diff --git a/README.md b/README.md index c1ba11a2..145b4328 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ -# epidemics: A library of compartmental epidemic scenario models +# epidemics: Composable epidemic scenario modelling @@ -15,13 +15,14 @@ public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostat status](https://www.r-pkg.org/badges/version/epidemics)](https://CRAN.R-project.org/package=epidemics) -*epidemics* is an R package that provides a convenient interface to a -library of compartmental models that can help to model epidemic -scenarios for directly transmitted respiratory infections such as -influenza or Covid-19 as well haemorrhagic fevers such as Ebola virus -disease. +*epidemics* is an R package that provides modular representations of +populations and public health response measures, allowing them to be +combined with epidemiological model structures curated from the +published literature, to conveniently compose and compare epidemic +scenario models. -The models in *epidemics* implement methods outlined in Bjørnstad et al. +The models in *epidemics* focus on directly transmitted infections, and +implement methods outlined in Bjørnstad et al. ([2020a](#ref-bjornstad2020a)) and Bjørnstad et al. ([2020b](#ref-bjornstad2020)). The models in *epidemics* can help provide rough estimates of the course of epidemics, and the @@ -199,25 +200,28 @@ vignettes](https://epiverse-trace.github.io/epidemics/), under ## Package models -*epidemics* currently provides three models: +*epidemics* provides a convenient interface to a library of +compartmental models that can help to model epidemic scenarios for +directly transmitted respiratory infections such as influenza or +Covid-19 as well haemorrhagic fevers such as Ebola virus disease: 1. A deterministic SEIR-V model with susceptible, exposed, infectious, recovered, and vaccinated compartments (SEIR-V), allowing for heterogeneity in social contacts, the implementation of a group-specific non-pharmaceutical intervention that reduces social contacts, and a vaccination regime with group-specific start and end - dates, + dates; 2. The deterministic Vacamole model developed at [RIVM, the Dutch Public Health Institute](https://www.rivm.nl/) for the Covid-19 pandemic, with a focus on scenario modelling for hospitalisation and - vaccination ([Ainslie et al. 2022](#ref-ainslie2022)), + vaccination ([Ainslie et al. 2022](#ref-ainslie2022)); 3. A stochastic, discrete-time, compartmental SEIR model suitable for modelling haemorrhagic fevers such as Ebola Virus Disease, including hospitalisation and hospital and funeral transmissions, adapted from Li et al. ([2019](#ref-li2019)) and Getz and Dougherty - ([2018](#ref-getz2018)), + ([2018](#ref-getz2018)); 4. An initial implementation of a compartmental model for diphtheria in the context of internally displaced persons camps, including a