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corTable <- function(data, use = "pairwise", method = "pearson", round = 2, significance = "stars", sd=FALSE, mean.sd.cols = FALSE) {
corr.test.out <- psych::corr.test(plyr::colwise(makeNumeric)(data), use = use, method = method) # calculate correlation
corr.test.out.r <- (data.frame(round(corr.test.out$r, round))) # get correlation coefs
corr.test.out.p <- (data.frame(round(corr.test.out$p, 3))) # get p-values
pasteStars <- function(x, y) paste(x, y, sep="")
pastePval <- function(x, y) paste(x, " (", y, ")", sep="")
if("stars" %in% significance && "p-values" %in% significance) {
star.table <- data.frame(ifelse(corr.test.out.p < .001, "***", ifelse(corr.test.out.p < .01, "** ", ifelse(corr.test.out.p < .05, "* ", "")))) # generate significance stars
significance.table <- data.frame(mapply(pastePval, star.table, corr.test.out.p))
cor.table <- mapply(pasteStars, corr.test.out.r, significance.table)
cor.table <- gsub("(0)", "(< 0.001)", cor.table, fixed=T)
} else if("stars" %in% significance) {
significance.table <- data.frame(ifelse(corr.test.out.p < .001, "***", ifelse(corr.test.out.p < .01, "** ", ifelse(corr.test.out.p < .05, "* ", "")))) # generate significance stars
cor.table <- mapply(pasteStars, corr.test.out.r, significance.table)
} else if("p-values" %in% significance){
cor.table <- mapply(pastePval, corr.test.out.r, corr.test.out.p)
cor.table <- gsub("(0)", "(< 0.001)", cor.table, fixed=T)
} else {
cor.table <- corr.test.out.r
}
rownames(cor.table) <- colnames(cor.table)
rownames(cor.table) <- paste(1:length(rownames(cor.table)), ". ", rownames(cor.table), sep="")
colnames(cor.table) <- paste("(", 1:length(rownames(cor.table)), ")", sep="")
cor.table[upper.tri(cor.table)] <- ""
cor.table <- as.matrix(cor.table)
diag(cor.table) <- ""
if(sd) {
sd2 <- function(x) sd(x, na.rm = TRUE)
diag(cor.table) <- paste("(", round(sapply(data, sd2), 2), ")", sep="")
} else {
diag(cor.table) <- "-"
}
if(mean.sd.cols) {
cor.table <- cbind(cor.table, M = round(colMeans(data, na.rm=TRUE), 2))
cor.table <- cbind(cor.table, SD = round(sapply(data, sd, na.rm=TRUE), 2))
order <- c("M", "SD", paste("(", 1:length(rownames(cor.table)), ")", sep=""))
cor.table <- cor.table[, order]
}
cor.table
}
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