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CITATION.cff

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+# -----------------------------------------------------------
+# CITATION file created with {cffr} R package, v0.5.0
+# 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
+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) <doi:10.1093/biostatistics/4.2.279>.
+authors:
+- family-names: Azam
+  given-names: James M.
+  email: [email protected]
+  orcid: https://orcid.org/0000-0001-5782-7330
+- family-names: Finger
+  given-names: Flavio
+  email: [email protected]
+  orcid: https://orcid.org/0000-0002-8613-5170
+- family-names: Funk
+  given-names: Sebastian
+  email: [email protected]
+  orcid: https://orcid.org/0000-0002-2842-3406
+preferred-citation:
+  type: manual
+  title: 'epichains: Analysing transmission chain statistics using branching process
+    models'
+  authors:
+  - name: Sebastian Funk
+  - name: Flavio Finger
+  - name: James M. Azam
+  year: '2023'
+  url: https://github.com/epiverse-trace/epichains/
+repository-code: https://github.com/epiverse-trace/epichains
+url: https://epiverse-trace.github.io/epichains/
+contact:
+- family-names: Azam
+  given-names: James M.
+  email: [email protected]
+  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
+  location:
+    name: Vienna, Austria
+  year: '2023'
+  institution:
+    name: R Foundation for Statistical Computing
+  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: [email protected]
+    orcid: https://orcid.org/0000-0001-9754-0393
+  year: '2023'
+- type: software
+  title: stats
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Imports
+  authors:
+  - name: R Core Team
+  location:
+    name: Vienna, Austria
+  year: '2023'
+  institution:
+    name: R Foundation for Statistical Computing
+- type: software
+  title: utils
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Imports
+  authors:
+  - name: R Core Team
+  location:
+    name: Vienna, Austria
+  year: '2023'
+  institution:
+    name: R Foundation for Statistical Computing
+- 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: [email protected]
+    orcid: https://orcid.org/0000-0003-0645-5666
+  year: '2023'
+- type: software
+  title: covr
+  abstract: 'covr: Test Coverage for Packages'
+  notes: Suggests
+  url: https://covr.r-lib.org
+  repository: https://CRAN.R-project.org/package=covr
+  authors:
+  - family-names: Hester
+    given-names: Jim
+    email: [email protected]
+  year: '2023'
+- 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: [email protected]
+    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: [email protected]
+    orcid: https://orcid.org/0000-0003-4777-038X
+  year: '2023'
+- type: software
+  title: epiparameter
+  abstract: 'epiparameter: Library of Epidemiological Parameters'
+  notes: Suggests
+  url: https://epiverse-trace.github.io/epiparameter/
+  authors:
+  - family-names: Lambert
+    given-names: Joshua W.
+    email: [email protected]
+    orcid: https://orcid.org/0000-0001-5218-3046
+  - family-names: Kucharski
+    given-names: Adam
+    email: [email protected]
+    orcid: https://orcid.org/0000-0001-8814-9421
+  year: '2023'
+- 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: [email protected]
+    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: [email protected]
+    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
+  year: '2023'
+- 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: [email protected]
+    orcid: https://orcid.org/0000-0003-0645-5666
+  year: '2023'
+- 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: [email protected]
+  - family-names: Grolemund
+    given-names: Garrett
+  - family-names: Wickham
+    given-names: Hadley
+  year: '2023'
+- 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: [email protected]
+  - family-names: Xie
+    given-names: Yihui
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-0645-5666
+  - family-names: Dervieux
+    given-names: Christophe
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-4474-2498
+  - family-names: McPherson
+    given-names: Jonathan
+    email: [email protected]
+  - family-names: Luraschi
+    given-names: Javier
+  - family-names: Ushey
+    given-names: Kevin
+    email: [email protected]
+  - family-names: Atkins
+    given-names: Aron
+    email: [email protected]
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  - family-names: Cheng
+    given-names: Joe
+    email: [email protected]
+  - family-names: Chang
+    given-names: Winston
+    email: [email protected]
+  - family-names: Iannone
+    given-names: Richard
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-3925-190X
+  year: '2023'
+- type: software
+  title: spelling
+  abstract: 'spelling: Tools for Spell Checking in R'
+  notes: Suggests
+  url: https://docs.ropensci.org/spelling/
+  repository: https://CRAN.R-project.org/package=spelling
+  authors:
+  - family-names: Ooms
+    given-names: Jeroen
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-4035-0289
+  - family-names: Hester
+    given-names: Jim
+    email: [email protected]
+  year: '2023'
+- 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: [email protected]
+  year: '2023'
+- 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: [email protected]
+  - family-names: Nadarajah
+    given-names: Saralees
+    email: [email protected]
+  year: '2023'
+- type: software
+  title: usethis
+  abstract: 'usethis: Automate Package and Project Setup'
+  notes: Suggests
+  url: https://usethis.r-lib.org
+  repository: https://CRAN.R-project.org/package=usethis
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-4757-117X
+  - family-names: Bryan
+    given-names: Jennifer
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-6983-2759
+  - family-names: Barrett
+    given-names: Malcolm
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-0299-5825
+  - family-names: Teucher
+    given-names: Andy
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-7840-692X
+  year: '2023'

DESCRIPTION

@@ -0,0 +1,53 @@
+Package: epichains
+Title: Simulating and Analysing Transmission Chain Statistics Using Branching Process
+    Models
+Version: 0.1.0
+Authors@R: c(
+    person("James M.", "Azam", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "https://orcid.org/0000-0001-5782-7330")),
+    person("Zhian N.", "Kamvar", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "https://orcid.org/0000-0003-1458-7108")),
+    person("Flavio", "Finger", , "[email protected]", role = "aut",
+           comment = c(ORCID = "https://orcid.org/0000-0002-8613-5170")),
+    person("Sebastian", "Funk", , "[email protected]", role = "aut",
+           comment = c(ORCID = "https://orcid.org/0000-0002-2842-3406"))
+           )
+Description: 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) <doi:10.1093/biostatistics/4.2.279>.
+License: MIT + file LICENSE
+URL: https://github.com/epiverse-trace/epichains,
+    https://epiverse-trace.github.io/epichains/
+BugReports: https://github.com/epiverse-trace/epichains/issues
+Depends:
+    R (>= 3.6.0)
+Imports: 
+    checkmate,
+    stats,
+    utils
+Suggests:
+    bookdown,
+    covr,
+    dplyr,
+    epiparameter,
+    ggplot2,
+    knitr,
+    lubridate,
+    rmarkdown,
+    spelling,
+    testthat,
+    truncdist,
+    usethis
+VignetteBuilder:
+    knitr
+Remotes:
+    github::epiverse-trace/epiparameter
+Config/Needs/website:epiverse-trace/epiversetheme
+Config/testthat/edition: 3
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Language: en-GB

LICENSE

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+YEAR: 2023
+COPYRIGHT HOLDER: epichains authors