https://github.com/antononcube/ecmmon-r
Epidemiologic Compartmental Modeling Monad in R
https://github.com/antononcube/ecmmon-r
compartmental-models epidemiology-models
Last synced: 5 months ago
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Epidemiologic Compartmental Modeling Monad in R
- Host: GitHub
- URL: https://github.com/antononcube/ecmmon-r
- Owner: antononcube
- License: gpl-3.0
- Created: 2020-04-09T04:04:23.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2021-04-16T14:00:52.000Z (about 5 years ago)
- Last Synced: 2025-08-30T23:42:57.247Z (10 months ago)
- Topics: compartmental-models, epidemiology-models
- Language: HTML
- Homepage:
- Size: 1.31 MB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Epidemiologic Compartmental Modeling Monad R package
[](https://www.repostatus.org/#active)
[](https://codecov.io/gh/antononcube/ECMMon-R?branch=master)
[](https://github.com/antononcube/ECMMon-R/actions)
## Introduction
This package has implementations of [epidemiologic compartmental models](https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology), [Wk1, HH1],
modified to fit better simulations of propagation of [COVID-19](https://en.wikipedia.org/wiki/Coronavirus_disease_2019), [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"](https://cran.r-project.org/web/packages/devtools/readme/README.html):
```r
devtools::install_github(repo = "antononcube/ECMMon-R")
```
**Remark:** The simulations done by the package functions rely on the R package
["deSolve"](https://cran.r-project.org/web/packages/deSolve/index.html),
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"](https://github.com/antononcube/ECMMon-R/blob/master/notebooks/Basic-experiments-workflow-for-simple-epidemiological-models.Rmd),
([HTML](https://htmlpreview.github.io/?https://github.com/antononcube/ECMMon-R/blob/master/notebooks/Basic-experiments-workflow-for-simple-epidemiological-models.nb.html)).
The package repository has [flexdashboard](https://rmarkdown.rstudio.com/flexdashboard/index.html) 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"](https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology).
[Wl2] Wikipedia entry, ["Coronavirus disease 2019"](https://en.wikipedia.org/wiki/Coronavirus_disease_2019).
[HH1] Herbert W. Hethcote (2000). ["The Mathematics of Infectious Diseases"](http://leonidzhukov.net/hse/2014/socialnetworks/papers/2000SiamRev.pdf). SIAM Review. 42 (4): 599–653. Bibcode:2000SIAMR..42..599H. doi:10.1137/s0036144500371907.
[AA1] Anton Antonov, ["Coronavirus propagation modeling considerations"](https://github.com/antononcube/SystemModeling/blob/master/Projects/Coronavirus-propagation-dynamics/Documents/Coronavirus-propagation-modeling-considerations.md), (2020), [SystemModeling at GitHub](https://github.com/antononcube/SystemModeling).
[AA2] Anton Antonov, ["Basic experiments workflow for simple epidemiological models"](https://github.com/antononcube/SystemModeling/blob/master/Projects/Coronavirus-propagation-dynamics/Documents/Basic-experiments-workflow-for-simple-epidemiological-models.md), (2020), [SystemModeling at GitHub](https://github.com/antononcube/SystemModeling).
[AA3] Anton Antonov, ["Scaling of Epidemiology Models with Multi-site Compartments"](https://github.com/antononcube/SystemModeling/blob/master/Projects/Coronavirus-propagation-dynamics/Documents/Scaling-of-epidemiology-models-with-multi-site-compartments.md), (2020), [SystemModeling at GitHub](https://github.com/antononcube/SystemModeling).
### Repositories, packages
[AAr1] Anton Antonov, [Coronavirus propagation dynamics project](https://github.com/antononcube/SystemModeling/tree/master/Projects/Coronavirus-propagation-dynamics), (2020), [SystemModeling at GitHub](https://github.com/antononcube/SystemModeling).
[AAp1] Anton Antonov, ["Epidemiology models Mathematica package"](https://github.com/antononcube/SystemModeling/blob/master/Projects/Coronavirus-propagation-dynamics/WL/EpidemiologyModels.m), (2020), [SystemModeling at GitHub](https://github.com/antononcube/SystemModeling).
[AAp2] Anton Antonov, ["Epidemiology models modifications Mathematica package"](https://github.com/antononcube/SystemModeling/blob/master/Projects/Coronavirus-propagation-dynamics/WL/EpidemiologyModelModifications.m), (2020), [SystemModeling at GitHub](https://github.com/antononcube/SystemModeling).
[AAp3] Anton Antonov, ["Epidemiology modeling visualization functions Mathematica package"](https://github.com/antononcube/SystemModeling/blob/master/Projects/Coronavirus-propagation-dynamics/WL/EpidemiologyModelingVisualizationFunctions.m), (2020), [SystemModeling at GitHub](https://github.com/antononcube/SystemModeling).
[AAp4] Anton Antonov, ["System dynamics interactive interfaces functions Mathematica package"](https://github.com/antononcube/SystemModeling/blob/master/WL/SystemDynamicsInteractiveInterfacesFunctions.m), (2020), [SystemModeling at GitHub](https://github.com/antononcube/SystemModeling).