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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 "EpiPvr" in publications use:'
type: software
license: GPL-3.0-only
title: 'EpiPvr: Estimating Plant Pathogen Epidemiology Parameters from Laboratory
  Assays'
version: 0.0.1
identifiers:
- type: doi
  value: 10.32614/CRAN.package.EpiPvr
abstract: Provides functions for estimating plant pathogen parameters from access
  period (AP) experiments. Separate functions are implemented for semi-persistently
  transmitted (SPT) and persistently transmitted (PT) pathogens. The common AP experiment
  exposes insect cohorts to infected source plants, healthy test plants, and intermediate
  plants (for PT pathogens). The package allows estimation of acquisition and inoculation
  rates during feeding, recovery rates, and latent progression rates (for PT pathogens).
  Additional functions support inference of epidemic risk from pathogen and local
  parameters, and also simulate AP experiment data. The functions implement probability
  models for epidemiological analysis, as derived in Donnelly et al. (2025), <https://doi.org/10.32942/X29K9P>.
  These models were originally implemented in the 'EpiPv' 'GitHub' package.
authors:
- family-names: Donnelly
  given-names: Ruairi
  email: rd501@cam.ac.uk
  orcid: https://orcid.org/0000-0001-7642-0317
preferred-citation:
  type: article
  title: Plant pathogen profiling with the EpiPv package
  authors:
  - family-names: Donnelly
    given-names: Ruairi
    email: rd501@cam.ac.uk
    orcid: https://orcid.org/0000-0001-7642-0317
  - family-names: Tankam
    given-names: Israel
  - family-names: Gilligan
    given-names: Chris
  year: '2025'
  journal: EcoEvoRxiv
  url: https://ecoevorxiv.org/repository/view/9081/
repository: https://cran.r-universe.dev
commit: 169bac7683165c85621d35d7d51608a2a2a8ecce
url: https://CRAN.R-project.org/package=EpiPvr
date-released: '2025-10-01'
contact:
- family-names: Donnelly
  given-names: Ruairi
  email: rd501@cam.ac.uk
  orcid: https://orcid.org/0000-0001-7642-0317