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finalsize

R package to calculate the final size of an SIR epidemic in populations with heterogeneity in social contacts and disease susceptibility

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

Science Score: 44.0%

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Keywords

epidemic-modelling epidemiology epiverse outbreak-analysis r r-package rcpp sdg-3
Last synced: 6 months ago · JSON representation ·

Repository

R package to calculate the final size of an SIR epidemic in populations with heterogeneity in social contacts and disease susceptibility

Basic Info
Statistics
  • Stars: 13
  • Watchers: 7
  • Forks: 6
  • Open Issues: 18
  • Releases: 3
Topics
epidemic-modelling epidemiology epiverse outbreak-analysis r r-package rcpp sdg-3
Created almost 4 years ago · Last pushed 9 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.Rmd 

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

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# {{ packagename }}: Calculate the final size of an epidemic 


Digital Public Good
[![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/finalsize)](https://CRAN.R-project.org/package=finalsize)


_{{ packagename }}_ is an R package to calculate the final size of a SIR epidemic in populations with heterogeneity in social contacts and infection susceptibility.

_{{ packagename }}_ provides estimates for the total proportion of a population infected over the course of an epidemic, and can account for a demographic distribution (such as age groups) and demography-specific contact patterns, as well as for heterogeneous susceptibility to infection between groups (such as due to age-group specific immune responses) and within groups (such as due to immunisation programs). An advantage of this approach is that it requires fewer parameters to be defined compared to a model that simulates the full transmission dynamics over time, such as models in the [_epidemics_ package](https://epiverse-trace.github.io/epidemics/articles/epidemics.html).

_{{ packagename }}_ implements methods outlined in @andreasen2011, @miller2012, @kucharski2014, and @bidari2016.

_{{ packagename }}_ can help provide rough estimates of the effectiveness of pharmaceutical interventions in the form of immunisation programmes, or the effect of naturally acquired immunity through previous infection (see the vignette).

_{{ packagename }}_ relies on [Eigen](https://gitlab.com/libeigen/eigen) via [RcppEigen](https://github.com/RcppCore/RcppEigen) for fast matrix algebra, 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](https://data.org/initiatives/epiverse/).

## Installation

The package can be installed from CRAN using

```r
install.packages("finalsize")
```

### Development version

The current development version of _{{ packagename }}_ can be installed from [Github](https://github.com/{{ gh_repo }}) using the `remotes` package.
The development version documentation can be found [here](https://epiverse-trace.github.io/finalsize/dev/).

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

## Quick start

The main function in _{{ packagename }}_ is `final_size()`, which calculates the final size of an epidemic given the $R_0$.

```{r}
# load finalsize
library(finalsize)

final_size(1.5)
```

Optionally, `final_size()` can estimate the epidemic size for populations with differences among demographic groups in their social contact patterns, in their susceptibility to infection.

We can use social contact data (here, from the _socialmixr_ package) to estimate the final size of an epidemic when the disease has an R0 of 1.5, and given three age groups of interest --- 0-19, 20-39 and 40+.
The under-20 age group is assumed to be fully susceptible to the disease, whereas individuals aged over 20 are only half as susceptible as those under 20.

```{r}
# Load example POLYMOD social contacts data included with the package
data(polymod_uk)

# Define contact matrix (entry {ij} is contacts in group i reported by group j)
contact_matrix <- polymod_uk$contact_matrix

# Define population in each age group
demography_vector <- polymod_uk$demography_vector

# Define susceptibility of each group
susceptibility <- matrix(
  data = c(1.0, 0.5, 0.5),
  nrow = length(demography_vector),
  ncol = 1
)

# Assume uniform susceptibility within age groups
p_susceptibility <- matrix(
  data = 1.0,
  nrow = length(demography_vector),
  ncol = 1
)

# R0 of the disease
r0 <- 1.5 # assumed for pandemic influenza

# Calculate the proportion of individuals infected in each age group
final_size(
  r0 = r0,
  contact_matrix = contact_matrix,
  demography_vector = demography_vector,
  susceptibility = susceptibility,
  p_susceptibility = p_susceptibility
)
```

Helper functions included in _{{ packagename }}_ are provided to calculate the effective $R_0$, called $R_{eff}$, from demographic and susceptibility distribution data, while other helpers can convert between $R_0$ and the transmission rate $\lambda$.

```{r}
# calculate the effective R0 using `r_eff()`
r_eff(
  r0 = r0,
  contact_matrix = contact_matrix,
  demography_vector = demography_vector,
  susceptibility = susceptibility,
  p_susceptibility = p_susceptibility
)
```

## Package vignettes

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

## Help

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

## Contribute

Contributions to _{{ packagename }}_ are welcomed. Please follow the [package contributing guide](https://github.com/{{ gh_repo }}/blob/main/.github/CONTRIBUTING.md).

