CITATION.cff

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# 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 "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
references:
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  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'
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  abstract: 'cli: Helpers for Developing Command Line Interfaces'
  notes: Imports
  url: https://cli.r-lib.org
  repository: https://CRAN.R-project.org/package=cli
  authors:
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  abstract: 'data.table: Extension of `data.frame`'
  notes: Imports
  url: https://r-datatable.com
  repository: https://CRAN.R-project.org/package=data.table
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  notes: Imports
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  repository: https://CRAN.R-project.org/package=glue
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- type: software
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  abstract: 'Rcpp: Seamless R and C++ Integration'
  notes: Imports
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  repository: https://CRAN.R-project.org/package=Rcpp
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  year: '2024'
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  abstract: 'RcppEigen: ''Rcpp'' Integration for the ''Eigen'' Templated Linear Algebra
    Library'
  notes: Imports
  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
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    given-names: Romain
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  year: '2024'
- type: software
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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: '2024'
- type: software
  title: utils
  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: withr
  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
  notes: Imports
  url: https://withr.r-lib.org
  repository: https://CRAN.R-project.org/package=withr
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Müller
    given-names: Kirill
    email: krlmlr+r@mailbox.org
  - family-names: Ushey
    given-names: Kevin
    email: kevinushey@gmail.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Chang
    given-names: Winston
  year: '2024'
- type: software
  title: bench
  abstract: 'bench: High Precision Timing of R Expressions'
  notes: Suggests
  url: https://bench.r-lib.org/
  repository: https://CRAN.R-project.org/package=bench
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
  year: '2024'
- type: software
  title: bookdown
  abstract: 'bookdown: Authoring Books and Technical Documents with R Markdown'
  notes: Suggests
  url: https://pkgs.rstudio.com/bookdown/
  repository: https://CRAN.R-project.org/package=bookdown
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2024'
- type: software
  title: colorspace
  abstract: 'colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes'
  notes: Suggests
  url: https://colorspace.R-Forge.R-project.org/contact.html
  repository: https://CRAN.R-project.org/package=colorspace
  authors:
  - family-names: Ihaka
    given-names: Ross
    email: ihaka@stat.auckland.ac.nz
  - family-names: Murrell
    given-names: Paul
    email: paul@stat.auckland.ac.nz
    orcid: https://orcid.org/0000-0002-3224-8858
  - family-names: Hornik
    given-names: Kurt
    email: Kurt.Hornik@R-project.org
    orcid: https://orcid.org/0000-0003-4198-9911
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    email: jfisher@usgs.gov
    orcid: https://orcid.org/0000-0001-9032-8912
  - family-names: Stauffer
    given-names: Reto
    email: Reto.Stauffer@uibk.ac.at
    orcid: https://orcid.org/0000-0002-3798-5507
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    given-names: Claus O.
    email: wilke@austin.utexas.edu
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: McWhite
    given-names: Claire D.
    email: claire.mcwhite@utmail.utexas.edu
    orcid: https://orcid.org/0000-0001-7346-3047
  - family-names: Zeileis
    given-names: Achim
    email: Achim.Zeileis@R-project.org
    orcid: https://orcid.org/0000-0003-0918-3766
  year: '2024'
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Suggests
  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: EpiEstim
  abstract: 'EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves'
  notes: Suggests
  url: https://github.com/mrc-ide/EpiEstim
  repository: https://CRAN.R-project.org/package=EpiEstim
  authors:
  - family-names: Cori
    given-names: Anne
    email: a.cori@imperial.ac.uk
    orcid: https://orcid.org/0000-0002-8443-9162
  year: '2024'
- type: software
  title: finalsize
  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
  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
  year: '2024'
- type: software
  title: ggdist
  abstract: 'ggdist: Visualizations of Distributions and Uncertainty'
  notes: Suggests
  url: https://mjskay.github.io/ggdist/
  repository: https://CRAN.R-project.org/package=ggdist
  authors:
  - family-names: Kay
    given-names: Matthew
    email: mjskay@northwestern.edu
  year: '2024'
- type: software
  title: ggplot2
  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
  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: 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: 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@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: 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: 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: '2024'
- 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: '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: 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: '2024'
- 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: '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'