Susceptible-Exposed-Infectious-Removed (SEIR) Model Framework

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

Usage

seir(
  wth,
  emergence,
  onset,
  duration,
  rhlim,
  rainlim,
  H0,
  I0,
  RcA,
  RcT,
  RcOpt,
  p,
  i,
  Sx,
  a,
  RRS,
  RRG,
  RcW = NULL,
  simple_wetness = TRUE
)

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). Described in Table 1 of Savary _et al. _ 2012.

onset

expected number of days until the onset of disease after emergence date (day, integer). Described in Table 1 of Savary et al. 2012.

duration

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

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.

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.

H0

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

I0

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

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 (1 to duration) 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). Described in Table 1 of Savary et al. 2012.

i

duration of infectious period (day, integer). 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). Described in Table 1 of Savary et al. 2012 and Table 1 of Savary et al. 2015. See further details in a - Aggregation section.

RRS

relative rate of physiological senescence (numeric). Described in Table 1 of Savary _et al. _ 2012.

RRG

relative rate of growth (numeric). 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 (1 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.

simple_wetness

Logical. If TRUE (default), the function uses a simple calculation of leaf wetness based on daily rhlim and rainlim values (wetness is either 0 or 24 hours). If FALSE, the function uses a more complex calculation of leaf wetness based on hourly temperature and humidity patterns derived from daily TMIN/TMAX values, requiring additional weather data columns (TMIN, TMAX, LAT, DOY), and applies RcW to determine the effect of leaf wetness duration on the infection rate.

Value

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

simday: Day of simulation (1-indexed, where 1 is the emergence date)
dates: Date of simulation
sites: Total number of healthy sites present on day "x"
latent: Number of latent sites present on day "x"
infectious: Number of infectious sites present on day "x"
removed: Number of removed sites present on day "x"
senesced: Number of senesced sites present on day "x"
rateinf: Rate of infection (new infections on day "x")
rtransfer: Rate of transfer from latent to infectious sites
rgrowth: Rate of growth of healthy sites
rsenesced: Rate of senescence of healthy sites
diseased: Number of diseased (latent + infectious + removed) sites on day "x"
intensity: Proportion of diseased sites (latent + infectious) per total living sites (excludes removed and senesced) on day "x"
AUDPC: Area under the disease progress curve (AUDPC) for the simulation
lat: Latitude value if provided by the wth object
lon: Longitude value if provided by the wth object

a – Aggregation Details

When a is set to 1 the assumption is that that there is no disease aggregation with new infections occurring at random among the healthy sites. When a is greater than 1 there is aggregation in the disease occurrence, the pathogen is unable to access the entire population of healthy sites, which results in disease aggregation. Refer to Savary _et al. _ (2012) for greater detail.

TMIN/TMAX Details

If simple_wetness is set to FALSE, the function will use the TMIN and TMAX columns in the wth object to calculate the leaf wetness value for 24 hours of the day using the rhlim and rainlim values and then uses RcW to calculate a value between 0 and 1 for the whole day. When simple_wetness is set to TRUE, the function only sets the leaf wetness to 0 or 1 for the day based on the rhlim and rainlim values.

LAT/LON Details

If the wth object provides LAT and LON columns, these will be included in the output for mapping purposes. Both values must be present. These columns are provided by default when using get_wth().

References

Sparks, A. H., P.D. Esker, M. Bates, W. Dall' Acqua, Z. Guo, V. Segovia, S.D. Silwal, S. Tolos, and K. A. Garrett, 2008. Ecology and Epidemiology in R: Disease Progress over Time. The Plant Health Instructor. doi:10.1094/PHI-A-2008-0129-02 .

Madden, L. V., G. Hughes, and F. van den Bosch. 2007. The Study of Plant Disease Epidemics. American Phytopathological Society, St. Paul, MN. doi:10.1094/9780890545058 .

Savary, S., Nelson, A., Willocquet, L., Pangga, I., and Aunario, J. Modeling and mapping potential epidemics of rice diseases globally. Crop Protection, Volume 34, 2012, Pages 6-17, ISSN 0261-2194 doi:10.1016/j.cropro.2011.11.009 .

Author

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

Examples

# get weather for IRRI Zeigler Experiment Station in wet season 2000
wth <- get_wth(
  lonlat = c(121.25562, 14.6774),
  dates = c("2000-06-30", "2000-12-31")
)

# provide suitable values for brown spot intensity
RcA <-
  cbind(
    c(0L, 20L, 40L, 60L, 80L, 100L, 120L),
    c(0.35, 0.35, 0.35, 0.47, 0.59, 0.71, 1.0)
  )
RcT <-
  cbind(
    c(15L, 20L, 25L, 30L, 35L, 40L),
    c(0, 0.06, 1.0, 0.85, 0.16, 0)
  )
emergence <- "2000-07-15"

seir(
  wth = wth,
  emergence = emergence,
  onset = 20,
  duration = 120,
  rhlim = 90,
  rainlim = 5,
  H0 = 600,
  I0 = 1,
  RcA = RcA,
  RcT = RcT,
  RcOpt = 0.61,
  p = 6,
  i = 19,
  Sx = 100000,
  a = 1,
  RRS = 0.01,
  RRG = 0.1
)
#> Error in seir(wth = wth, emergence = emergence, onset = 20, duration = 120,     rhlim = 90, rainlim = 5, H0 = 600, I0 = 1, RcA = RcA, RcT = RcT,     RcOpt = 0.61, p = 6, i = 19, Sx = 100000, a = 1, RRS = 0.01,     RRG = 0.1): `simple_wetness` must be a Boolean
#> (`TRUE/FALSE`) value.