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epidemics

A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes, to compose epidemic scenarios.

https://github.com/epiverse-trace/epidemics

Science Score: 54.0%

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Keywords

decision-support epidemic-modelling epidemic-simulations epidemiology epiverse infectious-disease-dynamics model-library non-pharmaceutical-interventions r r-package rcpp rcppeigen scenario-analysis vaccination

Keywords from Contributors

stan real-time-infectious-disease-modelling pandemic-preparedness outbreak-analysis nowcasting infectious-disease-surveillance effective-reproduction-number-estimation cmdstanr transmission-chain-reconstruction transmission-chain
Last synced: 6 months ago · JSON representation ·

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A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes, to compose epidemic scenarios.

Basic Info
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Topics
decision-support epidemic-modelling epidemic-simulations epidemiology epiverse infectious-disease-dynamics model-library non-pharmaceutical-interventions r r-package rcpp rcppeigen scenario-analysis vaccination
Created about 3 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License Citation

README.Rmd 

---
output: github_document
bibliography: vignettes/references.json
link-citations: true
---

```{r, include = FALSE}
knitr::opts_chunk[["set"]](
  collapse = TRUE,
  comment = "#>",
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  fig.path = "man/figures/README-",
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)
```

# {{ packagename }}: Composable epidemic scenario modelling 


[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/license/mit/)
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[![CRAN status](https://www.r-pkg.org/badges/version/{{ packagename }})](https://CRAN.R-project.org/package={{ packagename }})


_{{ packagename }}_ 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 _{{ packagename }}_ focus on directly transmitted infections, and implement methods outlined in @bjornstad2020a and @bjornstad2020.
The models in _{{ packagename }}_ can help provide rough estimates of the course of epidemics, and the effectiveness of pharmaceutical and non-pharmaceutical interventions.

_{{ packagename }}_ relies on [Eigen](https://gitlab.com/libeigen/eigen) via [{RcppEigen}](https://cran.r-project.org/package=RcppEigen), and on [Boost Odeint](https://www.boost.org/doc/libs/1_82_0/libs/numeric/odeint/doc/html/index.html) via [{BH}](https://cran.r-project.org/package=BH), and is developed at the [Centre for the Mathematical Modelling of Infectious Diseases](https://www.lshtm.ac.uk/research/centres/centre-mathematical-modelling-infectious-diseases) at the London School of Hygiene and Tropical Medicine as part of the [Epiverse-TRACE initiative](https://data.org/initiatives/epiverse/).

## Installation

The current development version of _{{ packagename }}_ can be installed from [GitHub](https://github.com/) using the _pak_ package.

```r
if(!require("pak")) install.packages("pak")
pak::pkg_install("{{ gh_repo }}")
```

Alternatively, install pre-compiled binaries from [the Epiverse TRACE R-universe](https://epiverse-trace.r-universe.dev/epidemics)

```r
install.packages("epidemics", repos = c("https://epiverse-trace.r-universe.dev", "https://cloud.r-project.org"))
```

### Installation Notes

1. Some users who are also using or developing packages that use Stan might face issues if they have modified their toolchain to accommodate packages such as [_cmdstanr_](https://mc-stan.org/cmdstanr/); see [this resolved issue](https://github.com/stan-dev/cmdstanr/issues/790) for a starting point if you face similar problems.

2. Users on Windows systems will need to have packages from the _RTools_ family installed and on their system path; see [this link for guidance on using _RTools_](https://cran.r-project.org/bin/windows/Rtools/) for your version of R.

## Quick start

Here we show an example of using the default model in _{{ packagename }}_ to model an epidemic in the U.K. population with an $R_0$ similar to that of pandemic influenza, with heterogeneity in social contacts among different age groups, and with the implementation of school closures to dampen the spread of the infection.

```{r}
# load epidemics
library(epidemics)
library(ggplot2)
library(dplyr)
```

Prepare the social contact pattern for a population (here, the U.K population), divided into three age groups: 0 -- 19, 20 -- 39, and 40+.

```{r}
# load contact and population data from socialmixr::polymod
polymod <- socialmixr::polymod
contact_data <- socialmixr::contact_matrix(
  polymod,
  countries = "United Kingdom",
  age.limits = c(0, 20, 40),
  symmetric = TRUE
)

# prepare contact matrix
contact_matrix <- t(contact_data[["matrix"]])

# prepare the demography vector
demography_vector <- contact_data[["demography"]][["population"]]
names(demography_vector) <- rownames(contact_matrix)
```

