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#' @title Summary of stacked frequencies as HTML table
#' @name tab_stackfrq
#'
#' @description Shows the results of stacked frequencies (such as likert scales) as HTML table.
#' This function is useful when several items with identical scale/categories
#' should be printed as table to compare their distributions (e.g.
#' when plotting scales like SF, Barthel-Index, Quality-of-Life-scales etc.).
#'
#' @param sort.frq logical, indicates whether the \code{items} should be ordered by
#' by highest count of first or last category of \code{items}.
#' \itemize{
#' \item Use \code{"first.asc"} to order ascending by lowest count of first category,
#' \item \code{"first.desc"} to order descending by lowest count of first category,
#' \item \code{"last.asc"} to order ascending by lowest count of last category,
#' \item \code{"last.desc"} to order descending by lowest count of last category,
#' \item or \code{NULL} (default) for no sorting.
#' }
#' @param show.total logical, if \code{TRUE}, an additional column with each
#' item's total N is printed.
#' @param string.total label for the total N column.
#' @param string.na label for the missing column/row.
#' @param show.skew logical, if \code{TRUE}, an additional column with each item's skewness is printed.
#' The skewness is retrieved from the \code{\link[psych]{describe}}-function
#' of the \pkg{psych}-package.
#' @param digits.stats amount of digits for rounding the skewness and kurtosis valuess.
#' Default is 2, i.e. skewness and kurtosis values have 2 digits after decimal point.
#'
#' @inheritParams tab_df
#' @inheritParams tab_itemscale
#' @inheritParams tab_xtab
#' @inheritParams plot_grpfrq
#' @inheritParams plot_stackfrq
#'
#' @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.
#'
#' @examples
#' # -------------------------------
#' # random sample
#' # -------------------------------
#' # prepare data for 4-category likert scale, 5 items
#' likert_4 <- data.frame(
#' as.factor(sample(1:4, 500, replace = TRUE, prob = c(0.2, 0.3, 0.1, 0.4))),
#' as.factor(sample(1:4, 500, replace = TRUE, prob = c(0.5, 0.25, 0.15, 0.1))),
#' as.factor(sample(1:4, 500, replace = TRUE, prob = c(0.25, 0.1, 0.4, 0.25))),
#' as.factor(sample(1:4, 500, replace = TRUE, prob = c(0.1, 0.4, 0.4, 0.1))),
#' as.factor(sample(1:4, 500, replace = TRUE, prob = c(0.35, 0.25, 0.15, 0.25)))
#' )
#'
#' # create labels
#' levels_4 <- c("Independent", "Slightly dependent",
#' "Dependent", "Severely dependent")
#'
#' # create item labels
#' items <- c("Q1", "Q2", "Q3", "Q4", "Q5")
#'
#' # plot stacked frequencies of 5 (ordered) item-scales
#' \dontrun{
#' if (interactive()) {
#' tab_stackfrq(likert_4, value.labels = levels_4, var.labels = items)
#'
#' # -------------------------------
#' # Data from the EUROFAMCARE sample dataset
#' # Auto-detection of labels
#' # -------------------------------
#' data(efc)
#' # recveive first item of COPE-index scale
#' start <- which(colnames(efc) == "c82cop1")
#' # recveive first item of COPE-index scale
#' end <- which(colnames(efc) == "c90cop9")
#'
#' tab_stackfrq(efc[, c(start:end)], alternate.rows = TRUE)
#'
#' tab_stackfrq(efc[, c(start:end)], alternate.rows = TRUE,
#' show.n = TRUE, show.na = TRUE)
#'
#' # --------------------------------
#' # User defined style sheet
#' # --------------------------------
#' tab_stackfrq(efc[, c(start:end)], alternate.rows = TRUE,
#' show.total = TRUE, show.skew = TRUE, show.kurtosis = TRUE,
#' CSS = list(css.ncol = "border-left:1px dotted black;",
#' css.summary = "font-style:italic;"))
#' }
#' }
#' @export
tab_stackfrq <- function(items,
weight.by = NULL,
title = NULL,
var.labels = NULL,
value.labels = NULL,
wrap.labels = 20,
sort.frq = NULL,
alternate.rows = FALSE,
digits = 2,
string.total = "N",
string.na = "NA",
show.n = FALSE,
show.total = FALSE,
show.na = FALSE,
show.skew = FALSE,
show.kurtosis = FALSE,
digits.stats = 2,
file = NULL,
encoding = NULL,
CSS = NULL,
use.viewer = TRUE,
remove.spaces = TRUE) {
# --------------------------------------------------------
# check sorting
# --------------------------------------------------------
if (!is.null(sort.frq)) {
if (sort.frq == "first.asc") {
sort.frq <- "first"
reverseOrder <- FALSE
} else if (sort.frq == "first.desc") {
sort.frq <- "first"
reverseOrder <- TRUE
} else if (sort.frq == "last.asc") {
sort.frq <- "last"
reverseOrder <- FALSE
