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#' @title Summary of factor analysis as HTML table
#' @name tab_fa
#'
#' @description Performs a factor analysis on a data frame or matrix
#' and displays the factors as HTML
#' table, or saves them as file. \cr \cr In case a data frame is used as
#' parameter, the Cronbach's Alpha value for each factor scale will be calculated,
#' i.e. all variables with the highest loading for a factor are taken for the
#' reliability test. The result is an alpha value for each factor dimension.
#'
#' @param show.comm Logical, if \code{TRUE}, show the communality column in the table.
#' @param method the factoring method to be used. \code{"ml"} will do a maximum likelihood factor analysis (default).
#' \code{"minres"} will do a minimum residual (OLS),
#' \code{"wls"} will do a weighted least squares (WLS) solution,
#' \code{"gls"} does a generalized weighted least squares (GLS),
#' \code{"pa"} will do the principal factor solution,
#' \code{"minchi"} will minimize the sample size weighted chi square
#' when treating pairwise correlations with different number of
#' subjects per pair. \code{"minrank"} will do a minimum rank factor analysis.
#' @param sort logical, if \code{TRUE}, sort the loadings for each factors
#' (items will be sorted in terms of their greatest loading, in descending
#' order)
#'
#' @inheritParams tab_pca
#' @inheritParams tab_model
#' @inheritParams tab_df
#' @inheritParams tab_xtab
#' @inheritParams plot_grpfrq
#' @inheritParams tab_corr
#'
#' @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}),
#' \item the html-table with inline-css for use with knitr (\code{knitr}),
#' \item the \code{factor.index}, i.e. the column index of each variable with the highest factor loading for each factor and
#' \item the \code{removed.items}, i.e. which variables have been removed because they were outside of the \code{fctr.load.tlrn}'s range.
#' }
#' for further use.
#'
#' @note This method for factor analysis relies on the functions
#' \code{\link[psych]{fa}} and \code{\link[psych]{fa.parallel}} from the psych package.
#'
#'
#' @examples
#' \dontrun{
#' # Data from the EUROFAMCARE sample dataset
#' library(sjmisc)
#' library(GPArotation)
#' data(efc)
#'
#' # recveive first item of COPE-index scale
#' start <- which(colnames(efc) == "c82cop1")
#' # recveive last item of COPE-index scale
#' end <- which(colnames(efc) == "c90cop9")
#' # auto-detection of labels
#' if (interactive()) {
#' tab_fa(efc[, start:end])
#' }}
#' @export
tab_fa <- function(data,
rotation = "promax",
method = c("ml", "minres", "wls", "gls", "pa", "minchi", "minrank"),
nmbr.fctr = NULL,
fctr.load.tlrn = 0.1,
sort = FALSE,
title = "Factor Analysis",
var.labels = NULL,
wrap.labels = 40,
show.cronb = TRUE,
show.comm = FALSE,
alternate.rows = FALSE,
digits = 2,
CSS = NULL,
encoding = NULL,
file = NULL,
use.viewer = TRUE,
remove.spaces = TRUE) {
# -------------------------------------
# check encoding
# -------------------------------------
encoding <- get.encoding(encoding, data)
# check arguments
method <- match.arg(method)
if (!requireNamespace("psych", quietly = TRUE)) {
stop("Package 'psych' required for this function to work. Please install it.", call. = FALSE)
}
# --------------------------------------------------------
# try to automatically set labels is not passed as parameter
# --------------------------------------------------------
if (is.null(var.labels) && is.data.frame(data)) {
var.labels <- sjlabelled::get_label(data, def.value = colnames(data))
}
# ----------------------------
# check if user has passed a data frame
# or a pca object
# ----------------------------
if (inherits(data, "fa")) {
if (sort == TRUE) {
fadata <- psych::fa.sort(data) #resort loadings
} else {
fadata <- data
}
dataframeparam <- FALSE
} else if (is.data.frame(data)) {
if (is.null(nmbr.fctr)) {
nr_factors <- psych::fa.parallel(data, fa = "fa", fm = method)$nfact
dev.off()
fadata <- psych::fa(data, nfactors = nr_factors, fm = method, rotate = rotation)
if (sort == TRUE) {
fadata <- psych::fa.sort(fadata) #resort loadings
}
} else {
fadata <- psych::fa(data, nfactors = nmbr.fctr, fm = method, rotate = rotation)
if (sort == TRUE) {
fadata <- psych::fa.sort(fadata) #resort loadings
}
}
dataframeparam <- TRUE
}
# -------------------------------------
# init header
# -------------------------------------
toWrite <- 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.centeralign <- "centeralign"
