Package: EpiPvr 0.0.1

Ruairi Donnelly

EpiPvr: Estimating Plant Pathogen Epidemiology Parameters from Laboratory Assays

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.

Authors:Ruairi Donnelly [aut, cre, cph]

EpiPvr_0.0.1.tar.gz
EpiPvr_0.0.1.tar.gz(r-4.7-arm64)EpiPvr_0.0.1.tar.gz(r-4.7-x86_64)EpiPvr_0.0.1.tar.gz(r-4.6-arm64)EpiPvr_0.0.1.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
EpiPvr/json (API)

# Install 'EpiPvr' in R:
install.packages('EpiPvr', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • ap_data_sim_PT - Simulated access period experiment Data for a hypothetical PT virus
  • ap_data_sim_SPT - Simulated access period experiment Data for a hypothetical SPT virus

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

2.30 score 252 downloads 4 exports 48 dependencies

Last updated from:169bac7683. Checks:5 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK318
linux-devel-x86_64OK331
source / vignettesOK460
linux-release-arm64OK316
linux-release-x86_64OK344
wasm-releaseFAIL205

Exports:AP_assay_simulatorcalculate_epidemic_probabilityestimate_virus_parameters_PTestimate_virus_parameters_SPT

Dependencies:abindbackportsBHcallrcheckmateclicpp11descdistributionalfarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglifecycleloomagrittrmatrixStatsnumDerivotelpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsS7scalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr

Using the EpiPvr package to analyse access period data
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Last update: 2025-10-01
Started: 2025-10-01

Using the EpiPvr package to create access period data
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Rendered fromassay_simulation_script.Rmdusingknitr::rmarkdown

Last update: 2025-10-01
Started: 2025-10-01