Epidemiologic Compartmental Modeling Monad R package

Introduction

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.)

Installation

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.

Usage

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.

Core 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

References

Articles

[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.

Repositories, packages

[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.