Prepare the initial conditions for the population by age group --- here, one in every million individuals is infected at the start of the epidemic (for a total of about 60 infections).

```{r}
# initial conditions: one in every 1 million is infected
initial_i <- 1e-6
initial_conditions <- c(
  S = 1 - initial_i, E = 0, I = initial_i, R = 0, V = 0
)

# build for all age groups
initial_conditions <- rbind(
  initial_conditions,
  initial_conditions,
  initial_conditions
)
rownames(initial_conditions) <- rownames(contact_matrix)
```

Prepare an object of the class ``, using the function `population()`.

```{r}
# prepare the population to model as affected by the epidemic
uk_population <- population(
  name = "UK",
  contact_matrix = contact_matrix,
  demography_vector = demography_vector,
  initial_conditions = initial_conditions
)
```

Define an intervention to close schools for two months. This intervention mostly only affects individuals in the age range 0 -- 19, and reduces their contacts by 50%, reducing the contacts of other age groups by 1%. This is an object of the class ``, created using the function `intervention()`, while setting `type = "contacts"`.

```{r}
# an intervention to close schools
close_schools <- intervention(
  type = "contacts",
  time_begin = 200,
  time_end = 260,
  reduction = matrix(c(0.5, 0.01, 0.01))
)

# view the intervention
close_schools
```

Run the default epidemic model, using the function `model_default()`. 
We assume an $R_0$ of 1.5 which is similar to pandemic influenza, an infectious period of 7 days, and a pre-infectious period of 3 days.
From these values we can calculate transmission rate $\beta$ `1.5 / 7.0`, infectiousness_rate $\alpha$ `1.0 / 3.0` and recovery_rate $\gamma$ `1.0 / 7.0`.

```{r message=FALSE}
# run an epidemic model using `epidemic()`
output <- model_default(
  population = uk_population,
  transmission_rate = 1.5 / 7.0,
  infectiousness_rate = 1.0 / 3.0,
  recovery_rate = 1.0 / 7.0,
  intervention = list(contacts = close_schools),
  time_end = 600, increment = 1.0
)
```

Visualise the development of individuals in the "infectious" compartment over model time. Note that these curves represent the number of individuals that are infectious, and not the number of newly infectious individuals.

```{r fig-modelout, echo=FALSE}
filter(output, compartment == "infectious") %>%
  ggplot() +
  geom_vline(
    xintercept = c(close_schools[["time_begin"]], close_schools[["time_end"]]),
    colour = "red",
    linetype = "dashed",
    linewidth = 0.2
  ) +
  annotate(
    geom = "text",
    label = "Schools closed",
    colour = "red",
    x = 230, y = 400e3,
    angle = 90,
    vjust = "outward"
  ) +
  geom_line(
    aes(time, value, colour = demography_group)
  ) +
  scale_colour_brewer(
    palette = "Dark2",
    labels = rownames(contact_matrix),
    name = "Age group"
  ) +
  scale_y_continuous(
    labels = scales::comma,
    name = "Individuals infected"
  ) +
  labs(
    x = "Model time (days)"
  ) +
  theme_bw() +
  theme(
    legend.position = "top"
  )
```

## Package vignettes

More details on how to use _{{ packagename }}_ can be found in the [online documentation as package vignettes](https://epiverse-trace.github.io/{{ packagename }}/), under "Articles".

## Package models

_{{ packagename }}_ 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;

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 [@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 @li2019 and @getz2018;

4. An initial implementation of a compartmental model for diphtheria in the context of internally displaced persons camps, including a reporting rate, hospitalisation rate, and delays in entering and leaving hospital, taken from @finger2019.

More models are planned to be added in the near future.
Please get in touch if you would like to see your model added to the _{{ packagename }}_ model library --- we are happy to help with translating it into our framework, with a special focus on making the model applicable to LMIC settings.

