Susceptible-Exposed-Infectious-Removed (SEIR) Model Framework with Lesion Expansion

This function is originally used by specific disease models in ‘EPIRICE’ and ‘EPIWHEAT’ to model disease intensity of several rice diseases and two wheat diseases respectively. Given proper values it can be used with other pathosystems as well.

Usage

seir(
  wth,
  emergence,
  onset,
  duration,
  H0,
  I0,
  RcA,
  RcT,
  RcOpt,
  p,
  i,
  Sx,
  a = 1,
  rhlim = 90,
  rainlim = 5,
  RRS = NULL,
  RRG = NULL,
  RcW = NULL,
  RRLEX = NULL,
  simple_wetness = TRUE,
  weighted_wetness = FALSE,
  age_driver = c("day", "dvs"),
  thermal_time = NULL,
  steps_per_day = 1L,
  infection_window = NULL
)

Arguments

wth

a data.frame of class epicrop.wth from either get_wth() or format_wth() containing weather on a daily time-step with the following field names:

Field Name	Value
YYYYMMDD	Date as Year Month Day (ISO8601)
DOY	Consecutive day of year, commonly called "Julian date"
TEMP	Mean daily temperature (°C)
RHUM	Mean daily relative humidity (%)
RAIN	Mean daily rainfall (mm)
TMIN	Optional Minimum daily temperature (°C), see TMIN/TMAX Details
TMAX	Optional Maximum daily temperature (°C), see TMIN/TMAX Details
LAT	Optional latitude of weather observation, see LAT/LON Details
LON	Optional longitude of weather observation, see LAT/LON Details

emergence

Expected date of plant emergence (or transplanting for rice) entered in YYYY-MM-DD format (character).

onset

expected number of days until the onset of disease after emergence date (day, integer). For this modern seir() variant onset is 1-indexed (1 = emergence day). When comparing with legacy SEIR(), translate as legacy_onset = onset - 1.

duration

simulation duration i. e., growing season length (day, integer). Described in Table 1 of Savary et al. 2012.

H0

initial number of plant's healthy sites (integer). Described in Table 1 of Savary et al. 2012.

I0

initial number of infective sites (scalar integer). Described in Table 1 of Savary et al. 2012. I0 is injected as new infections (become infectious after p days).

RcA

modifier for Rc (the basic infection rate corrected for removals) for crop age as a numeric two-column matrix with the first column being the crop age in days (0 to duration-1) or DVS (0 to 2) and the second being the modifier (bounded by 0 and 1). Described in Tables 1 and 2 of Savary et al. 2012.

RcT

modifier for Rc (the basic infection rate corrected for removals) for temperature as a numeric two-column matrix with the first column being temperature in °C and the second the modifier (bounded by 0 and 1). Described in Tables 1 and 2 of Savary et al. 2012.

RcOpt

potential basic infection rate corrected for removals (numeric). Described in Table 1 of Savary et al. 2012. This value can be modified to reflect crop cultivar resistance ratings as well, see Kim _et al. _ 2015 for more details.

p

duration of latent period (day, integer or function of temperature). Described in Table 1 of Savary et al. 2012.

i

duration of infectious period (day, integer or function of temperature). Described in Table 1 of Savary et al. 2012.

Sx

maximum number of sites (integer). Described in Table 1 of Savary et al. 2012.

a

aggregation coefficient, values are from 1 to >1 (numeric or function of DVS). Described in Table 1 of Savary et al. 2012 and Table 1 of Savary et al. 2015. See further details in a - Aggregation section. Defaults to 1.

rhlim

relative humidity value threshold to decide whether leaves are wet or not (numeric). Described in Table 1 of Savary et al. 2012. Savary et al. 2012 used 90. Defaults to 90.

rainlim

rainfall amount (mm) threshold to decide whether leaves are wet or not (numeric). Described in Table 1 of Savary et al. 2012. Savary et al. 2012 used 5. Defaults to 5.

RRS

relative rate of physiological senescence (numeric, vector, or function of DVS). Described in Table 1 of Savary et al. 2012.

RRG

relative rate of growth (numeric, vector, or function of time). Described in Table 1 of Savary et al. 2012.

RcW

Optional modifier for Rc to calculate leaf wetness effect from 1 if wet to 0 if dry. This is a numeric two-column matrix with the first column being hours (0 to 24) and the second the modifier (bounded by 0 and 1). Used when simple_wetness = FALSE (hourly/derived wetness). If NULL (default), a linear relationship is used where 0 hours wet = 0 and 24 hours wet = 1. Ignored if simple_wetness = TRUE.

RRLEX

Rate of lesion expansion (scalar, vector, or function). Allows healthy sites to be directly converted to infectious sites without passing through latent stage. Set to 0 (default) for standard SEIR behavior.

simple_wetness

Logical. If TRUE (default), uses binary wetness calculation (0 or 1) based on rhlim and rainlim thresholds. If FALSE, uses hourly wetness duration calculation (requires TMIN, TMAX, LAT, DOY in wth) and applies RcW curve.

weighted_wetness

Logical. If TRUE, compute weighted hourly wetness (0 to 24); if FALSE, count hours where hourly RH >= rhlim (0 to 24). Only used when simple_wetness = FALSE. Defaults to FALSE.

age_driver

Character. Use "day" (default, 0-indexed days from emergence) or "dvs" (development stage 0-2) for age-based modifiers in RcA. When "dvs", thermal_time parameter is required. Defaults to "day".

thermal_time

List with base_temp (°C) and gdd_to_maturity (°C·days). Only required when age_driver = "dvs". Determines how growing degree days are accumulated and converted to development stage (DVS).

steps_per_day

Integer. Number of sub-daily time steps for numerical integration. Default is 1 (daily steps). Values of 2, 4, or 8 can improve accuracy for stiff systems at cost of computation time. Should be a power of 2. Defaults to 1.

infection_window

Optional list defining DVS-based infection window:

dvs_start: DVS when susceptibility begins
dvs_end: DVS when susceptibility ends
base_temp: Base temperature for GDD (optional, uses thermal_time if present)
gdd_to_maturity: GDD to maturity (optional, uses thermal_time if present)

Value

A data.table::data.table() object containing the following columns:

... (documentation omitted for brevity) ...

Author

Adam H. Sparks, adamhsparks@gmail.com from original by Robert J. Hijmans, Rene Pangga and Jorrel Aunario.