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 "epichains" in publications use:'
type: software
license: MIT
title: 'epichains: Simulating and Analysing Transmission Chain Statistics Using Branching
  Process Models'
version: 0.1.0.9000
abstract: Provides methods to simulate and analyse the size and length of branching
  processes with an arbitrary offspring distribution. These can be used, for example,
  to analyse the distribution of chain sizes or length of infectious disease outbreaks,
  as discussed in Farrington et al. (2003) <https://doi.org/10.1093/biostatistics/4.2.279>.
authors:
- family-names: Azam
  given-names: James M.
  email: james.azam@lshtm.ac.uk
  orcid: https://orcid.org/0000-0001-5782-7330
- family-names: Funk
  given-names: Sebastian
  email: sebastian.funk@lshtm.ac.uk
  orcid: https://orcid.org/0000-0002-2842-3406
- family-names: Finger
  given-names: Flavio
  email: flavio.finger@epicentre.msf.org
  orcid: https://orcid.org/0000-0002-8613-5170
repository-code: https://github.com/epiverse-trace/epichains
url: https://epiverse-trace.github.io/epichains/
contact:
- family-names: Azam
  given-names: James M.
  email: james.azam@lshtm.ac.uk
  orcid: https://orcid.org/0000-0001-5782-7330
keywords:
- branching-processes
- epidemic-dynamics
- epidemic-modelling
- epidemic-simulations
- epidemiology
- epidemiology-models
- outbreak-simulator
- r-package
- r-stats
- transmission-chain
- transmission-chain-reconstruction
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: '>= 3.6.0'
- 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: stats
  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: 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: 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: epicontacts
  abstract: 'epicontacts: Handling, Visualisation and Analysis of Epidemiological
    Contacts'
  notes: Suggests
  url: https://www.repidemicsconsortium.org/epicontacts/
  repository: https://CRAN.R-project.org/package=epicontacts
  authors:
  - family-names: Campbell
    given-names: Finlay
    email: finlaycampbell93@gmail.com
  - family-names: Jombart
    given-names: Thibaut
    email: thibautjombart@gmail.com
  - family-names: Randhawa
    given-names: Nistara
    email: nrandhawa@ucdavis.edu
  - family-names: Sudre
    given-names: Bertrand
    email: Bertrand.Sudre@ecdc.europa.eu
  - family-names: Nagraj
    given-names: VP
    email: nagraj@nagraj.net
  - family-names: Crellen
    given-names: Thomas
    email: tc13@sanger.ac.uk
  - family-names: Kamvar
    given-names: Zhian N.
    email: zkamvar@gmail.com
  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: lubridate
  abstract: 'lubridate: Make Dealing with Dates a Little Easier'
  notes: Suggests
  url: https://lubridate.tidyverse.org
  repository: https://CRAN.R-project.org/package=lubridate
  authors:
  - family-names: Spinu
    given-names: Vitalie
    email: spinuvit@gmail.com
  - family-names: Grolemund
    given-names: Garrett
  - family-names: Wickham
    given-names: Hadley
  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'
- type: software
  title: truncdist
  abstract: 'truncdist: Truncated Random Variables'
  notes: Suggests
  repository: https://CRAN.R-project.org/package=truncdist
  authors:
  - family-names: Novomestky
    given-names: Frederick
    email: fn334@nyu.edu
  - family-names: Nadarajah
    given-names: Saralees
    email: saralees.nadarajah@manchester.ac.uk
  year: '2024'