CITATION.cff

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# CITATION file created with {cffr} R package, v0.5.0
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "epinowcast" in publications use:'
type: software
license: MIT
title: 'epinowcast: Flexible Hierarchical Nowcasting'
version: 0.2.3.2000
doi: 10.5281/zenodo.5637165
abstract: 'Tools to enable flexible and efficient hierarchical nowcasting of right-truncated
  epidemiological time-series using a semi-mechanistic Bayesian model with support
  for a range of reporting and generative processes. Nowcasting, in this context,
  is gaining situational awareness using currently available observations and the
  reporting patterns of historical observations. This can be useful when tracking
  the spread of infectious disease in real-time: without nowcasting, changes in trends
  can be obfuscated by partial reporting or their detection may be delayed due to
  the use of simpler methods like truncation. While the package has been designed
  with epidemiological applications in mind, it could be applied to any set of right-truncated
  time-series count data.'
authors:
- name: Sam Abbott
  email: contact@samabbott.co.uk
  orcid: https://orcid.org/0000-0001-8057-8037
- family-names: Lison
  given-names: Adrian
  email: adrian.lison@bsse.ethz.ch
  orcid: https://orcid.org/0000-0002-6822-8437
- family-names: Funk
  given-names: Sebastian
  email: sebastian.funk@lshtm.ac.uk
- family-names: Pearson
  given-names: Carl
  email: carl.ab.pearson@gmail.com
  orcid: https://orcid.org/0000-0003-0701-7860
- family-names: Gruson
  given-names: Hugo
  email: hugo.gruson@normalesup.org
  orcid: https://orcid.org/0000-0002-4094-1476
- family-names: Guenther
  given-names: Felix
  email: felixguenther1@gmx.de
  orcid: https://orcid.org/0000-0001-6582-1174
preferred-citation:
  type: manual
  title: 'epinowcast: Flexible Hierarchical Nowcasting'
  authors:
  - name: Sam Abbott
    email: contact@samabbott.co.uk
    orcid: https://orcid.org/0000-0001-8057-8037
  - family-names: Lison
    given-names: Adrian
    email: adrian.lison@bsse.ethz.ch
    orcid: https://orcid.org/0000-0002-6822-8437
  - family-names: Funk
    given-names: Sebastian
    email: sebastian.funk@lshtm.ac.uk
  - family-names: Pearson
    given-names: Carl
    email: carl.ab.pearson@gmail.com
    orcid: https://orcid.org/0000-0003-0701-7860
  - family-names: Gruson
    given-names: Hugo
    email: hugo.gruson@normalesup.org
    orcid: https://orcid.org/0000-0002-4094-1476
  - family-names: Guenther
    given-names: Felix
    email: felixguenther1@gmx.de
    orcid: https://orcid.org/0000-0001-6582-1174
  year: 'NULL'
  doi: 10.5281/zenodo.5637165
repository-code: https://github.com/epinowcast/epinowcast/issues/
url: https://package.epinowcast.org
contact:
- name: Sam Abbott
  email: contact@samabbott.co.uk
  orcid: https://orcid.org/0000-0001-8057-8037
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: '>= 3.5.0'
- type: software
  title: data.table
  abstract: 'data.table: Extension of `data.frame`'
  notes: Imports
  url: https://r-datatable.com
  repository: https://CRAN.R-project.org/package=data.table
  authors:
  - family-names: Dowle
    given-names: Matt
    email: mattjdowle@gmail.com
  - family-names: Srinivasan
    given-names: Arun
    email: asrini@pm.me
  year: '2023'
- type: software
  title: lubridate
  abstract: 'lubridate: Make Dealing with Dates a Little Easier'
  notes: Imports
  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: '2023'
- 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
  year: '2023'
- 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: '2023'
- 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: '2023'
- type: software
  title: scales
  abstract: 'scales: Scale Functions for Visualization'
  notes: Imports
  url: https://scales.r-lib.org
  repository: https://CRAN.R-project.org/package=scales
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Seidel
    given-names: Dana
  year: '2023'
- type: software
  title: lifecycle
  abstract: 'lifecycle: Manage the Life Cycle of your Package Functions'
  notes: Imports
  url: https://lifecycle.r-lib.org/
  repository: https://CRAN.R-project.org/package=lifecycle
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@rstudio.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
  year: '2023'
- 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: '2023'
- type: software
  title: loo
  abstract: 'loo: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models'
  notes: Suggests
  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: '2023'
  version: '>= 2.4.1'
- 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: '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: 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: '2023'
- type: software
  title: scoringutils
  abstract: 'scoringutils: Utilities for Scoring and Assessing Predictions'
  notes: Suggests
  url: https://epiforecasts.io/scoringutils/
  repository: https://CRAN.R-project.org/package=scoringutils
  authors:
  - family-names: Bosse
    given-names: Nikos
    email: nikosbosse@gmail.com
    orcid: https://orcid.org/0000-0002-7750-5280
  - name: Sam Abbott
    email: contact@samabbott.co.uk
    orcid: https://orcid.org/0000-0001-8057-8037
  - family-names: Gruson
    given-names: Hugo
    email: hugo.gruson@lshtm.ac.uk
    orcid: https://orcid.org/0000-0002-4094-1476
  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: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
  - family-names: Hester
    given-names: Jim
    email: james.hester@rstudio.com
  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: hadley@posit.co
  year: '2023'
  version: '>= 3.1.9'
- 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: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  - family-names: Barrett
    given-names: Malcolm
    email: malcolmbarrett@gmail.com
    orcid: https://orcid.org/0000-0003-0299-5825
  - family-names: Teucher
    given-names: Andy
    email: andy.teucher@posit.co
    orcid: https://orcid.org/0000-0002-7840-692X
  year: '2023'
identifiers:
- type: url
  value: https://github.com/epinowcast/epinowcast/