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serofoi

Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies

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

Science Score: 44.0%

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Keywords

antibodies bayesian-methods epidemiology epiverse r r-package serological-surveys stan-language
Last synced: 6 months ago · JSON representation ·

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Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies

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  • Stars: 20
  • Watchers: 4
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  • Open Issues: 25
  • Releases: 4
Topics
antibodies bayesian-methods epidemiology epiverse r r-package serological-surveys stan-language
Created over 3 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog License Citation

README.Rmd 

---
output: github_document
editor_options: 
  markdown: 
    wrap: 72
bibliography: vignettes/references.bib
link-citations: true
---

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

## *serofoi*: force-of-infection from population based serosurveys with age-disaggregated data 



[![License:
MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
[![R-CMD-check](https://github.com/epiverse-trace/serofoi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/serofoi/actions/workflows/R-CMD-check.yaml)
[![Codecov test
coverage](https://codecov.io/gh/epiverse-trace/serofoi/branch/dev/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/serofoi/tree/dev/R?displayType=list)
[![lifecycle-maturing](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-maturing.svg)](https://www.reconverse.org/lifecycle.html#maturing)



_{{ packagename }}_ is an R package to estimate the *Force-of-Infection (FoI)* of a given pathogen from age-disaggregated population-based cross-sectional serosurveys, using a Bayesian framework. The package provides a set of features for assessing model fitting, convergence and visualisation. 

_{{ packagename }}_ relies on the [`rstan`](https://mc-stan.org/users/interfaces/rstan) package, which provides an R interface for the Stan programming language for statistical Bayesian modelling. Particularly, _{{ packagename }}_ relies on the use of a *Hamiltonian Monte Carlo (HMC)* algorithm implemented by *Stan for Markov chain Monte Carlo (MCMC)* sampling. The implemented methods are outlined in [@cucunubá2017] and [@carrera2020] (see [FoI Models](https://epiverse-trace.github.io/serofoi/articles/foi_models.html) for further details). A compelling mathematical treatment of the implemented serocatalytic models can be found in [@kamau2025].

_{{ packagename }}_ is part of the [Epiverse Initiative](https://data.org/initiatives/epiverse/).

## Installation

You can install _{{ packagename }}_ from CRAN using:

```{r install_from_cran, eval = FALSE}
install.packages("serofoi")
```

You can install the **development version** of _{{ packagename }}_ from [GitHub](https://github.com/epiverse-trace/serofoi) running:

```{r install_with_pak, eval = FALSE}
if(!require("pak")) install.packages("pak")
pak::pak("epiverse-trace/serofoi")
```
or:
```{r install_with_remotes, eval = FALSE}
if(!require("remotes")) install.packages("remotes")
remotes::install_github("epiverse-trace/serofoi")
```
## Quick start

```{r load_package, include = FALSE, echo = TRUE}
library(serofoi)
```

_{{ packagename }}_ provides some minimal serosurvey datasets that can be used to test out the package. For instance, the dataset `chagas2012` contains seroprevalence measures of IgG antibodies against Trypanosoma cruzi infection corresponding to a serological survey conducted in Colombia during 2012 on a rural indigenous community that is known to present long-term endemic transmission 

```{r load_data, include = TRUE}
# Load example dataset chagas2012 included with the package
data(chagas2012)
head(chagas2012, 5)
```

A visualisation of the serological data can be obtained using the function `plot_serosurvey`:

```{r data_test, fig.cap = "Seroprevalence plot for the chagas2012 dataset.", include = TRUE, out.fig.height="30%", out.width="50%", fig.align="center", message=FALSE, warning=FALSE}
plot_serosurvey(chagas2012, bin_serosurvey = TRUE, size_text = 15)
```
Here, the error bars correspond to the binomial confidence interval and the point size represents the sample size for each age group.

A constant FoI model can easily be implemented by means of `fit_seromodel`:

```{r constant_model, include = TRUE, eval = FALSE}
seromodel <- fit_seromodel(serosurvey = chagas2012)
```

For further details on how to visualise the results and other available models, please refer to the [online documentation](https://epiverse-trace.github.io/serofoi/).

### Contributions

Contributors to the project include:

-   [Zulma M. Cucunubá](https://github.com/zmcucunuba) (author,
    maintainer)

-   [Nicolás Torres](https://github.com/ntorresd) (author)

-   [Ben Lambert](https://ben-lambert.com/about/) (author)

-   [Pierre Nouvellet](https://github.com/pnouvellet) (author)

-   [Geraldine Gómez](https://github.com/megamezl) (contributor)

-   [Jaime A. Pavlich-Mariscal](https://github.com/jpavlich) (contributor)

-   [Miguel Gamez](https://github.com/megamezl) (contributor)

-   [Hugo Gruson](https://github.com/Bisaloo) (contributor)

-   [David Santiago Quevedo](https://github.com/davidsantiagoquevedo) (contributor)

-   [Everlyn Kamau](https://github.com/ekamau) (contributor)

-   [Richard Creswell](https://github.com/rccreswell) (contributor)

-   [Sumali Bajaj](https://github.com/sumalibajaj) (contributor)


## 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".

## 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/epiverse-trace/.github/blob/main/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.