## Related projects

_epidemics_ aims to be a library of published epidemiological models, and the following projects may be useful for building your own models:

- The [R package _finalsize_](https://cran.r-project.org/package=finalsize) is also developed by Epiverse-TRACE and helps to calculate the final size of an epidemic in a heterogeneous population, and is a quicker option for estimates of total infections when the temporal dynamics are less important;
- The [Epirecipes project](http://epirecip.es/epicookbook/) is a cookbook-style guide that focuses on different ways to implement epidemic models in R and other languages;
- The [R package _odin_](https://cran.r-project.org/package=odin) generates systems of ordinary differential equations (ODE) and integrate them, using a domain specific language (DSL), and is widely used to translate compartmental models from R to C code for performance gains;
- Many R packages provide modelling options, and these can be found on the [CRAN Epidemiology Task View](https://cran.r-project.org/view=Epidemiology) under the section "Infectious disease modelling".

## Help

To report a bug please open an [issue](https://github.com/{{ gh_repo }}/issues/new/choose).

## Contribute

Contributions to _{{ packagename }}_ are welcomed via [pull requests](https://github.com/{{ gh_repo }}/pulls).

## Code of conduct

Please note that the _{{ packagename }}_ project is released with a [Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.

## References

Owner

  • Name: Epiverse-TRACE
  • Login: epiverse-trace
  • Kind: organization

Citation (CITATION.cff) 

