R: The Area Under the Disease Progress Stairs

audps {agricolae} | R Documentation

## 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

### 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.

### Value

`evaluation` | data frame, matrix or numeric vector
`dates` | a numeric vector
`type` | text

### Author(s)

Felipe de Mendiburu

### References

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

### Examples

    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)

[Package agricolae version 1.2-6 Index]