EpiPvr (version 0.0.1)

AP_assay_simulator: Main function for AP assay simulation

Description

This function simulates the assay data of an AP experiment (calling the helper function AP_insect_simulator.r to simulate on a per insect basis).

Usage

AP_assay_simulator(
  assayinput_in,
  fixedComponent_in,
  WF_in,
  smarkpams_in,
  isVerbose = 0,
  virusTypeIn
)

Value

A numeric array with 3 rows corresponding to assay structure and outcome: The first row specifies the assay variable durations, the second the reps per duration, the third the simulated number of infected test plants.

Arguments

assayinput_in

Numeric array with 3 rows (required): [1,] assay variable durations, [2,] reps per duration, [3,] zero entries for infected test plants (to be populated with simulated values).

fixedComponent_in

Numeric vector of 3 fixed durations in the order AAP, LAP, IAP; nb. one of these 3 will not be relevant for the sub-assay as it is varied in the assay (code -1) e.g. if AAP sub-assay [1] is -1, if LAP sub-assay [2] is -1, if IAP sub-assay [3] is -1 (required).

WF_in

Number of insect vectors in cohort (required).

smarkpams_in

Numeric vector: 4 elements representing virus rate parameters (hr^-1) (required): [1], acquisition rate; [2], inoculation rate; [3], latent progression rate WITH code -1 for SPT (no significant latency for SPT virus); [4], insect recovery rate.

isVerbose

Binary (optional, default = 0). If 1, prints information from nested functions.

virusTypeIn

Character. Plant virus type, either "SPT" or "PT" (required).

Examples

assay1=AP_assay_simulator(
  assayinput_in=rbind(c(6,7,8),rep(10,3),rep(0,3)),
  fixedComponent_in=c(10,-1,10),WF_in=5,
  smarkpams_in=rep(0.1,4),isVerbose=0,virusTypeIn='PT'
)