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "epidemics" in publications use:'
type: software
license: MIT
title: 'epidemics: Composable Epidemic Scenario Modelling'
version: 0.4.0.9000
abstract: A library of compartmental epidemic models taken from the published literature,
  and classes to represent affected populations, public health response measures including
  non-pharmaceutical interventions on social contacts, non-pharmaceutical and pharmaceutical
  interventions that affect disease transmissibility, vaccination regimes, and disease
  seasonality, which can be combined to compose epidemic scenario models.
authors:
- family-names: Gupte
  given-names: Pratik
  email: pratik.gupte@lshtm.ac.uk
  orcid: https://orcid.org/0000-0001-5294-7819
- family-names: Eggo
  given-names: Rosalind
  email: rosalind.eggo@lshtm.ac.uk
  orcid: https://orcid.org/0000-0002-0362-6717
- family-names: Van Leeuwen
  given-names: Edwin
  email: edwin.vanleeuwen@ukhsa.gov.uk
  orcid: https://orcid.org/0000-0002-2383-5305
repository-code: https://github.com/epiverse-trace/epidemics
url: https://epiverse-trace.github.io/epidemics/
contact:
- family-names: Eggo
  given-names: Rosalind
  email: rosalind.eggo@lshtm.ac.uk
  orcid: https://orcid.org/0000-0002-0362-6717
keywords:
- decision-support
- epidemic-modelling
- epidemic-simulations
- epidemiology
- epiverse
- infectious-disease-dynamics
- model-library
- non-pharmaceutical-interventions
- r
- r-package
- rcpp
- rcppeigen
- scenario-analysis
- vaccination
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    email: rich.fitzjohn@gmail.com
  year: '2025'
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  repository: https://CRAN.R-project.org/package=cli
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    given-names: Matt
    email: mattjdowle@gmail.com
  - family-names: Srinivasan
    given-names: Arun
    email: asrini@pm.me
  - family-names: Gorecki
    given-names: Jan
  - family-names: Chirico
    given-names: Michael
    orcid: https://orcid.org/0000-0003-0787-087X
  - family-names: Hocking
    given-names: Toby
    orcid: https://orcid.org/0000-0002-3146-0865
  - family-names: Schwendinger
    given-names: Benjamin
    orcid: https://orcid.org/0000-0003-3315-8114
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    given-names: Ivan
    email: ikrylov@disroot.org
    orcid: https://orcid.org/0000-0002-0172-3812
  year: '2025'
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  notes: Imports
  url: https://glue.tidyverse.org/
  repository: https://CRAN.R-project.org/package=glue
  authors:
  - family-names: Hester
    given-names: Jim
    orcid: https://orcid.org/0000-0002-2739-7082
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2025'
  doi: 10.32614/CRAN.package.glue
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  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
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  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: utils
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
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  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
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  notes: Imports
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  repository: https://CRAN.R-project.org/package=withr
  authors:
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    given-names: Jim
  - family-names: Henry
    given-names: Lionel
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  - family-names: Ushey
    given-names: Kevin
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  - family-names: Wickham
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    email: hadley@posit.co
  - family-names: Chang
    given-names: Winston
  year: '2025'
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    given-names: Hadley
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  - family-names: Henry
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  notes: Suggests
  url: https://github.com/mrc-ide/EpiEstim
  repository: https://CRAN.R-project.org/package=EpiEstim
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- type: software
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  abstract: 'finalsize: Calculate the Final Size of an Epidemic'
  notes: Suggests
  url: https://epiverse-trace.github.io/finalsize/
  repository: https://CRAN.R-project.org/package=finalsize
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  - family-names: Gupte
    given-names: Pratik
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  abstract: 'ggdist: Visualizations of Distributions and Uncertainty'
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  url: https://mjskay.github.io/ggdist/
  repository: https://CRAN.R-project.org/package=ggdist
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  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Suggests
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
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  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
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  - family-names: Pedersen
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    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
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  - family-names: Woo
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  - family-names: Dunnington
    given-names: Dewey
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  - family-names: Brand
    given-names: Teun
    name-particle: van den
    orcid: https://orcid.org/0000-0002-9335-7468
  year: '2025'
  doi: 10.32614/CRAN.package.ggplot2
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: purrr
  abstract: 'purrr: Functional Programming Tools'
  notes: Suggests
  url: https://purrr.tidyverse.org/
  repository: https://CRAN.R-project.org/package=purrr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.purrr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2025'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: scales
  abstract: 'scales: Scale Functions for Visualization'
  notes: Suggests
  url: https://scales.r-lib.org
  repository: https://CRAN.R-project.org/package=scales
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Seidel
    given-names: Dana
  year: '2025'
  doi: 10.32614/CRAN.package.scales
- type: software
  title: socialmixr
  abstract: 'socialmixr: Social Mixing Matrices for Infectious Disease Modelling'
  notes: Suggests
  url: https://epiforecasts.io/socialmixr/
  repository: https://CRAN.R-project.org/package=socialmixr
  authors:
  - family-names: Funk
    given-names: Sebastian
    email: sebastian.funk@lshtm.ac.uk
  - family-names: Willem
    given-names: Lander
  - family-names: Gruson
    given-names: Hugo
  year: '2025'
  doi: 10.32614/CRAN.package.socialmixr
- type: software
  title: spelling
  abstract: 'spelling: Tools for Spell Checking in R'
  notes: Suggests
  url: https://ropensci.r-universe.dev/spelling
  repository: https://CRAN.R-project.org/package=spelling
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroenooms@gmail.com
    orcid: https://orcid.org/0000-0002-4035-0289
  - family-names: Hester
    given-names: Jim
    email: james.hester@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.spelling
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.testthat
  version: '>= 3.0.0'
- type: software
  title: tibble
  abstract: 'tibble: Simple Data Frames'
  notes: Suggests
  url: https://tibble.tidyverse.org/
  repository: https://CRAN.R-project.org/package=tibble
  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.tibble
- type: software
  title: tidyr
  abstract: 'tidyr: Tidy Messy Data'
  notes: Suggests
  url: https://tidyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=tidyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
  - family-names: Girlich
    given-names: Maximilian
  year: '2025'
  doi: 10.32614/CRAN.package.tidyr
- type: software
  title: BH
  abstract: 'BH: Boost C++ Header Files'
  notes: LinkingTo
  url: https://dirk.eddelbuettel.com/code/bh.html
  repository: https://CRAN.R-project.org/package=BH
  authors:
  - family-names: Eddelbuettel
    given-names: Dirk
    email: edd@debian.org
    orcid: https://orcid.org/0000-0001-6419-907X
  - family-names: Emerson
    given-names: John W.
  - family-names: Kane
    given-names: Michael J.
    orcid: https://orcid.org/0000-0003-1899-6662
  year: '2025'
  doi: 10.32614/CRAN.package.BH
- type: software
  title: Rcpp
  abstract: 'Rcpp: Seamless R and C++ Integration'
  notes: LinkingTo
  url: https://www.rcpp.org
  repository: https://CRAN.R-project.org/package=Rcpp
  authors:
  - family-names: Eddelbuettel
    given-names: Dirk
    email: edd@debian.org
    orcid: https://orcid.org/0000-0001-6419-907X
  - family-names: Francois
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Allaire
    given-names: JJ
    orcid: https://orcid.org/0000-0003-0174-9868
  - family-names: Ushey
    given-names: Kevin
    orcid: https://orcid.org/0000-0003-2880-7407
  - family-names: Kou
    given-names: Qiang
    orcid: https://orcid.org/0000-0001-6786-5453
  - family-names: Russell
    given-names: Nathan
  - family-names: Ucar
    given-names: Iñaki
    orcid: https://orcid.org/0000-0001-6403-5550
  - family-names: Bates
    given-names: Doug
    orcid: https://orcid.org/0000-0001-8316-9503
  - family-names: Chambers
    given-names: John
  year: '2025'
  doi: 10.32614/CRAN.package.Rcpp
- type: software
  title: RcppEigen
  abstract: 'RcppEigen: ''Rcpp'' Integration for the ''Eigen'' Templated Linear Algebra
    Library'
  notes: LinkingTo
  url: https://dirk.eddelbuettel.com/code/rcpp.eigen.html
  repository: https://CRAN.R-project.org/package=RcppEigen
  authors:
  - family-names: Bates
    given-names: Doug
    orcid: https://orcid.org/0000-0001-8316-9503
  - family-names: Eddelbuettel
    given-names: Dirk
    email: edd@debian.org
    orcid: https://orcid.org/0000-0001-6419-907X
  - family-names: Francois
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Qiu
    given-names: Yixuan
    orcid: https://orcid.org/0000-0003-0109-6692
  year: '2025'
  doi: 10.32614/CRAN.package.RcppEigen

