## Overwrite function in radiant.basics/correlation.R
##
summary.correlation_ <- function(object,
cutoff = 0,
covar = FALSE,
dec = 2,
...) {
## using correlation_ to avoid print method conflict with nlme
## calculate the correlation matrix with p.values using the psych package
cmat <- sshhr( psych::corr.test(object$dat, method = object$method) )
cr <- apply(cmat$r, 2, formatnr, dec = dec) %>%
format(justify = "right") %>%
set_rownames(rownames(cmat$r))
cr[is.na(cmat$r)] <- "-"
cr[abs(cmat$r) < cutoff] <- ""
ltmat <- lower.tri(cr)
cr[!ltmat] <- ""
## Use format.pval instead if formatnr and get more decimals
cp <- apply(cmat$p, 2, format.pval, digits = 3,eps=0.001) %>%
format(justify = "right") %>%
set_rownames(rownames(cmat$p))
cp[is.na(cmat$p)] <- "-"
cp[abs(cmat$r) < cutoff] <- ""
cp[!ltmat] <- ""
cat("Correlation\n")
cat("Data :", object$dataset, "\n")
cat("Method :", object$method, "\n")
if (cutoff > 0)
cat("Cutoff :", cutoff, "\n")
if (object$data_filter %>% gsub("\\s","",.) != "")
cat("Filter :", gsub("\\n","", object$data_filter), "\n")
cat("Variables:", paste0(object$vars, collapse = ", "), "\n")
cat("Null hyp.: variables x and y are not correlated\n")
cat("Alt. hyp.: variables x and y are correlated\n\n")
cat("Correlation matrix:\n")
print(cr[-1,-ncol(cr), drop = FALSE], quote = FALSE)
cat("\np.values:\n")
print(cp[-1,-ncol(cp), drop = FALSE], quote = FALSE)
if (covar) {
cvmat <- sshhr( cov(object$dat, method = object$method) )
cvr <- apply(cvmat, 2, formatnr, dec = dec) %>%
format(justify = "right") %>%
set_rownames(rownames(cvmat))
cvr[abs(cmat$r) < cutoff] <- ""
ltmat <- lower.tri(cvr)
cvr[!ltmat] <- ""
cat("\nCovariance matrix:\n")
print(cvr[-1,-ncol(cvr), drop = FALSE], quote = FALSE)
}
rm(object)
}
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