## 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 "serofoi" in publications use:'
type: software
license: MIT
title: 'serofoi: Bayesian Estimation of the Force of Infection from Serological Data'
version: 1.0.3
abstract: Estimating the force of infection from time varying, age varying, or constant
  serocatalytic models from population based seroprevalence studies using a Bayesian
  framework, including data simulation functions enabling the generation of serological
  surveys based on this models. This tool also provides a flexible prior specification
  syntax for the force of infection and the seroreversion rate, as well as methods
  to assess model convergence and comparison criteria along with useful visualisation
  functions.
authors:
- family-names: Cucunubá
  given-names: Zulma M.
  email: zulma.cucunuba@javeriana.edu.co
  orcid: https://orcid.org/0000-0002-8165-3198
- family-names: T. Domínguez
  given-names: Nicolás
  email: ex-ntorres@javeriana.edu.co
  orcid: https://orcid.org/0009-0002-8484-1298
- family-names: Lambert
  given-names: Ben
- family-names: Nouvellet
  given-names: Pierre
repository-code: https://github.com/epiverse-trace/serofoi
url: https://epiverse-trace.github.io/serofoi/
contact:
- family-names: Cucunubá
  given-names: Zulma M.
  email: zulma.cucunuba@javeriana.edu.co
  orcid: https://orcid.org/0000-0002-8165-3198
keywords:
- antibodies
- bayesian-methods
- epidemiology
- epiverse
- r
- r-package
- serological-surveys
- stan-language
references:
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  notes: Depends
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  version: '>= 4.1.0'
- type: software
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  abstract: 'bayesplot: Plotting for Bayesian Models'
  notes: Imports
  url: https://mc-stan.org/bayesplot/
  repository: https://CRAN.R-project.org/package=bayesplot
  authors:
  - family-names: Gabry
    given-names: Jonah
    email: jsg2201@columbia.edu
  - family-names: Mahr
    given-names: Tristan
  year: '2025'
  doi: 10.32614/CRAN.package.bayesplot
- 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: '2025'
  doi: 10.32614/CRAN.package.checkmate
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  title: config
  abstract: 'config: Manage Environment Specific Configuration Values'
  notes: Imports
  url: https://rstudio.github.io/config/
  repository: https://CRAN.R-project.org/package=config
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.config
- type: software
  title: cowplot
  abstract: 'cowplot: Streamlined Plot Theme and Plot Annotations for ''ggplot2'''
  notes: Imports
  url: https://wilkelab.org/cowplot/
  repository: https://CRAN.R-project.org/package=cowplot
  authors:
  - family-names: Wilke
    given-names: Claus O.
    email: wilke@austin.utexas.edu
    orcid: https://orcid.org/0000-0002-7470-9261
  year: '2025'
  doi: 10.32614/CRAN.package.cowplot
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
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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: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
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    given-names: Lionel
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    orcid: https://orcid.org/0000-0002-1416-3412
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- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Imports
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
  authors:
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    given-names: Hadley
    email: hadley@posit.co
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    given-names: Lionel
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    orcid: https://orcid.org/0000-0002-5147-4711
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    given-names: Kohske
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    orcid: https://orcid.org/0000-0002-7470-9261
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    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
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    orcid: https://orcid.org/0000-0002-9415-4582
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    given-names: Teun
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  notes: Imports
  url: https://glue.tidyverse.org/
  repository: https://CRAN.R-project.org/package=glue
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    given-names: Jim
    orcid: https://orcid.org/0000-0002-2739-7082
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  abstract: 'loo: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models'
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  url: https://mc-stan.org/loo/
  repository: https://CRAN.R-project.org/package=loo
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    given-names: Aki
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  url: https://R-forge.R-project.org/tracker/?atid=472&group_id=107
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    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
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  notes: Imports
  url: https://purrr.tidyverse.org/
  repository: https://CRAN.R-project.org/package=purrr
  authors:
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  notes: Imports
  url: https://www.rcpp.org
  repository: https://CRAN.R-project.org/package=Rcpp
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  notes: Imports
  url: https://mc-stan.org/rstan/
  repository: https://CRAN.R-project.org/package=rstan
  authors:
  - family-names: Guo
    given-names: Jiqiang
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  notes: Imports
  url: https://mc-stan.org/rstantools/
  repository: https://CRAN.R-project.org/package=rstantools
  authors:
  - family-names: Gabry
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  - family-names: Johnson
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  year: '2025'
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  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
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  abstract: 'tibble: Simple Data Frames'
  notes: Imports
  url: https://tibble.tidyverse.org/
  repository: https://CRAN.R-project.org/package=tibble
  authors:
  - family-names: Müller
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  notes: Imports
  url: https://tidyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=tidyr
  authors:
  - family-names: Wickham
    given-names: Hadley
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  notes: Suggests
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  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
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  notes: LinkingTo
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  repository: https://CRAN.R-project.org/package=BH
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    given-names: Dirk
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GitHub Events

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Last Year
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  • Pull request review event: 56
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Issues and Pull Requests

Last synced: 6 months ago

All Time
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CRAN (8) refactor (5) documentation (3) testing (3) discussion (2) question (2) fix (2) enhancement (2) simdata (1) warning (1) help wanted (1) serodata (1)
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 200 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
cran.r-project.org: serofoi

Bayesian Estimation of the Force of Infection from Serological Data

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 200 Last month
Rankings
Dependent packages count: 26.9%
Dependent repos count: 33.1%
Average: 49.0%
Downloads: 87.0%
Maintainers (1)
zulma.cucunuba@javeriana.edu.co
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • Hmisc * imports
  • bayesplot * imports
  • config * imports
  • dplyr * imports
  • gridExtra * imports
  • gsubfn * imports
  • loo * imports
  • reshape2 * imports
  • rstan * imports
  • tidyverse * imports
  • knitr * suggests
  • rmarkdown * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 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 v4.4.1 composite
  • actions/checkout v3 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
tests/docker/Dockerfile docker
  • rocker/tidyverse 4.2.2 build