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#' @title Summary of correlations as HTML table
#' @name tab_corr
#'
#' @description Shows the results of a computed correlation as HTML table. Requires either
#' a \code{\link{data.frame}} or a matrix with correlation coefficients
#' as returned by the \code{\link{cor}}-function.
#'
#' @param data Matrix with correlation coefficients as returned by the
#' \code{\link{cor}}-function, or a \code{data.frame} of variables where
#' correlations between columns should be computed.
#' @param na.deletion Indicates how missing values are treated. May be either
#' \code{"listwise"} (default) or \code{"pairwise"}. May be
#' abbreviated.
#' @param corr.method Indicates the correlation computation method. May be one of
#' \code{"pearson"} (default), \code{"spearman"} or \code{"kendall"}.
#' May be abbreviated.
#' @param p.numeric Logical, if \code{TRUE}, the p-values are printed
#' as numbers. If \code{FALSE} (default), asterisks are used.
#' @param fade.ns Logical, if \code{TRUE} (default), non-significant correlation-values
#' appear faded (by using a lighter grey text color). See 'Note'.
#' @param triangle Indicates whether only the upper right (use \code{"upper"}), lower left (use \code{"lower"})
#' or both (use \code{"both"}) triangles of the correlation table is filled with values. Default
#' is \code{"both"}. You can specifiy the inital letter only.
#' @param val.rm Specify a number between 0 and 1 to suppress the output of correlation values
#' that are smaller than \code{val.rm}. The absolute correlation values are used, so
#' a correlation value of \code{-.5} would be greater than \code{val.rm = .4} and thus not be
#' omitted. By default, this argument is \code{NULL}, hence all values are shown in the table.
#' If a correlation value is below the specified value of \code{val.rm}, it is still printed to
#' the HTML table, but made "invisible" with white foreground color. You can use the \code{CSS}
#' argument (\code{"css.valueremove"}) to change color and appearance of those correlation value that are smaller than
#' the limit specified by \code{val.rm}.
#' @param string.diag A vector with string values of the same length as \code{ncol(data)} (number of
#' correlated items) that can be used to display content in the diagonal cells
#' where row and column item are identical (i.e. the "self-correlation"). By defauilt,
#' this argument is \code{NULL} and the diagnal cells are empty.
#'
#' @inheritParams tab_model
#' @inheritParams tab_xtab
#' @inheritParams plot_grpfrq
#' @inheritParams plot_gpt
#'
#' @return Invisibly returns
#' \itemize{
#' \item the web page style sheet (\code{page.style}),
#' \item the web page content (\code{page.content}),
#' \item the complete html-output (\code{page.complete}) and
#' \item the html-table with inline-css for use with knitr (\code{knitr})
#' }
#' for further use.
#'
#' @note If \code{data} is a matrix with correlation coefficients as returned by
#' the \code{\link{cor}}-function, p-values can't be computed.
#' Thus, \code{show.p}, \code{p.numeric} and \code{fade.ns}
#' only have an effect if \code{data} is a \code{\link{data.frame}}.
#'
#' @examples
#' \dontrun{
#' if (interactive()) {
#' # Data from the EUROFAMCARE sample dataset
#' library(sjmisc)
#' data(efc)
#'
#' # retrieve variable and value labels
#' varlabs <- get_label(efc)
#'
#' # recveive first item of COPE-index scale
#' start <- which(colnames(efc) == "c83cop2")
#' # recveive last item of COPE-index scale
#' end <- which(colnames(efc) == "c88cop7")
#'
#' # create data frame with COPE-index scale
#' mydf <- data.frame(efc[, c(start:end)])
#' colnames(mydf) <- varlabs[c(start:end)]
#'
#' # we have high correlations here, because all items
#' # belong to one factor.
