Rice and Wheat Disease Models — disease

Helper functions with pre-loaded parameter tables for optimal performance. Custom parameter tables can be provided to override defaults.

Usage

bacterial_blight(
  wth,
  emergence,
  RcA = NULL,
  RcT = NULL,
  RRS = NULL,
  RRG = NULL,
  ...
)

brown_spot(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

leaf_blast(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

sheath_blight(
  wth,
  emergence,
  RcA = NULL,
  RcT = NULL,
  RRS = NULL,
  RRG = NULL,
  ...
)

tungro(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

modified_kim_leaf_blast(
  wth,
  emergence,
  RcA = NULL,
  RcT = NULL,
  RRS = NULL,
  RRG = NULL,
  ...
)

modified_kim_sheath_blight(
  wth,
  emergence,
  RcA = NULL,
  RcT = NULL,
  RRS = NULL,
  RRG = NULL,
  ...
)

leaf_rust(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

s_tritici_blotch(
  wth,
  emergence,
  RcA = NULL,
  RcT = NULL,
  RRS = NULL,
  RRG = NULL,
  ...
)

bb(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

bs(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

lb(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

sb(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

tg(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

mk_lb(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

mk_sb(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

lr(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

brown_rust(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = NULL, ...)

stb(wth, emergence, RcA = NULL, RcT = NULL, RRS = NULL, RRG = 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).

RcA

Optional custom age modifier table (2-column matrix).

RcT

Optional custom temperature modifier table (2-column matrix).

RRS

Optional custom senescence rate (scalar, vector, or function).

RRG

Optional custom growth rate (scalar, vector, or table).

...

Other parameters passed to seir() allowing the user to override the default values from published papers.

References

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

Kim, K. H., Cho, J., Lee, Y. H., & Lee, W. S. (2015). Predicting potential epidemics of rice leaf blast and sheath blight in South Korea. Agricultural and Forest Meteorology, 203: 191-207. doi:10.1016/j.agrformet.2015.01.011

Savary, S., Stetkiewicz, S., Brun, F., & Willocquet, L. (2015). Modelling and mapping potential epidemics of wheat diseases. European Journal of Plant Pathology, 142: 771-790. doi:10.1007/s10658-015-0650-7

Author

Adam H. Sparks, adamhsparks@gmail.com