zakoks.original.model: Classical SEIR model for plant diseases from Zadoks (1971)

Description

Model description. This model is a classical SEIR model for plant disease. It was written from it description included in the original publication of Zadoks (1971)

Usage

zakoks.original.model(nlpd = 4 * 10, nipd = 1 * 10, dmfr = 16,
  SITE0 = 5 * 10^9, weather, sdate = 145, ldate = 145 + 50,
  XLAT0 = 1)

Arguments

nlpd

: latent period (in degree.day) - default value for Puccinia triticina : ~10 days at 20degC

nipd

: infectious period (in degree.day) - default value for Puccinia triticina : ~20 days at 20degC

dmfr

: daily multiplication factor - default value number of effective spores produced by lesion

SITE0

weather

: weather data.frame for one single year

sdate

: starting date

ldate

: ending date

XLAT0

Value

list with a data.frame with daily day, DACE, XVAC, XLAT, XINF, XCTR ,XTO1, XSEV= XSEV, severity and a vector of parameter value (nlpd, nipd, dmfr, SITE0).

Details

This model is a classical SEIR model proposed by Zadoks (1971) to simulate epidemics of diseases of crops. It is a Susceptible-Exposed-Infectious-Removed (SEIR) model. This simple model of an epidemic is based on the epidemiological concepts "latent period", "infectious period", and "multiplication factor". The crop is considered to consist of a large but finite number of infectious sites. The physical dimensions of an infectious site roughly coincide with the reproductive unit of the parasite studied. Different pathosystems (with different infectious site definitions) can be considered with this model. A full description, is available in the original paper: The model has four essential state variables representing the number of sites in each state XVAC for vacant (healthy) sites, XLAT for latent site, XINF for infectant sites and XCTR for the cumulative total of removal (post infectious) sites. Two supplementary variables based on the state variables are used defined as XTO1 = XLAT+XINF+XCTR and XSEV = XINF+XCTR. Fluxes or rates between the state variables are defined as rocc for occupation, rapp for apparition and rrem for removal. The model has a time step of one day (dt=1). The system modeled is one hectare of a wheat crop.

Examples

Run this code

# NOT RUN {
weather=subset(weather_FranceWest, WEYR==1997 & idsite==39)
out=zakoks.original.model(nlpd=4*10,nipd=1*10,dmfr=16,SITE0 = 5*10^9,
weather, sdate = 145, ldate = 145+50 , XLAT0=1)
plot(out$sim$DACE,out$sim$severity, type="l")
# }