#' tab_corr(mydf, p.numeric = TRUE)
#'
#' # auto-detection of labels, only lower triangle
#' tab_corr(efc[, c(start:end)], triangle = "lower")
#'
#' # auto-detection of labels, only lower triangle, all correlation
#' # values smaller than 0.3 are not shown in the table
#' tab_corr(efc[, c(start:end)], triangle = "lower", val.rm = 0.3)
#'
#' # auto-detection of labels, only lower triangle, all correlation
#' # values smaller than 0.3 are printed in blue
#' tab_corr(efc[, c(start:end)], triangle = "lower",val.rm = 0.3,
#' CSS = list(css.valueremove = 'color:blue;'))
#' }}
#' @importFrom stats na.omit cor cor.test
#' @export
tab_corr <- function(data,
na.deletion = c("listwise", "pairwise"),
corr.method = c("pearson", "spearman", "kendall"),
title = NULL,
var.labels = NULL,
wrap.labels = 40,
show.p = TRUE,
p.numeric = FALSE,
fade.ns = TRUE,
val.rm = NULL,
digits = 3,
triangle = "both",
string.diag = NULL,
CSS = NULL,
encoding = NULL,
file = NULL,
use.viewer = TRUE,
remove.spaces = TRUE) {
# --------------------------------------------------------
# check p-value-style option
# --------------------------------------------------------
opt <- getOption("p_zero")
if (is.null(opt) || opt == FALSE) {
p_zero <- ""
} else {
p_zero <- "0"
}
# --------------------------------------------------------
# check args
# --------------------------------------------------------
na.deletion <- match.arg(na.deletion)
corr.method <- match.arg(corr.method)
# --------------------------------------------------------
# check encoding
# --------------------------------------------------------
encoding <- get.encoding(encoding, data)
# --------------------------------------------------------
# argument check
# --------------------------------------------------------
if (is.null(triangle)) {
triangle <- "both"
} else if (triangle == "u" || triangle == "upper") {
triangle <- "upper"
} else if (triangle == "l" || triangle == "lower") {
triangle <- "lower"
} else triangle <- "both"
# --------------------------------------------------------
# try to automatically set labels is not passed as argument
# --------------------------------------------------------
if (is.null(var.labels) && is.data.frame(data)) {
var.labels <- sjlabelled::get_label(data, def.value = colnames(data))
}
# ----------------------------
# check for valid argument
# ----------------------------
if (corr.method != "pearson" && corr.method != "spearman" && corr.method != "kendall") {
stop("argument 'corr.method' must be one of: pearson, spearman or kendall")
}
# ----------------------------
# check if user has passed a data frame
# or a pca object
# ----------------------------
if (is.matrix(data)) {
corr <- data
cpvalues <- NULL
} else {
# missing deletion corresponds to
# SPSS listwise
if (na.deletion == "listwise") {
data <- stats::na.omit(data)
corr <- stats::cor(data, method = corr.method)
} else {
# missing deletion corresponds to
# SPSS pairwise
corr <- stats::cor(data,
method = corr.method,
use = "pairwise.complete.obs")
}
#---------------------------------------
# if we have a data frame as argument,
# compute p-values of significances
#---------------------------------------
computePValues <- function(df) {
cp <- c()
for (i in 1:ncol(df)) {
pv <- c()
for (j in 1:ncol(df)) {
test <- suppressWarnings(
stats::cor.test(
df[[i]],
df[[j]],
alternative = "two.sided",
method = corr.method
)
)
pv <- cbind(pv, round(test$p.value, 5))
}
cp <- rbind(cp, pv)
}
return(cp)
}
cpvalues <- computePValues(data)
}
# --------------------------------------------------------
# save original p-values
# --------------------------------------------------------
cpv <- cpvalues
# --------------------------------------------------------
# add column with significance value
# --------------------------------------------------------
if (!is.null(cpvalues)) {
if (!p.numeric) {
# --------------------------------------------------------
# prepare function for apply-function. replace sig. p
# with asterisks
# --------------------------------------------------------
fun.star <- function(x) {
x <- get_p_stars(x)
