inoc_durtn_calculator

Helper function for effective inoculation period calculator

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

EpiPvr

Estimating Plant Pathogen Epidemiology Parameters from
Laboratory Assays

inoc_durtn_calculator function

<dl><dt>lmark_in</dt>
<dd>Numeric vector of length 3 specifying assay durations.</dd>
<dt>sim_Ts_in</dt>
<dd>Numeric vector of length 4 specifying sampled event times (hours) related to virus parameters (rates hr^-1) (rates per hour)</dd>
<dt>isitVerbose</dt>
<dd>Logical (default: <code>FALSE</code>). If <code>TRUE</code>, prints information from nested functions.</dd></dl>

Arguments

Helper function for effective inoculation period calculator — inoc_durtn_calculator

<dl>

<dt>lmark_in</dt>
<dd>Numeric vector of length 3 specifying assay durations.</dd>


<dt>sim_Ts_in</dt>
<dd>Numeric vector of length 4 specifying sampled event times (hours) related to virus parameters (rates hr^-1) (rates per hour)</dd>


<dt>isitVerbose</dt>
<dd>Logical (default: <code>FALSE</code>). If <code>TRUE</code>, prints information from nested functions.</dd>

</dl>

inoc_durtn_calculator: Helper function for effective inoculation period calculator

Description

Usage

Value

Arguments