R/paircomp.jt.R

In onewaytests: One-Way Tests in Independent Groups Designs

paircomp.jt<- function(x, adjust.method = c("bonferroni", "none"), verbose = TRUE, ...){
    
    if(x$statistic<x$criticalValue) stop(paste("Pairwise comparisons could not be performed since difference is not statistically significant (alpha = ",x$alpha,").",sep = ""))
    
    data<-x$data
    
    dp=as.character(x$formula)
    
    y=data[[dp[[2L]]]]
    group=as.factor(data[[dp[[3L]]]])
    
    
    if (is.character(group)) group <- as.factor(group)
    
    if (length(levels(group))==2) stop("The group variable must have more than two levels to make pairwise comparison.")
    
    
    
    alpha <- x$alpha
    id <- levels(group)
    comb <- t(combn((id), 2))
    comb2 <- dim(comb)[1]
    
    adjust.method <- match.arg(adjust.method)
    if (adjust.method == "bonferroni"){ 
        alpha_adj=alpha/comb2
        method.name = paste("Bonferroni Correction (alpha = ",alpha_adj,")",sep = "")
    }
    if (adjust.method == "none"){ 
        alpha_adj=alpha
        method.name = paste("No Correction (alpha = ",alpha_adj,")",sep = "")
    }
    
    
    statistics <- NULL
    cvs <- NULL
    for (i in 1:comb2){
        data_sub <- data[(group == comb[i,1])|(group == comb[i,2]),]
        data_sub[[dp[[3L]]]] <- factor(data_sub[[dp[[3L]]]])
        if (x$method == "James Second Order Test") {
            statistics <- c(statistics , james.test(x$formula,data_sub,alpha=alpha_adj,verbose=F)$statistic)
            cvs <- c(cvs , james.test(x$formula,data_sub, alpha=alpha_adj,verbose=F)$criticalValue)
            
        }
    }
    
    
    store = data.frame(matrix(NA, nrow = comb2, ncol = 5))
    
    store$X1 = comb[,1]
    store$X2 = comb[,2]
    store$X3 = statistics 
    store$X4 = cvs 
    store$X5 = ifelse(store$X3 < store$X4 , "Not reject", "Reject")
    colnames(store) = c("Level (a)", "Level (b)", "statistic","criticalValue", "  No difference")
    
    if (verbose) {
        cat("\n", "",method.name, "\n", sep = " ")
        cat("----------------------------------------------------------------", "\n", sep = " ")
        print(store)
        cat("----------------------------------------------------------------", "\n\n", sep = " ")
    }
    
    invisible(store)
    
}