptible, Exposed, Infected two, Hospitalized, Recovered” populations with Economic extensions
[Wk1] Wikipedia entry, "Compartmental models in epidemiology".
[Wl2] Wikipedia entry, "Coronavirus disease 2019".
[HH1] Herbert W. Hethcote (2000). "The Mathematics of Infectious Diseases". SIAM Review. 42 (4): 599–653. Bibcode:2000SIAMR..42..599H. doi:10.1137/s0036144500371907.
[AA1] Anton Antonov, "Coronavirus propagation modeling considerations", (2020), SystemModeling at GitHub.
[AA2] Anton Antonov, "Basic experiments workflow for simple epidemiological models", (2020), SystemModeling at GitHub.
[AA3] Anton Antonov, "Scaling of Epidemiology Models with Multi-site Compartments", (2020), SystemModeling at GitHub.
[AAr1] Anton Antonov, Coronavirus propagation dynamics project, (2020), SystemModeling at GitHub.
[AAp1] Anton Antonov, "Epidemiology models Mathematica package", (2020), SystemModeling at GitHub.
[AAp2] Anton Antonov, "Epidemiology models modifications Mathematica package", (2020), SystemModeling at GitHub.
[AAp3] Anton Antonov, "Epidemiology modeling visualization functions Mathematica package", (2020), SystemModeling at GitHub.
[AAp4] Anton Antonov, "System dynamics interactive interfaces functions Mathematica package", (2020), SystemModeling at GitHub.