} else if (sort.frq == "last.desc") {
sort.frq <- "last"
reverseOrder <- TRUE
} else {
sort.frq <- NULL
reverseOrder <- FALSE
}
} else {
reverseOrder <- FALSE
}
# --------------------------------------------------------
# check encoding
# --------------------------------------------------------
encoding <- get.encoding(encoding, items)
# --------------------------------------------------------
# try to automatically set labels is not passed as parameter
# --------------------------------------------------------
if (is.null(value.labels)) {
value.labels <- sjlabelled::get_labels(
items[[1]],
attr.only = F,
values = "n",
non.labelled = T
)
}
if (is.null(var.labels)) {
var.labels <- sjlabelled::get_label(items, def.value = colnames(items))
}
# ----------------------------
# retrieve min and max values
# ----------------------------
minval <- as.numeric(min(apply(items, 2, function(x) min(x, na.rm = TRUE))))
maxval <- as.numeric(max(apply(items, 2, function(x) max(x, na.rm = TRUE))))
# ----------------------------
# if we have no value labels, set default labels and find amount
# of unique categories
# ----------------------------
if (is.null(value.labels)) value.labels <- as.character(minval:maxval)
# check whether missings should be shown
if (show.na) value.labels <- c(value.labels, `NA` = string.na)
# save amolunt of values
catcount <- length(value.labels)
# check length of x-axis-labels and split longer strings at into new lines
value.labels <- sjmisc::word_wrap(value.labels, wrap.labels, "<br>")
# ----------------------------
# if we have no variable labels, use row names
# ----------------------------
if (is.null(var.labels)) var.labels <- colnames(items)
# check length of x-axis-labels and split longer strings at into new lines
var.labels <- sjmisc::word_wrap(var.labels, wrap.labels, "<br>")
# ----------------------------
# additional statistics required from psych-package?
# ----------------------------
if (show.skew) pstat_skewness <- datawizard::skewness(items)
if (show.kurtosis) pstat_kurtosis <- datawizard::kurtosis(items)
if (is.null(weight.by)) {
dummy <- sjmisc::frq(items, show.strings = TRUE, show.na = show.na)
} else {
items$weights <- weight.by
dummy <- sjmisc::frq(items, weights = items$weights, show.strings = TRUE, show.na = show.na)
}
mat.n <- .transform_data(dummy, col = "frq")
mat <- .transform_data(dummy, col = ifelse(isTRUE(show.na), "raw.prc", "valid.prc"))
# ----------------------------
# Check if ordering was requested
# ----------------------------
# default order
facord <- seq_len(nrow(mat))
if (!is.null(sort.frq)) {
if (sort.frq == "first")
facord <- order(mat.n$V1)
else
facord <- order(mat.n[, ncol(mat.n)])
}
# ----------------------------
# reverse order
# ----------------------------
if (reverseOrder) facord <- rev(facord)
# -------------------------------------
# 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.arc <- "arc"
tag.centeralign <- "centeralign"
tag.firsttablecol <- "firsttablecol"
tag.ncol <- "ncol"
tag.skewcol <- "skewcol"
tag.kurtcol <- "kurtcol"
tag.summary <- "summary"
css.table <- "border-collapse:collapse; border:none; border-bottom:double black;"
css.caption <- "font-weight: bold; text-align:left;"
css.thead <- "border-top:double black; border-bottom:1px solid black; padding:0.2cm;"
css.tdata <- "padding:0.2cm;"
css.arc <- "background-color:#eaeaea;"
css.centeralign <- "text-align:center;"
css.firsttablecol <- "font-style:italic;"
css.ncol <- ""
css.summary <- ""
css.skewcol <- ""
css.kurtcol <- ""
# ------------------------
# 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.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.arc']])) css.arc <- ifelse(substring(CSS[['css.arc']],1,1) == '+', paste0(css.arc, substring(CSS[['css.arc']],2)), CSS[['css.arc']])
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.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.ncol']])) css.ncol <- ifelse(substring(CSS[['css.ncol']],1,1) == '+', paste0(css.ncol, substring(CSS[['css.ncol']],2)), CSS[['css.ncol']])
if (!is.null(CSS[['css.skewcol']])) css.skewcol <- ifelse(substring(CSS[['css.skewcol']],1,1) == '+', paste0(css.skewcol, substring(CSS[['css.skewcol']],2)), CSS[['css.skewcol']])
if (!is.null(CSS[['css.kurtcol']])) css.kurtcol <- ifelse(substring(CSS[['css.kurtcol']],1,1) == '+', paste0(css.kurtcol, substring(CSS[['css.kurtcol']],2)), CSS[['css.kurtcol']])
}