}
} else {
# --------------------------------------------------------
# prepare function for apply-function.
# round p-values, keeping the numeric values
# --------------------------------------------------------
fun.star <- function(x) {
round(x, digits)
}
}
cpvalues <- apply(cpvalues, c(1,2), fun.star)
if (p.numeric) {
cpvalues <-
apply(
cpvalues,
c(1,2),
function(x) {
if (x < 0.001)
x <- sprintf("<%s.001", p_zero)
else
x <- sub("0", p_zero, sprintf("%.*f", digits, x))
}
)
}
} else {
show.p <- FALSE
}
# ----------------------------
# check if user defined labels have been supplied
# if not, use variable names from data frame
# ----------------------------
if (is.null(var.labels)) {
var.labels <- row.names(corr)
}
# check length of x-axis-labels and split longer strings at into new lines
var.labels <- sjmisc::word_wrap(var.labels, wrap.labels, "<br>")
# -------------------------------------
# init header
# -------------------------------------
toWrite <- table.header <- sprintf("<html>\n<head>\n<meta http-equiv=\"Content-type\" content=\"text/html;charset=%s\">\n", encoding)
# -------------------------------------
# init style sheet and tags used for css-definitions
# we can use these variables for string-replacement
# later for return value
# -------------------------------------
tag.table <- "table"
tag.caption <- "caption"
tag.thead <- "thead"
tag.tdata <- "tdata"
tag.notsig <- "notsig"
tag.pval <- "pval"
tag.valueremove <- "valueremove"
tag.summary <- "summary"
tag.centeralign <- "centeralign"
tag.firsttablecol <- "firsttablecol"
css.table <- "border-collapse:collapse; border:none;"
css.thead <- "font-style:italic; font-weight:normal; border-top:double black; border-bottom:1px solid black; padding:0.2cm;"
css.tdata <- "padding:0.2cm;"
css.caption <- "font-weight: bold; text-align:left;"
css.valueremove <- "color:white;"
css.centeralign <- "text-align:center;"
css.firsttablecol <- "font-style:italic;"
css.notsig <- "color:#999999;"
css.summary <- "border-bottom:double black; border-top:1px solid black; font-style:italic; font-size:0.9em; text-align:right;"
css.pval <- "vertical-align:super;font-size:0.8em;"
if (p.numeric) css.pval <- "font-style:italic;"
# ------------------------
# check user defined style sheets
# ------------------------
if (!is.null(CSS)) {
if (!is.null(CSS[['css.table']])) css.table <- ifelse(substring(CSS[['css.table']], 1, 1) == '+', paste0(css.table, substring(CSS[['css.table']], 2)), CSS[['css.table']])
if (!is.null(CSS[['css.thead']])) css.thead <- ifelse(substring(CSS[['css.thead']], 1, 1) == '+', paste0(css.thead, substring(CSS[['css.thead']], 2)), CSS[['css.thead']])
if (!is.null(CSS[['css.tdata']])) css.tdata <- ifelse(substring(CSS[['css.tdata']], 1, 1) == '+', paste0(css.tdata, substring(CSS[['css.tdata']], 2)), CSS[['css.tdata']])
if (!is.null(CSS[['css.caption']])) css.caption <- ifelse(substring(CSS[['css.caption']], 1, 1) == '+', paste0(css.caption, substring(CSS[['css.caption']], 2)), CSS[['css.caption']])
if (!is.null(CSS[['css.summary']])) css.summary <- ifelse(substring(CSS[['css.summary']], 1, 1) == '+', paste0(css.summary, substring(CSS[['css.summary']], 2)), CSS[['css.summary']])
if (!is.null(CSS[['css.centeralign']])) css.centeralign <- ifelse(substring(CSS[['css.centeralign']], 1, 1) == '+', paste0(css.centeralign, substring(CSS[['css.centeralign']], 2)), CSS[['css.centeralign']])
if (!is.null(CSS[['css.firsttablecol']])) css.firsttablecol <- ifelse(substring(CSS[['css.firsttablecol']], 1, 1) == '+', paste0(css.firsttablecol, substring(CSS[['css.firsttablecol']], 2)), CSS[['css.firsttablecol']])
if (!is.null(CSS[['css.notsig']])) css.notsig <- ifelse(substring(CSS[['css.notsig']], 1, 1) == '+', paste0(css.notsig, substring(CSS[['css.notsig']], 2)), CSS[['css.notsig']])
if (!is.null(CSS[['css.pval']])) css.pval <- ifelse(substring(CSS[['css.pval']], 1, 1) == '+', paste0(css.pval, substring(CSS[['css.pval']], 2)), CSS[['css.pval']])
