EpiPvr0.0.1 package

Estimating Plant Pathogen Epidemiology Parameters from Laboratory Assays

AP_assay_simulator

Main function for AP assay simulation

AP_insect_simulator

Simulate AP assay data for individual insects

calculate_epidemic_probability

Main function for calculating epidemic probability

EpiPvr-package

The EpiPvr package

estimate_virus_parameters_PT

Estimate PT virus parameters using Bayesian inference with rstan

estimate_virus_parameters_SPT

Estimate SPT virus parameters using Bayesian inference with rstan

gen_exp

Safely generate random exponential data

inoc_durtn_calculator

Helper function for effective inoculation period calculator

solveInoculumStatesBP

Compute Epidemic Probability via Transition and Fertility Matrices

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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.