EpiPvr: Estimating Plant Pathogen Epidemiology Parameters from Laboratory Assays (original) (raw)

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.

Version:	0.0.1
Depends:	R (≥ 3.5)
Imports:	methods, stats, Rcpp (≥ 0.12.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), rstantools (≥ 2.5.0), posterior
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)
Suggests:	bayesplot, knitr, rmarkdown, testthat (≥ 3.0.0), ggplot2
Published:	2025-10-01
DOI:	10.32614/CRAN.package.EpiPvr
Author:	Ruairi Donnelly [aut, cre, cph]
Maintainer:	Ruairi Donnelly
License:	GPL-3
URL:	https://CRAN.R-project.org/package=EpiPvr
NeedsCompilation:	yes
SystemRequirements:	GNU make
Citation:	EpiPvr citation info
CRAN checks:	EpiPvr results

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