if (!is.null(CSS[['css.valueremove']])) css.valueremove <- ifelse(substring(CSS[['css.valueremove']], 1, 1) == '+', paste0(css.valueremove, substring(CSS[['css.valueremove']], 2)), CSS[['css.valueremove']])
}
# ------------------------
# set page style
# ------------------------
page.style <- sprintf("<style>\nhtml, body { background-color: white; }\n%s { %s }\n%s { %s }\n.%s { %s }\n.%s { %s }\n.%s { %s }\n.%s { %s }\n.%s { %s }\n.%s { %s }\n.%s { %s }\n.%s { %s }\n</style>",
tag.table, css.table, tag.caption, css.caption,
tag.thead, css.thead, tag.tdata, css.tdata,
tag.firsttablecol, css.firsttablecol,
tag.centeralign, css.centeralign,
tag.notsig, css.notsig,
tag.pval, css.pval,
tag.summary, css.summary,
tag.valueremove, css.valueremove)
# ------------------------
# start content
# ------------------------
toWrite <- paste0(toWrite, page.style)
toWrite = paste(toWrite, "\n</head>\n<body>", "\n")
# -------------------------------------
# start table tag
# -------------------------------------
page.content <- "<table>\n"
# -------------------------------------
# table caption, variable label
# -------------------------------------
if (!is.null(title)) page.content <- paste0(page.content, sprintf(" <caption>%s</caption>\n", title))
# -------------------------------------
# header row
# -------------------------------------
# write tr-tag
page.content <- paste0(page.content, " <tr>\n")
# first column
page.content <- paste0(page.content, " <th class=\"thead\"> </th>\n")
# iterate columns
for (i in 1:ncol(corr)) {
page.content <- paste0(page.content, sprintf(" <th class=\"thead\">%s</th>\n", var.labels[i]))
}
# close table row
page.content <- paste0(page.content, " </tr>\n")
# -------------------------------------
# data rows
# -------------------------------------
# iterate all rows of df
for (i in 1:nrow(corr)) {
# write tr-tag
page.content <- paste0(page.content, " <tr>\n")
# print first table cell
page.content <- paste0(page.content, sprintf(" <td class=\"firsttablecol\">%s</td>\n", var.labels[i]))
# --------------------------------------------------------
# iterate all columns
# --------------------------------------------------------
for (j in 1:ncol(corr)) {
# --------------------------------------------------------
# leave out self-correlations
# --------------------------------------------------------
if (j == i) {
if (is.null(string.diag) || length(string.diag) > ncol(corr)) {
page.content <- paste0(page.content, " <td class=\"tdata centeralign\"> </td>\n")
} else {
page.content <- paste0(page.content, sprintf(" <td class=\"tdata centeralign\">%s</td>\n",
string.diag[j]))
}
} else {
# --------------------------------------------------------
# check whether only lower or upper triangle of correlation
# table should be printed
# --------------------------------------------------------
if ((triangle == "upper" && j > i) || (triangle == "lower" && i > j) || triangle == "both") {
# --------------------------------------------------------
# print table-cell-data (cor-value)
# --------------------------------------------------------
cellval <- sprintf("%.*f", digits, corr[i, j])
# --------------------------------------------------------
# check whether we want to show P-Values
# --------------------------------------------------------
if (show.p) {
if (p.numeric) {
# --------------------------------------------------------
# if we have p-values as number, print them in new row
# --------------------------------------------------------
cellval <- sprintf("%s<br><span class=\"pval\">(%s)</span>", cellval, cpvalues[i, j])
} else {
# --------------------------------------------------------
# if we have p-values as "*", add them
# --------------------------------------------------------
cellval <- sprintf("%s<span class=\"pval\">%s</span>", cellval, cpvalues[i, j])
}
}
