{"id":23029782,"url":"https://github.com/antononcube/ecmmon-r","last_synced_at":"2026-02-11T18:35:00.412Z","repository":{"id":71383350,"uuid":"254267550","full_name":"antononcube/ECMMon-R","owner":"antononcube","description":"Epidemiologic Compartmental Modeling Monad in 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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["compartmental-models","epidemiology-models"],"created_at":"2024-12-15T14:17:05.940Z","updated_at":"2026-02-11T18:35:00.408Z","avatar_url":"https://github.com/antononcube.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Epidemiologic Compartmental Modeling Monad R package\n\n\u003c!-- badges: start --\u003e\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![Codecov test coverage](https://codecov.io/gh/antononcube/ECMMon-R/branch/master/graph/badge.svg)](https://codecov.io/gh/antononcube/ECMMon-R?branch=master)\n[![R-CMD-check](https://github.com/antononcube/ECMMon-R/workflows/R-CMD-check/badge.svg)](https://github.com/antononcube/ECMMon-R/actions)\n\u003c!-- badges: end --\u003e\n  \n## Introduction\n\nThis package has implementations of [epidemiologic compartmental models](https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology), [Wk1, HH1], \nmodified to fit better simulations of propagation of [COVID-19](https://en.wikipedia.org/wiki/Coronavirus_disease_2019), [Wk2]. \n\nThe models implemented in this package deal with one, two, or all three of the rectangles in this diagram:\n\n![0y1f7ckbmwf5i](https://github.com/antononcube/SystemModeling/raw/master/Projects/Coronavirus-propagation-dynamics/Diagrams/Coronavirus-propagation-simple-dynamics.jpeg)\n\nThe content of the package corresponds to the Mathematica packages and notebooks referenced below. \n(But there are some significant differences.)\n\n## Installation\n\nHere is an installation command using [\"devtools\"](https://cran.r-project.org/web/packages/devtools/readme/README.html):\n\n```r\ndevtools::install_github(repo = \"antononcube/ECMMon-R\")\n```\n\n**Remark:** The simulations done by the package functions rely on the R package \n[\"deSolve\"](https://cran.r-project.org/web/packages/deSolve/index.html),\nwhich in turn relies on FORTRAN code. For example, on Mac OS X the installation of `gfortran` is needed.\n\n## Usage\n\nHere is a notebook that demonstrates usage of the provided objects and functions:\n[\"Basic experiments workflow for simple epidemiological models\"](https://github.com/antononcube/ECMMon-R/blob/master/notebooks/Basic-experiments-workflow-for-simple-epidemiological-models.Rmd),\n([HTML](https://htmlpreview.github.io/?https://github.com/antononcube/ECMMon-R/blob/master/notebooks/Basic-experiments-workflow-for-simple-epidemiological-models.nb.html)).\n  \nThe package repository has [flexdashboard](https://rmarkdown.rstudio.com/flexdashboard/index.html) interfaces for the more important models. \n\n### Core models\n\nHere are the core (single-site) models \n\n  - SIR   \n    “Susceptible, Infected, Recovered” populations\n\n  - SEIR   \n    “Susceptible, Exposed, Infected, Recovered” populations\n\n  - SEI2R   \n    “Susceptible, Exposed, Infected two, Recovered” populations\n\n  - SEI2HR   \n    “Susceptible, Exposed, Infected two, Hospitalized, Recovered” populations\n\n  - SEI2HREcon   \n    “Susceptible, Exposed, Infected two, Hospitalized, Recovered” populations with Economic extensions\n\n\n\n## References\n\n### Articles\n\n[Wk1] Wikipedia entry, [\"Compartmental models in epidemiology\"](https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology).\n\n[Wl2] Wikipedia entry, [\"Coronavirus disease 2019\"](https://en.wikipedia.org/wiki/Coronavirus_disease_2019).\n\n[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.\n\n[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).\n\n[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).\n\n[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).\n\n### Repositories, packages\n\n[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).\n\n[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).\n\n[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).\n\n[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).\n\n[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).\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fantononcube%2Fecmmon-r","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fantononcube%2Fecmmon-r","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fantononcube%2Fecmmon-r/lists"}