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Predict Rice Leaf Blast Intensity Using Modified Kim Model

modified_kim_leaf_blast.Rd

A helper function to provide values used by Kim _et al. 2015 for a dynamic mechanistic simulation of leaf blast disease of rice, causal agent Magnaporthe oryzae. The model is driven by daily weather data, which can easily be accessed using get_wth to download weather data from NASA POWER.

Usage

modified_kim_leaf_blast(wth, emergence, ...)

mk_lb(wth, emergence, ...)

Source

Kim, Kwang-hyung (2015). Modified EPIRICE Ref.. figshare. Dataset. doi:doi.org/10.6084/m9.figshare.1515884.v1

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 NameValue
YYYYMMDDDate as Year Month Day (ISO8601)
DOYConsecutive day of year, commonly called "Julian date"
TEMPMean daily temperature (°C)
RHUMMean daily relative humidity (%)
RAINMean daily rainfall (mm)
TMINOptional Minimum daily temperature (°C), see TMIN/TMAX Details
TMAXOptional Maximum daily temperature (°C), see TMIN/TMAX Details
LATOptional latitude of weather observation, see LAT/LON Details
LONOptional 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 44 mm2 of a rice plant's leaf.

Note

The original code for this function from Kim _et al. 2015 had an incorrect matrix for the RcW modifier. The original code had the following values:

  • Hours: c(0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L)

  • Modifier: c(0, 0.24, 0.41, 0.68, 0.94, 0.97, 1, 1, 1, 1 ,1) These have been corrected to:

  • Hours: c(4L, 6L, 8L, 10L, 12L, 14L, 16L, 18L, 20L, 22L, 24L)

  • Modifier: c(0, 0.24, 0.41, 0.68, 0.94, 0.97, 1, 1, 1, 1, 1) providing modifiers for hours 4-24, inclusive rather than stopping at 10 hours.

Function Provenance and Modifications

This function is adapted from Kim et al. by Adam H. Sparks, Curtin University, with assistance from Kwang-Hyung Kim, APEC Climate Center, 12 Centum7-ro, Haeundae-gu, Busan 612-020, South Korea. Original model development: Serge Savary & Rene Pangga (IRRI). Original R implementation by Robert J. Hijmans, Rene Pangga, & Jorrel Aunario (IRRI). While the paper by Kim et al. 2015 indicates that the leaf wetness duration changed with time rather than being 0 or 1 as in Savary et al. 2012, the original code available does not implement this. epicrop offers the option to do this by setting simple_wetness = FALSE, but the results may differ from the published values if this is used.

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 leaf blast as presented in Table 2 of Savary et al. 2012 has a typo. The optimal value should be 20 °C, not 25 °C as shown. The correct value, 20 °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

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 under the RCP 4.5 and RCP 8.5 climate change scenarios using a rice disease epidemiology model, EPIRICE. Agricultural and forest meteorology, 203, 191-207. doi:10.1016/j.agrformet.2015.01.011

El Refaei, M.I., 1977. Epidemiology of rice blast disease in the tropics with special reference to the leaf wetness in relation to disease development. PhD Thesis, Indian Agricultural Research Institute, New Delhi, India. 195 p.

Hemmi, T., Abe, T., Ikaya, J., and Inoue, Y. 1936. Studies on the rice blast disease. IV. Relation of the environment to the development of blast disease and physiologic specialization in the rice blast fungus. Materials for Rural Improvement, Department of Agriculture and Forestry, Japan No. 105, 145p.

Hwang, B.K., Koh, Y.J., Chung, H.S., 1987. Effects of adult-plant resistance on blast severity and yield of rice. Plant Disease 71:1035-1038. DOI: doi:10.1094/PD-71-1035 .

Kato, H. and Kozaka, T., 1974. Effect of temperature on lesion enlargement and sporulation of Pyricularia oryzae in rice leaves. Phytopathology 64:828-830. DOI: doi:10.1094/Phyto-64-828 .

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

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: doi:10.1016/j.cropro.2011.11.009 .

Torres, C.Q., 1986. Effect of plant age on the expression of resistance to Pyricularia oryzae Cav. in upland rice varieties. PhD Thesis, University of the Philippines at Los Baños, 82 p.

See also

seir

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

Author

Kwang-Hyung Kim, Serge Savary, Ireneo Pangga, Robert Hijmans, Jorrel Khalil Aunario, and Adam H. Sparks

Examples


# get weather for IRRI Zeigler Experiment Station in wet season 2000
wth <- get_wth(
  lonlat = c(121.25562, 14.6774),
  dates = c("2000-05-01", "2000-09-01")
)
#> No encoding supplied: defaulting to UTF-8.
#> No encoding supplied: defaulting to UTF-8.

# use 25 May as transplanting date (`emergence`) as in Kim et al. 2015
lb_sim <- modified_kim_leaf_blast(wth, emergence = "2000-05-25")
plot(x = lb_sim$dates, y = lb_sim$intensity, type = "l")

# use shorthand function
mk_lb <- mk_lb(wth, emergence = "2000-07-01")
#> Error in seir(wth = wth, emergence = emergence, onset = 15L, duration = 100L,     rhlim = 90L, rainlim = 5L, H0 = 600L, I0 = 1L, RcA = cbind(c(0L,         5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L,         60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L), c(1, 1,         1, 1, 1, 1, 1, 1, 1, 0.4, 0.3, 0.1, 0.1, 0.05, 0.03,         0.03, 0.02, 0.02, 0.02, 0.01, 0.01)), RcT = cbind(c(9L,         12L, 15L, 18L, 21L, 24L, 27L, 30L, 33L, 36L, 39L), c(0,         0.4, 0.72, 0.88, 1, 0.9, 0.45, 0.2, 0.05, 0.01, 0)),     RcOpt = 0.86, p = 4L, i = 20L, a = 1L, Sx = 90000L, RRS = 0.005,     RRG = cbind(c(0L, 10L, 20L, 30L, 40L, 50L, 60L, 70L, 80L,         90L, 100L), c(0.12, 0.12, 0.11, 0.11, 0.09, 0.09, 0.09,         0.09, 0.09, 0.09, 0.05)), RcW = cbind(c(4L, 6L, 8L, 10L,         12L, 14L, 16L, 18L, 20L, 22L, 24L), c(0, 0.24, 0.41,         0.68, 0.94, 0.97, 1, 1, 1, 1, 1)), simple_wetness = TRUE): Incomplete weather data or dates do not align.
plot(x = mk_lb$dates, y = mk_lb$intensity, type = "l")
#> Error in mk_lb$dates: object of type 'closure' is not subsettable