# --------------------------------------------------------
# prepare css for not significant values
# --------------------------------------------------------
notsig <- ""
# --------------------------------------------------------
# check whether non significant values should be blurred
# --------------------------------------------------------
if (fade.ns && !is.null(cpv)) {
# set css-class-attribute
if (cpv[i, j] >= 0.05) notsig <- " notsig"
}
# --------------------------------------------------------
# prepare css for values that shoould be removed due to low
# correlation value
# --------------------------------------------------------
value.remove <- ""
# --------------------------------------------------------
# check whether correlation value is too small and should
# be omitted
# --------------------------------------------------------
if (!is.null(val.rm) && abs(corr[i, j]) < abs(val.rm)) {
value.remove <- " valueremove"
}
page.content <- paste0(page.content, sprintf(" <td class=\"tdata centeralign%s%s\">%s</td>\n",
notsig,
value.remove,
cellval))
} else {
page.content <- paste0(page.content, " <td class=\"tdata centeralign\"> </td>\n")
}
}
}
# close row
page.content <- paste0(page.content, " </tr>\n")
}
# -------------------------------------
# feedback...
# -------------------------------------
page.content <- paste0(page.content, " <tr>\n")
page.content <- paste0(page.content, sprintf(" <td colspan=\"%i\" class=\"summary\">", ncol(corr) + 1))
page.content <- paste0(page.content, sprintf("Computed correlation used %s-method with %s-deletion.", corr.method, na.deletion))
page.content <- paste0(page.content, "</td>\n </tr>\n")
# -------------------------------------
# finish table
# -------------------------------------
page.content <- paste(page.content, "\n</table>")
# -------------------------------------
# finish html page
# -------------------------------------
toWrite <- paste(toWrite, page.content, "\n")
toWrite <- paste0(toWrite, "</body></html>")
# -------------------------------------
# replace class attributes with inline style,
# useful for knitr
# -------------------------------------
# copy page content
# -------------------------------------
knitr <- page.content
# -------------------------------------
# set style attributes for main table tags
# -------------------------------------
knitr <- gsub("class=", "style=", knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub("<table", sprintf("<table style=\"%s\"", css.table), knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub("<caption", sprintf("<caption style=\"%s\"", css.caption), knitr, fixed = TRUE, useBytes = TRUE)
# -------------------------------------
# replace class-attributes with inline-style-definitions
# -------------------------------------
knitr <- gsub(tag.tdata, css.tdata, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.thead, css.thead, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.centeralign, css.centeralign, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.notsig, css.notsig, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.pval, css.pval, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.summary, css.summary, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.firsttablecol, css.firsttablecol, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.valueremove, css.valueremove, knitr, fixed = TRUE, useBytes = TRUE)
# -------------------------------------
# remove spaces?
# -------------------------------------
if (remove.spaces) {
knitr <- sju.rmspc(knitr)
toWrite <- sju.rmspc(toWrite)
page.content <- sju.rmspc(page.content)
}
# -------------------------------------
# return results
# -------------------------------------
structure(
class = c("sjTable", "sjtcorr"),
list(
page.style = page.style,
page.content = page.content,
page.complete = toWrite,
header = table.header,
knitr = knitr,
file = file,
viewer = use.viewer
)
)
}
|
