agricolae (version 1.2-8)

audps: The Area Under the Disease Progress Stairs

Description

A better estimate of disease progress is the area under the disease progress stairs (AUDPS). The AUDPS approach improves the estimation of disease progress by giving a weight closer to optimal to the first and last observations.

Usage

audps(evaluation, dates, type = "absolute")

Arguments

evaluation

Table of data of the evaluations: Data frame

dates

Vector of dates corresponding to each evaluation

type

relative, absolute

Value

Vector with relative or absolute audps.

Details

AUDPS. For the illustration one considers three evaluations (14, 21 and 28 days) and percentage of damage in the plant 40, 80 and 90 (interval between dates of evaluation 7 days). AUDPS = 1470. The evaluations can be at different interval. AUDPS= sum( rectangle area by interval in times evaluation ) see example.

References

Ivan Simko, and Hans-Peter Piepho, (2012). The area under the disease progress stairs: Calculation, advantage, and application. Phytopathology 102:381- 389.

Examples

# NOT RUN {
library(agricolae)
dates<-c(14,21,28) # days
# example 1: evaluation - vector
evaluation<-c(40,80,90)
audps(evaluation,dates)
audps(evaluation,dates,"relative")
x<-seq(10.5,31.5,7)
y<-c(40,80,90,90)
plot(x,y,"s",ylim=c(0,100),xlim=c(10,32),axes=FALSE,col="red" ,ylab="",xlab="")
title(cex.main=0.8,main="Absolute or Relative AUDPS\nTotal area=(31.5-10.5)*100=2100",
ylab="evaluation",xlab="dates" )
points(x,y,type="h")
z<-c(14,21,28)
points(z,y[-3],col="blue",lty=2,pch=19)
points(z,y[-3],col="blue",lty=2,pch=19)
axis(1,x,pos=0)
axis(2,c(0,40,80,90,100),las=2)
text(dates,evaluation+5,dates,col="blue")
text(14,20,"A = (17.5-10.5)*40",cex=0.8)
text(21,40,"B = (24.5-17.5)*80",cex=0.8)
text(28,60,"C = (31.5-24.5)*90",cex=0.8)
text(14,95,"audps = A+B+C = 1470")
text(14,90,"relative = audps/area = 0.7")
# It calculates audpc absolute
absolute<-audps(evaluation,dates,type="absolute")
print(absolute)
rm(evaluation, dates, absolute)
# }