ap_data_sim_SPT

This dataset contains simulated AP assay results for an SPT virus (AAP and IAP sub-assays)

datasets

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

EpiPvr

Estimating Plant Pathogen Epidemiology Parameters from
Laboratory Assays

ap_data_sim_SPT function

A List that is a collection of 5 data objects and 3 attributes<dl>
<dt>d_AAP</dt>
<dd>Numeric 3 x n array for acquistion access sub-assay: variable duration; reps per duration, no. infected test plants per duration</dd><dt>d_IAP</dt>
<dd>Numeric 3 x n array for inoculation access sub-assay: variable duration; reps per duration, no. infected test plants per duration</dd><dt>d_durations</dt>
<dd>Numeric 2 x 2 assay of fixed durations (FD): row 1, FDs for acquistion access sub-assay; row 2, FDs acquistion access sub-assay. nb diagonal entries must be '-1' indicating redundancy since these elements correspond to the variable durations</dd><dt>d_vectorspp</dt>
<dd>Numeric number of insects per plant</dd><dt>d_pathogen</dt>
<dd>Character representing underlying virus</dd>
</dl>#'<dl>
<dt>"alpha"</dt>
<dd>Numeric: acquisition rate (h^-1); used to generate the data or '-1' if unknown</dd><dt>"beta"</dt>
<dd>Numeric: inoculation rate (h^-1); used to generate the data or '-1' if unknown</dd><dt>"mu"</dt>
<dd>Numeric: insect recovery rate (h^-1); used to generate the data or '-1' if unknown</dd>
</dl>

Format

Simulated access period experiment Data for a hypothetical SPT virus — ap_data_sim_SPT

A List that is a collection of 5 data objects and 3 attributes<dl>
<dt>d_AAP</dt>
<dd>Numeric 3 x n array for acquistion access sub-assay: variable duration; reps per duration, no. infected test plants per duration</dd>

<dt>d_IAP</dt>
<dd>Numeric 3 x n array for inoculation access sub-assay: variable duration; reps per duration, no. infected test plants per duration</dd>

<dt>d_durations</dt>
<dd>Numeric 2 x 2 assay of fixed durations (FD): row 1, FDs for acquistion access sub-assay; row 2, FDs acquistion access sub-assay. nb diagonal entries must be '-1' indicating redundancy since these elements correspond to the variable durations</dd>

<dt>d_vectorspp</dt>
<dd>Numeric number of insects per plant</dd>

<dt>d_pathogen</dt>
<dd>Character representing underlying virus</dd>


</dl>#'<dl>
<dt>"alpha"</dt>
<dd>Numeric: acquisition rate (h^-1); used to generate the data or '-1' if unknown</dd>

<dt>"beta"</dt>
<dd>Numeric: inoculation rate (h^-1); used to generate the data or '-1' if unknown</dd>

<dt>"mu"</dt>
<dd>Numeric: insect recovery rate (h^-1); used to generate the data or '-1' if unknown</dd>


</dl>

ap_data_sim_SPT: Simulated access period experiment Data for a hypothetical SPT virus

Description

Usage

Arguments

Format