AUDPC.cal: Calculation of Area Under Disease / Pest Progress Curve

In plantbreeding: Analysis and visualization of data from plant breeding and genetics experiments

Description

The function calculates area under disease / pest progress curve (Jeger and Viljanen-Rollinson 2001; Madden et al. 2007). The area under the disease / pest progress curve (AUDPC) is a useful quantitative summary of disease or pest intensity over time. The trapezoidal method is the most frequently used method for estimating the AUDPC.This method discretize the time in different units(hours, days, weeks, months, or years) and then calculate the average disease or pest intensity between each pair of adjacent time points which are summed over time intervals (Madden et al. 2007).

Usage

AUDPC.cal(reading.dates, severity.data)

Arguments

reading.dates	Vector disease reading dates
severity.data	Matrix of severity data, first column is ID of the individuals

Author(s)

Umesh Rosyara

References

Jeger M.J., Viljanen-Rollinson S.L.H. (2001) The use of the area under the disease-progress curve (AUDPC) to assess quantitative disease resistance in crop cultivars, Theor Appl Genet 102:32-40

Madden L.V., Hughes, G., van den Bosch, F. (2007) The study of plant disease epidemics. The American Phytopathological Society, APS Press St. Paul, Minnesota.

Examples

# Example 
reading.dates <- as.Date(c("2012-02-13","2012-02-20","2012-02-28"))

mydat <- data.frame (ID = c("A", "B", "C", "D"), Date1 = c(1:4), Date2 = c(5:8),
 Date3 = c(11:14))

cd <- AUDPC.cal (reading.dates, mydat)
print(cd)

plantbreeding documentation built on May 2, 2019, 4:54 p.m.