R/multcompmatrix.R

In smatr: (Standardised) Major Axis Estimation and Testing Routines

multcompmatrix <- function(smfit, sort=TRUE){
	
	if(smfit$multcompdone == "none")stop("Call sma() with multcomp=TRUE to use this function")
	
	ngr <- length(smfit$groups)
	x <- smfit$multcompresult
	m <- matrix(nrow=ngr, ncol=ngr)
	cn <- combn(1:ngr,2)

	for(i in 1:ncol(cn)){
		m[cn[1,i],cn[2,i]] <- x$Pval[i]
		m[cn[2,i],cn[1,i]] <- x$Pval[i]
	}

	m2 <- matrix(rep("",ngr^2), nrow=ngr)
	diag(m2) <- "-"
	m2[m < 0.1] <- ".  "
	m2[m < 0.05] <- "*  "
	m2[m < 0.01] <- "** "
	m2[m < 0.001] <- "***"
	l <- list(x=smfit$groups, y=smfit$groups)
	names(l) <- names(x)[1:2]
	dimnames(m2) <- l

	if(sort){
		neworder <- c(0, order(tapply(x[,6], x[,1], mean))) + 1
		m2 <- m2[neworder,neworder]
	}
	
	cat("Multiple comparison matrix.\n")
	cat("Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1\n\n")
	print.table(m2, justify="left")
return(invisible(m2))
}