# ------------------------
# 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.%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.arc, css.arc,
tag.centeralign, css.centeralign, tag.ncol, css.ncol,
tag.summary, css.summary, tag.kurtcol, css.kurtcol,
tag.skewcol, css.skewcol)
# ------------------------
# start content
# ------------------------
toWrite <- paste0(toWrite, page.style)
toWrite = paste(toWrite, "\n</head>\n<body>", "\n")
# -------------------------------------
# start table tag
# -------------------------------------
page.content <- "<table>\n"
# -------------------------------------
# table caption
# -------------------------------------
if (!is.null(title)) page.content <- paste(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:catcount) {
page.content <- paste0(page.content, sprintf(" <th class=\"thead\">%s</th>\n", value.labels[i]))
}
# add N column
if (show.total) page.content <- paste0(page.content, sprintf(" <th class=\"thead ncol summary\">%s</th>\n", string.total))
# add skew column
if (show.skew) page.content <- paste0(page.content, " <th class=\"thead skewcol summary\">Skew</th>\n")
# add kurtosis column
if (show.kurtosis) page.content <- paste0(page.content, " <th class=\"thead kurtcol summary\">Kurtosis</th>\n")
# close table row
page.content <- paste0(page.content, " </tr>\n")
# -------------------------------------
# data rows
# -------------------------------------
# iterate all rows of df
for (i in seq_len(nrow(mat))) {
# default row string for alternative row colors
arcstring <- ""
# if we have alternating row colors, set css
if (alternate.rows) arcstring <- ifelse(sjmisc::is_even(i), " arc", "")
# write tr-tag
page.content <- paste0(page.content, " <tr>\n")
# print first table cell
page.content <- paste0(page.content, sprintf(" <td class=\"firsttablecol%s\">%s</td>\n", arcstring, var.labels[facord[i]]))
# --------------------------------------------------------
# iterate all columns
# --------------------------------------------------------
for (j in seq_len(ncol(mat))) {
if (show.n) {
page.content <- paste0(page.content, sprintf(" <td class=\"tdata centeralign%s\">%i<br>(%.*f %%)</td>\n", arcstring, as.integer(mat.n[facord[i], j]), digits, mat[facord[i], j]))
} else {
page.content <- paste0(page.content, sprintf(" <td class=\"tdata centeralign%s\">%.*f %%</td>\n", arcstring, digits, mat[facord[i], j]))
}
}
# add column with N's
if (show.total) page.content <- paste0(page.content, sprintf(" <td class=\"tdata centeralign ncol summary%s\">%i</td>\n", arcstring, as.integer(sum(mat.n[facord[i], ]))))
# add column with Skew's
if (show.skew) page.content <- paste0(page.content, sprintf(" <td class=\"tdata centeralign skewcol summary%s\">%.*f</td>\n", arcstring, digits.stats, pstat_skewness[facord[i]]))
# add column with Kurtosis's
if (show.kurtosis) page.content <- paste0(page.content, sprintf(" <td class=\"tdata centeralign kurtcol summary%s\">%.*f</td>\n", arcstring, digits.stats, pstat_kurtosis[facord[i]]))
# close row
page.content <- paste0(page.content, " </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.firsttablecol, css.firsttablecol, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.ncol, css.ncol, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.skewcol, css.skewcol, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.kurtcol, css.kurtcol, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.summary, css.summary, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.arc, css.arc, 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", "sjtstackfrq"),
list(page.style = page.style,
page.content = page.content,
page.complete = toWrite,
header = table.header,
knitr = knitr,
file = file,
viewer = use.viewer))
}
.transform_data <- function(x, col) {
dat <- suppressWarnings(Reduce(function(x, y) merge(x, y, all = TRUE, sort = FALSE, by = "val"), x))
if (is.factor(dat$val)) {
reihe <- levels(dat$val)
if (anyNA(dat$val))
reihe <- c(reihe, NA)
dat <- dat[order(dat$val, reihe), ]
} else {
dat <- dat[order(dat$val), ]
}
colnames(dat) <- make.names(colnames(dat), unique = TRUE)
keep <- (colnames(dat) == "val") | grepl(paste0("^", col), colnames(dat))
dat <- as.data.frame(t(dat[, keep, drop = FALSE]))
dat <- as.data.frame(sapply(dat[-1, ], function(i) as.numeric(as.character(i))))
dat[is.na(dat)] <- 0
colnames(dat) <- sprintf("V%i", 1:ncol(dat))
dat
}
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