{"id":22151657,"url":"https://github.com/epiverse-trace/serofoi","last_synced_at":"2025-07-26T05:31:36.642Z","repository":{"id":65506420,"uuid":"522740861","full_name":"epiverse-trace/serofoi","owner":"epiverse-trace","description":"Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies","archived":false,"fork":false,"pushed_at":"2025-06-26T15:31:48.000Z","size":17051,"stargazers_count":20,"open_issues_count":25,"forks_count":4,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-07-20T13:48:55.752Z","etag":null,"topics":["antibodies","bayesian-methods","epidemiology","epiverse","r","r-package","serological-surveys","stan-language"],"latest_commit_sha":null,"homepage":"https://epiverse-trace.github.io/serofoi/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/epiverse-trace.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-08-08T23:45:21.000Z","updated_at":"2025-04-23T23:38:11.000Z","dependencies_parsed_at":"2023-11-27T18:26:38.377Z","dependency_job_id":"e95b3c54-75b2-4c5e-94fa-8cfc0e177ccf","html_url":"https://github.com/epiverse-trace/serofoi","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/epiverse-trace/serofoi","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fserofoi","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fserofoi/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fserofoi/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fserofoi/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epiverse-trace","download_url":"https://codeload.github.com/epiverse-trace/serofoi/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fserofoi/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267123423,"owners_count":24039456,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-07-26T02:00:08.937Z","response_time":62,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["antibodies","bayesian-methods","epidemiology","epiverse","r","r-package","serological-surveys","stan-language"],"created_at":"2024-12-02T00:35:01.602Z","updated_at":"2025-07-26T05:31:36.623Z","avatar_url":"https://github.com/epiverse-trace.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\neditor_options: \n  markdown: \n    wrap: 72\nbibliography: vignettes/references.bib\nlink-citations: true\n---\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\"\n)\n```\n\n## *serofoi*: force-of-infection from population based serosurveys with age-disaggregated data \u003cimg src=\"man/figures/logo.png\" align=\"right\" width=\"130\"/\u003e\n\n\u003c!-- badges: start --\u003e\n\n[![License:\nMIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n[![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)\n[![Codecov test\ncoverage](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)\n[![lifecycle-maturing](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-maturing.svg)](https://www.reconverse.org/lifecycle.html#maturing)\n\n\u003c!-- badges: end --\u003e\n\n_{{ 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. \n\n_{{ 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].\n\n_{{ packagename }}_ is part of the [Epiverse Initiative](https://data.org/initiatives/epiverse/).\n\n## Installation\n\nYou can install _{{ packagename }}_ from CRAN using:\n\n```{r install_from_cran, eval = FALSE}\ninstall.packages(\"serofoi\")\n```\n\nYou can install the **development version** of _{{ packagename }}_ from [GitHub](https://github.com/epiverse-trace/serofoi) running:\n\n```{r install_with_pak, eval = FALSE}\nif(!require(\"pak\")) install.packages(\"pak\")\npak::pak(\"epiverse-trace/serofoi\")\n```\nor:\n```{r install_with_remotes, eval = FALSE}\nif(!require(\"remotes\")) install.packages(\"remotes\")\nremotes::install_github(\"epiverse-trace/serofoi\")\n```\n## Quick start\n\n```{r load_package, include = FALSE, echo = TRUE}\nlibrary(serofoi)\n```\n\n_{{ 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 \n\n```{r load_data, include = TRUE}\n# Load example dataset chagas2012 included with the package\ndata(chagas2012)\nhead(chagas2012, 5)\n```\n\nA visualisation of the serological data can be obtained using the function `plot_serosurvey`:\n\n```{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}\nplot_serosurvey(chagas2012, bin_serosurvey = TRUE, size_text = 15)\n```\nHere, the error bars correspond to the binomial confidence interval and the point size represents the sample size for each age group.\n\nA constant FoI model can easily be implemented by means of `fit_seromodel`:\n\n```{r constant_model, include = TRUE, eval = FALSE}\nseromodel \u003c- fit_seromodel(serosurvey = chagas2012)\n```\n\nFor further details on how to visualise the results and other available models, please refer to the [online documentation](https://epiverse-trace.github.io/serofoi/).\n\n### Contributions\n\nContributors to the project include:\n\n-   [Zulma M. Cucunubá](https://github.com/zmcucunuba) (author,\n    maintainer)\n\n-   [Nicolás Torres](https://github.com/ntorresd) (author)\n\n-   [Ben Lambert](https://ben-lambert.com/about/) (author)\n\n-   [Pierre Nouvellet](https://github.com/pnouvellet) (author)\n\n-   [Geraldine Gómez](https://github.com/megamezl) (contributor)\n\n-   [Jaime A. Pavlich-Mariscal](https://github.com/jpavlich) (contributor)\n\n-   [Miguel Gamez](https://github.com/megamezl) (contributor)\n\n-   [Hugo Gruson](https://github.com/Bisaloo) (contributor)\n\n-   [David Santiago Quevedo](https://github.com/davidsantiagoquevedo) (contributor)\n\n-   [Everlyn Kamau](https://github.com/ekamau) (contributor)\n\n-   [Richard Creswell](https://github.com/rccreswell) (contributor)\n\n-   [Sumali Bajaj](https://github.com/sumalibajaj) (contributor)\n\n\n## Package vignettes\n\nMore details on how to use _{{ packagename }}_ can be found in the [online documentation as package vignettes](https://epiverse-trace.github.io/{{ packagename }}/), under \"Articles\".\n\n## Help\n\nTo report a bug please open an [issue](https://github.com/{{ gh_repo }}/issues/new/choose).\n\n## Contribute\n\nContributions to _{{ packagename }}_ are welcomed. Please follow the [package contributing guide](https://github.com/epiverse-trace/.github/blob/main/CONTRIBUTING.md).\n\n## Code of conduct\n\nPlease 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.\n\n## References\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiverse-trace%2Fserofoi","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fepiverse-trace%2Fserofoi","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiverse-trace%2Fserofoi/lists"}