EpiPvr

EpiPvr-package

Tools for epidemic parameter estimation using Stan.

internal

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.

Ruairi Donnelly

Estimating Plant Pathogen Epidemiology Parameters from
Laboratory Assays

EpiPvr-package function

Maintainer: Ruairi Donnelly <a href="/link/rd501%40cam.ac.uk?package=EpiPvr&version=0.0.1" data-mini-rdoc="EpiPvr::rd501@cam.ac.uk">rd501@cam.ac.uk</a> (<a href="https://orcid.org/0000-0001-7642-0317">ORCID</a>) [copyright holder]

Author

The EpiPvr package — EpiPvr-package

Maintainer: Ruairi Donnelly <a href='mailto:rd501@cam.ac.uk'>rd501@cam.ac.uk</a> (<a href='https://orcid.org/0000-0001-7642-0317'>ORCID</a>) [copyright holder]

EpiPvr-package: The EpiPvr package

Description

Arguments

Author

References

See Also