GitHub Events

Total
  • Create event: 6
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Last Year
  • Create event: 6
  • Issues event: 10
  • Watch event: 4
  • Delete event: 4
  • Member event: 1
  • Issue comment event: 57
  • Push event: 94
  • Pull request review comment event: 14
  • Pull request review event: 29
  • Pull request event: 14
  • Fork event: 10

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 700
  • Total Committers: 11
  • Avg Commits per committer: 63.636
  • Development Distribution Score (DDS): 0.147
Past Year
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  • Avg Commits per committer: 63.455
  • Development Distribution Score (DDS): 0.146
Top Committers
Name Email Commits
Pratik Gupte p****e@l****k 597
GitHub Action a****n@g****m 32
James Azam j****m@g****m 18
jamesaazam j****m@l****k 17
Pratik Gupte p****6@g****m 11
Hugo Gruson B****o 9
bahadzie b****e@g****m 7
Edwin van Leeuwen e****l@t****o 5
adamkucharski a****i@l****k 2
Tim Taylor t****r@h****k 1
banky 4****e 1
Committer Domains (Top 20 + Academic)
lshtm.ac.uk: 3 hiddenelephants.co.uk: 1 tuta.io: 1 github.com: 1

Issues and Pull Requests

Last synced: 6 months ago

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  • Bot pull requests: 6
Past Year
  • Issues: 7
  • Pull requests: 9
  • Average time to close issues: 4 months
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  • Issue authors: 4
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  • Average comments per pull request: 0.0
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Top Authors
Issue Authors
  • pratikunterwegs (109)
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Pull Request Authors
  • pratikunterwegs (103)
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Top Labels
Issue Labels
Discussion (22) R frontend (21) ODE model (19) Documentation (17) Helper functions (12) Enhancement (10) Interventions (9) R code (9) C++ backend (8) Bug (7) Vaccination (7) good first issue (6) Stale (6) Cleanup (6) C++ (5) Population (4) question (4) New model (3) Infection (2) CI (2) Active (2) known-issue (1) Stochastic models (1) Testing (1)
Pull Request Labels
CI (9) Documentation (6) Enhancement (5) ODE model (5) Helper functions (5) C++ backend (4) Bug (4) Vaccination (4) R frontend (3) New model (2) Cleanup (2) C++ (2) Interventions (1) Testing (1) Scenarios (1)

Dependencies

.github/workflows/Cpp-lint-check.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v2 composite
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action 4.1.4 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/render_readme.yml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • Rcpp * imports
  • data.table * imports
  • deSolve * imports
  • covr * suggests
  • testthat >= 3.0.0 suggests