## 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.


## Citing this package

```{r message=FALSE, warning=FALSE}
citation("finalsize")
```

## 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 "finalsize" in publications use:'
type: software
license: MIT
title: 'finalsize: Calculate the Final Size of an Epidemic'
version: 0.2.1.9000
abstract: Calculate the final size of a susceptible-infectious-recovered epidemic
  in a population with demographic variation in contact patterns and susceptibility
  to disease, as discussed in Miller (2012) <https://doi.org/10.1007/s11538-012-9749-6>.
authors:
- family-names: Gupte
  given-names: Pratik
  email: pratik.gupte@lshtm.ac.uk
  orcid: https://orcid.org/0000-0001-5294-7819
- family-names: Van Leeuwen
  given-names: Edwin
  email: edwin.vanleeuwen@ukhsa.gov.uk
  orcid: https://orcid.org/0000-0002-2383-5305
- family-names: Kucharski
  given-names: Adam
  email: adam.kucharski@lshtm.ac.uk
  orcid: https://orcid.org/0000-0001-8814-9421
- family-names: Eggo
  given-names: Rosalind
  email: r.eggo@lshtm.ac.uk
  orcid: https://orcid.org/0000-0002-0362-6717
repository: https://CRAN.R-project.org/package=finalsize
repository-code: https://github.com/epiverse-trace/finalsize
url: https://epiverse-trace.github.io/finalsize/
contact:
- family-names: Eggo
  given-names: Rosalind
  email: r.eggo@lshtm.ac.uk
  orcid: https://orcid.org/0000-0002-0362-6717
keywords:
- epidemic-modelling
- epidemiology
- epiverse
- outbreak-analysis
- r
- r-package
- rcpp
- sdg-3
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
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  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
  version: '>= 2.10'
- type: software
  title: checkmate
  abstract: 'checkmate: Fast and Versatile Argument Checks'
  notes: Imports
  url: https://mllg.github.io/checkmate/
  repository: https://CRAN.R-project.org/package=checkmate
  authors:
  - family-names: Lang
    given-names: Michel
    email: michellang@gmail.com
    orcid: https://orcid.org/0000-0001-9754-0393
  year: '2024'
- type: software
  title: Rcpp
  abstract: 'Rcpp: Seamless R and C++ Integration'
  notes: Imports
  url: https://www.rcpp.org
  repository: https://CRAN.R-project.org/package=Rcpp
  authors:
  - family-names: Eddelbuettel
    given-names: Dirk
  - family-names: Francois
    given-names: Romain
  - family-names: Allaire
    given-names: JJ
  - family-names: Ushey
    given-names: Kevin
  - family-names: Kou
    given-names: Qiang
  - family-names: Russell
    given-names: Nathan
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    given-names: Inaki
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    given-names: Douglas
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  title: bookdown
  abstract: 'bookdown: Authoring Books and Technical Documents with R Markdown'
  notes: Suggests
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  repository: https://CRAN.R-project.org/package=bookdown
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    given-names: Yihui
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  abstract: 'colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes'
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    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
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    given-names: Lionel
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    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
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    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
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    given-names: Hadley
    email: hadley@rstudio.com
  year: '2024'
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  notes: Suggests
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  repository: https://CRAN.R-project.org/package=ggplot2
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    given-names: Hadley
    email: hadley@posit.co
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    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
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    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
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    given-names: Kohske
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    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
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    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
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    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
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    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
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    given-names: Teun
    name-particle: van den
    orcid: https://orcid.org/0000-0002-9335-7468
  year: '2024'
- type: software
  title: ggtext
  abstract: 'ggtext: Improved Text Rendering Support for ''ggplot2'''
  notes: Suggests
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  repository: https://CRAN.R-project.org/package=ggtext
  authors:
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    given-names: Claus O.
    email: wilke@austin.utexas.edu
    orcid: https://orcid.org/0000-0002-7470-9261
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  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
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  repository: https://CRAN.R-project.org/package=knitr
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    given-names: Yihui
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    orcid: https://orcid.org/0000-0003-0645-5666
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  abstract: 'purrr: Functional Programming Tools'
  notes: Suggests
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  repository: https://CRAN.R-project.org/package=purrr
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    given-names: Hadley
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    orcid: https://orcid.org/0000-0003-4757-117X
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    given-names: Lionel
    email: lionel@rstudio.com
  year: '2024'
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
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  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
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    email: xie@yihui.name
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    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
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    given-names: Hadley
    email: hadley@posit.co
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    given-names: Joe
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    given-names: Winston
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    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2024'
- type: software
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  notes: Suggests
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    given-names: Hadley
    email: hadley@posit.co
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    given-names: Thomas Lin
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    orcid: https://orcid.org/0000-0002-5147-4711
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    given-names: Dana
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  abstract: 'socialmixr: Social Mixing Matrices for Infectious Disease Modelling'
  notes: Suggests
  url: https://epiforecasts.io/socialmixr/
  repository: https://CRAN.R-project.org/package=socialmixr
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  - family-names: Funk
    given-names: Sebastian
    email: sebastian.funk@lshtm.ac.uk
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    email: jeroen@berkeley.edu
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    email: james.hester@rstudio.com
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  abstract: 'testthat: Unit Testing for R'
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    given-names: Hadley
    email: hadley@posit.co
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    email: kirill@cynkra.com
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cran.r-project.org: finalsize

Calculate the Final Size of an Epidemic

  • Versions: 3
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Rankings
Forks count: 12.8%
Stargazers count: 22.5%
Dependent packages count: 29.8%
Average: 31.5%
Dependent repos count: 35.5%
Downloads: 57.0%
Maintainers (1)
pratik.gupte@lshtm.ac.uk
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • Rcpp * imports
  • RcppEigen * imports
  • checkmate * imports
  • covr * suggests
  • socialmixr * suggests
  • testthat >= 3.0.0 suggests
  • xml2 * suggests
.github/workflows/Cpp-lint-check.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v2 composite
.github/workflows/R-CMD-check.yaml actions
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  • 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
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  • 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
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.github/workflows/test-coverage.yaml actions
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.github/workflows/update-citation-cff.yaml actions
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.github/workflows/dependency-change.yaml actions
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.github/workflows/lint-changed-files.yaml actions
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