Package: EpiPvr
Title: Estimating Plant Pathogen Epidemiology Parameters from
        Laboratory Assays
Version: 0.0.1
Authors@R: person("Ruairi","Donnelly",email = "rd501@cam.ac.uk",
      role = c("aut", "cre", "cph"),comment = c(ORCID = "0000-0001-7642-0317"))
Description: 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), <doi:10.32942/X29K9P>. These models were originally
    implemented in the 'EpiPv' 'GitHub' package.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.2
Biarch: true
Depends: R (>= 3.5)
Imports: methods, stats, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1),
        rstan (>= 2.18.1), rstantools (>= 2.5.0), posterior
Suggests: bayesplot, knitr, rmarkdown, testthat (>= 3.0.0), ggplot2
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0),
        RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>=
        2.18.0)
SystemRequirements: GNU make
VignetteBuilder: knitr
URL: https://CRAN.R-project.org/package=EpiPvr
LazyData: true
NeedsCompilation: yes
Packaged: 2025-09-25 00:22:14 UTC; ruair
Author: Ruairi Donnelly [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0001-7642-0317>)
Maintainer: Ruairi Donnelly <rd501@cam.ac.uk>
Repository: CRAN
Date/Publication: 2025-10-01 07:30:14 UTC
Built: R 4.5.2; x86_64-w64-mingw32; 2026-01-13 17:45:13 UTC; windows
Archs: x64
