Predict Rice Brown Spot Intensity

A helper function to provide sensible defaults for a dynamic mechanistic simulation of rice brown spot, causal agent Cochliobolus miyabeanus. The model is driven by daily weather data, which can easily be accessed using get_wth to download weather data from NASA POWER.

Usage

brown_spot(wth, emergence, ...)

bs(wth, emergence, ...)

Arguments

wth

Weather data with a daily time-step, normally NASA POWER data from get_wth, but any base::data.frame object that has been formatted using format_wth will have the following properly named columns and will work.

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 crop emergence

...

Additional arguments passed to seir.

Value

A data.table::data.table of disease intensity and infection sites. See seir for a full description of the column values.

Details

The model represents site size as 10 mm² of a rice plant's leaf.

Default values for this disease model are derived from Table 2 (Savary et al. 2012).

bs is a shorthand alias for brown_spot.

Note

Adapted from cropsim package version 0.2.0-5 by Adam H. Sparks, Department of Primary Industries and Regional Development, WA, AU. Original model development: Serge Savary & Rene Pangga (IRRI). Original R implementation by Robert J. Hijmans, Rene Pangga, & Jorrel Aunario (IRRI).

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.

The optimum temperature for brown spot as presented in Table 2 of Savary et al. 2012 has a typo. The optimal value should be 25 °C, not 20 °C as shown. The correct value, 25 °C, is used in this implementation.

TMIN/TMAX Details

If simple_wetness is set to FALSE, the function will use the TMIN and TMAXcolumns in thewthobject to calculate the leaf wetness value for 24 hours of the day using therhlimandrainlimvalues and then usesRcWto calculate a value between 0 and 1 for the whole day. Whensimple_wetnessis set toTRUE, the function only sets the leaf wetness to 0 or 1 for the day based on the rhlimandrainlim` 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

Klomp, A.O., 1977. Early senescence of rice and Drechslera oryzae in the Wageningen polder, Surinam. PhD Thesis, 97p.

Levy, Y. and Cohen, Y., 1980. Sporulation of Helminthosporium turcicum on sweet corn: Effects of temperature and dew period. Canadian Journal of Plant Pathology 2:65-69. doi:10.1080/07060668009501440 .

Luo Wei-Hong, 1996. Simulation and measurement of leaf wetness formation in paddy rice crops. PhD, Wageningen Agricultural University, 87 p.

Padmanabhan, S.Y. and Ganguly, D. 1954. Relation between the age of rice plant and its susceptibility to Helminthosporium and blast disease. Proceedings of the Indian Academy of Sciences B 29:44-50.

Sarkar, A.K. and Sen Gupta, P.K., 1977. Effect of temperature and humidity on disease development and sporulation of Helminthosporium oryzae on rice. Indian Phytopathology 30:258-259.

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 .

Waggoner. P.E., Horsfall, J.G., and Lukens, R.J. 1972. EPIMAY. A Simulator of Southern Corn Leaf Blight. Bulletin of the Connecticut Experiment Station, New Haven, 85p.

See also

seir

Other helper functions: bacterial_blight(), leaf_blast(), modified_kim_leaf_blast(), modified_kim_sheath_blight(), sheath_blight(), tungro()

Author

Serge Savary, Ireneo Pangga, Robert Hijmans, Jorrel Khalil 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")
)
#> No encoding supplied: defaulting to UTF-8.
#> No encoding supplied: defaulting to UTF-8.
bs_sim <- brown_spot(wth, emergence = "2000-07-01")
plot(x = bs_sim$dates, y = bs_sim$intensity, type = "l")

# use shorthand function
bs <- bs(wth, emergence = "2000-07-01")
plot(x = bs$dates, y = bs$intensity, type = "l")