CompMuCens: Survival analysis for quantitative ordinal scale data

In r4pde: Tools for Quantitative Plant Disease Epidemiology

Survival analysis for quantitative ordinal scale data

Description

Survival analysis for quantitative ordinal scale data

Usage

CompMuCens(dat, scale, grade = TRUE, ckData = FALSE)

Arguments

dat	Data frame containing the data to be processed.
scale	A numeric vector indicating the scale or order of classes.
grade	Logical. If TRUE, uses the class value. If FALSE, uses the NPE (Non-Parametric Estimate).
ckData	Logical. If TRUE, returns the input data along with the results. If FALSE, returns only the results.

Details

This function supports analysis of quantitative ordinal scale data via interval-censored methods. The approach follows the workflow described by Chiang et al. (2023) and the reference implementation provided in the CompMuCens repository.

Value

A list containing the score statistic, hypothesis tests, adjusted significance level, and conclusion based on pairwise comparisons.

References

Chiang, K.S., Chang, Y.M., Liu, H.I., Lee, J.Y., El Jarroudi, M. and Bock, C. (2023). Survival Analysis as a Basis to Test Hypotheses When Using Quantitative Ordinal Scale Disease Severity Data. Phytopathology. https://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-02-23-0055-R

See Also

Other Disease quantification: DSI(), DSI2()

Examples

if (requireNamespace("interval", quietly = TRUE)) {
  trAs <- c(5,4,2,5,5,4,4,2,5,2,2,3,4,3,2,2,6,2,2,4,2,4,2,4,5,3,4,2,2,3)
  trBs <- c(5,3,2,4,4,5,4,5,4,4,6,4,5,5,5,2,6,2,3,5,2,6,4,3,2,5,3,5,4,5)
  trCs <- c(2,3,1,4,1,1,4,1,1,3,2,1,4,1,1,2,5,2,1,3,1,4,2,2,2,4,2,3,2,2)
  trDs <- c(5,5,4,5,5,6,6,4,6,4,3,5,5,6,4,6,5,6,5,4,5,5,5,3,5,6,5,5,5,6)
  inputData <- data.frame(
    treatment = c(rep("A",30), rep("B",30), rep("C",30), rep("D",30)),
    x = c(trAs, trBs, trCs, trDs)
  )
  CompMuCens(dat = inputData,
             scale = c(0,3,6,12,25,50,75,88,94,97,100,100),
             ckData = TRUE)
}

r4pde documentation built on Sept. 8, 2026, 1:10 a.m.