CITATION.cff

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "serofoi" in publications use:'
type: software
license: MIT
title: 'serofoi: Estimates the Force-of-Infection of a Given Pathogen from Population
  Based Seroprevalence Studies'
version: 1.0.2
abstract: Estimate time-varying Force-of-Infection of a given pathogen from population
  based seroprevalence studies using a bayesian framework.
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:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
  version: '>= 3.5.0'
- type: software
  title: bayesplot
  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: '2024'
- 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: 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: '2024'
- 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
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2024'
- 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:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Chang
    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: Woo
    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
  - family-names: Yutani
    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
  - family-names: Dunnington
    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
  - family-names: Brand
    given-names: Teun
    name-particle: van den
    orcid: https://orcid.org/0000-0002-9335-7468
  year: '2024'
- type: software
  title: Hmisc
  abstract: 'Hmisc: Harrell Miscellaneous'
  notes: Imports
  url: https://hbiostat.org/R/Hmisc/
  repository: https://CRAN.R-project.org/package=Hmisc
  authors:
  - family-names: Harrell Jr
    given-names: Frank E
    email: fh@fharrell.com
    orcid: https://orcid.org/0000-0002-8271-5493
  year: '2024'
- type: software
  title: loo
  abstract: 'loo: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models'
  notes: Imports
  url: https://mc-stan.org/loo/
  repository: https://CRAN.R-project.org/package=loo
  authors:
  - family-names: Vehtari
    given-names: Aki
    email: Aki.Vehtari@aalto.fi
  - family-names: Gabry
    given-names: Jonah
    email: jsg2201@columbia.edu
  - family-names: Magnusson
    given-names: Mans
  - family-names: Yao
    given-names: Yuling
  - family-names: Bürkner
    given-names: Paul-Christian
  - family-names: Paananen
    given-names: Topi
  - family-names: Gelman
    given-names: Andrew
  year: '2024'
- type: software
  title: methods
  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: '2024'
- type: software
  title: purrr
  abstract: 'purrr: Functional Programming Tools'
  notes: Imports
  url: https://purrr.tidyverse.org/
  repository: https://CRAN.R-project.org/package=purrr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Henry
    given-names: Lionel
    email: lionel@rstudio.com
  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
  - family-names: Ucar
    given-names: Inaki
  - family-names: Bates
    given-names: Douglas
  - family-names: Chambers
    given-names: John
  year: '2024'
  version: '>= 0.12.0'
- type: software
  title: rstan
  abstract: 'rstan: R Interface to Stan'
  notes: Imports
  url: https://mc-stan.org/rstan/
  repository: https://CRAN.R-project.org/package=rstan
  authors:
  - family-names: Guo
    given-names: Jiqiang
    email: guojq28@gmail.com
  - family-names: Gabry
    given-names: Jonah
    email: jsg2201@columbia.edu
  - family-names: Goodrich
    given-names: Ben
    email: benjamin.goodrich@columbia.edu
  - family-names: Johnson
    given-names: Andrew
    email: andrew.johnson@arjohnsonau.com
  - family-names: Weber
    given-names: Sebastian
    email: sdw.post@waebers.de
  - family-names: Badr
    given-names: Hamada S.
    email: badr@jhu.edu
    orcid: https://orcid.org/0000-0002-9808-2344
  year: '2024'
  version: '>= 2.18.1'
- type: software
  title: rstantools
  abstract: 'rstantools: Tools for Developing R Packages Interfacing with ''Stan'''
  notes: Imports
  url: https://mc-stan.org/rstantools/
  repository: https://CRAN.R-project.org/package=rstantools
  authors:
  - family-names: Gabry
    given-names: Jonah
    email: jsg2201@columbia.edu
  - family-names: Goodrich
    given-names: Ben
    email: benjamin.goodrich@columbia.edu
  - family-names: Lysy
    given-names: Martin
    email: mlysy@uwaterloo.ca
  - family-names: Johnson
    given-names: Andrew
  year: '2024'
  version: '>= 2.3.1'
- 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: '2024'
- 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: '2024'
- 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: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
  - family-names: Hester
    given-names: Jim
    email: james.hester@rstudio.com
  year: '2024'
- 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: '2024'
  version: '>= 3.0.0'
- type: software
  title: vdiffr
  abstract: 'vdiffr: Visual Regression Testing and Graphical Diffing'
  notes: Suggests
  url: https://vdiffr.r-lib.org/
  repository: https://CRAN.R-project.org/package=vdiffr
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Luciani
    given-names: T Jake
    email: jake@apache.org
  - family-names: Decorde
    given-names: Matthieu
    email: matthieu.decorde@ens-lyon.fr
  - family-names: Lise
    given-names: Vaudor
    email: lise.vaudor@ens-lyon.fr
  year: '2024'
- 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
  - family-names: Emerson
    given-names: John W.
  - family-names: Kane
    given-names: Michael J.
  year: '2024'
  version: '>= 1.66.0'
- 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: Douglas
  - family-names: Eddelbuettel
    given-names: Dirk
  - family-names: Francois
    given-names: Romain
  - family-names: Eigen
    given-names: Yixuan Qiu; the authors of Eigen for the included version of
  year: '2024'
  version: '>= 0.3.3.3.0'
- type: software
  title: RcppParallel
  abstract: 'RcppParallel: Parallel Programming Tools for ''Rcpp'''
  notes: LinkingTo
  url: https://rcppcore.github.io/RcppParallel/
  repository: https://CRAN.R-project.org/package=RcppParallel
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  - family-names: Francois
    given-names: Romain
  - family-names: Ushey
    given-names: Kevin
    email: kevin@rstudio.com
  - family-names: Vandenbrouck
    given-names: Gregory
  - family-names: Geelnard
    given-names: Marcus
    website: https://tinythreadpp.bitsnbites.eu/
  - name: Intel
    website: https://www.threadingbuildingblocks.org/
  year: '2024'
  version: '>= 5.0.1'
- type: software
  title: StanHeaders
  abstract: 'StanHeaders: C++ Header Files for Stan'
  notes: LinkingTo
  url: https://mc-stan.org/
  repository: https://CRAN.R-project.org/package=StanHeaders
  authors:
  - family-names: Goodrich
    given-names: Ben
    email: benjamin.goodrich@columbia.edu
  - family-names: Gelman
    given-names: Andrew
  - family-names: Carpenter
    given-names: Bob
  - family-names: Hoffman
    given-names: Matt
  - family-names: Lee
    given-names: Daniel
  - family-names: Betancourt
    given-names: Michael
  - family-names: Brubaker
    given-names: Marcus
  - family-names: Guo
    given-names: Jiqiang
  - family-names: Li
    given-names: Peter
  - family-names: Riddell
    given-names: Allen
  - family-names: Inacio
    given-names: Marco
  - family-names: Morris
    given-names: Mitzi
  - family-names: Arnold
    given-names: Jeffrey
  - family-names: Goedman
    given-names: Rob
  - family-names: Lau
    given-names: Brian
  - family-names: Trangucci
    given-names: Rob
  - family-names: Gabry
    given-names: Jonah
  - family-names: Kucukelbir
    given-names: Alp
  - family-names: Grant
    given-names: Robert
  - family-names: Tran
    given-names: Dustin
  - family-names: Malecki
    given-names: Michael
  - family-names: Gao
    given-names: Yuanjun
  - family-names: Badr
    given-names: Hamada S.
    email: badr@jhu.edu
    orcid: https://orcid.org/0000-0002-9808-2344
  year: '2024'
  version: '>= 2.18.0'