tag.rightalign <- "rightalign"
tag.cronbach <- "cronbach"
tag.comm <- "comm"
tag.rotation <- "rotation"
tag.kmo <- "kmo"
tag.arc <- "arc"
tag.minval <- "minval"
tag.removable <- "removable"
tag.firsttablerow <- "firsttablerow"
tag.firsttablecol <- "firsttablecol"
css.table <- "border-collapse:collapse; border:none;"
css.caption <- "font-weight: bold; text-align:left;"
css.thead <- "border-top:double black; padding:0.2cm;"
css.tdata <- "padding:0.2cm;"
css.centeralign <- "text-align:center;"
css.rightalign <- "text-align:right;"
css.cronbach <- "font-style:italic; border-bottom:double;"
css.comm <- "font-style:italic; color:#666666;"
css.kmo <- "font-style:italic;"
css.rotation <- "font-style:italic; font-size:0.9em;"
css.minval <- "color:#cccccc;"
css.arc <- "background-color:#eaeaea;"
css.removable <- "background-color:#eacccc;"
css.firsttablerow <- "border-top:1px solid black;"
css.firsttablecol <- ""
if (!show.comm && show.cronb) css.cronbach <- sprintf("%s border-bottom:double;", css.cronbach)
# ------------------------
# 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.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.rightalign']])) css.rightalign <- ifelse(substring(CSS[['css.rightalign']], 1, 1) == '+', paste0(css.rightalign, substring(CSS[['css.rightalign']], 2)), CSS[['css.rightalign']])
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.firsttablerow']])) css.firsttablerow <- ifelse(substring(CSS[['css.firsttablerow']], 1, 1) == '+', paste0(css.firsttablerow, substring(CSS[['css.firsttablerow']], 2)), CSS[['css.firsttablerow']])
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.cronbach']])) css.cronbach <- ifelse(substring(CSS[['css.cronbach']], 1, 1) == '+', paste0(css.cronbach, substring(CSS[['css.cronbach']], 2)), CSS[['css.cronbach']])
if (!is.null(CSS[['css.comm']])) css.comm <- ifelse(substring(CSS[['css.comm']], 1, 1) == '+', paste0(css.comm, substring(CSS[['css.comm']], 2)), CSS[['css.comm']])
if (!is.null(CSS[['css.kmo']])) css.kmo <- ifelse(substring(CSS[['css.kmo']], 1, 1) == '+', paste0(css.kmo, substring(CSS[['css.kmo']], 2)), CSS[['css.kmo']])
if (!is.null(CSS[['css.rotation']])) css.rotation <- ifelse(substring(CSS[['css.rotation']], 1, 1) == '+', paste0(css.rotation, substring(CSS[['css.rotation']], 2)), CSS[['css.rotation']])
if (!is.null(CSS[['css.minval']])) css.minval <- ifelse(substring(CSS[['css.minval']], 1, 1) == '+', paste0(css.minval, substring(CSS[['css.minval']], 2)), CSS[['css.minval']])
if (!is.null(CSS[['css.removable']])) css.removable <- ifelse(substring(CSS[['css.removable']], 1, 1) == '+', paste0(css.removable, substring(CSS[['css.removable']], 2)), CSS[['css.removable']])
}
# ------------------------
# 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.%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.cronbach, css.cronbach, tag.minval, css.minval,
tag.removable, css.removable, tag.firsttablerow, css.firsttablerow,
tag.firsttablecol, css.firsttablecol, tag.centeralign, css.centeralign,
tag.rightalign, css.rightalign, tag.rotation, css.rotation,
tag.comm, css.comm, tag.kmo, css.kmo, tag.arc, css.arc)
# ------------------------
# start content
# ------------------------
toWrite <- paste0(toWrite, page.style)
toWrite = paste(toWrite, "\n</head>\n<body>", "\n")
# create data frame with factor loadings
loadings <- fadata$loadings[]
names <- rownames(fadata$loadings)
df <- as.data.frame(loadings, row.names = names)
# ----------------------------
# check if user defined labels have been supplied
# if not, use variable names from data frame
# ----------------------------
if (is.null(var.labels)) var.labels <- row.names(df)
# ----------------------------
# Prepare length of labels
# ----------------------------
if (!is.null(var.labels)) {
# wrap long variable labels
var.labels <- sjmisc::word_wrap(var.labels, wrap.labels, "<br>")
# resort labels when sort == TRUE
if (sort == TRUE) {
var.labels <- var.labels[fadata$order]
}
}
# --------------------------------------------------------
# this function checks which items have unclear factor loadings,
# i.e. which items do not strongly load on a single factor but
# may load almost equally on several factors
# --------------------------------------------------------
getRemovableItems <- function(dataframe) {
# clear vector
removers <- c()
# iterate each row of the data frame. each row represents
# one item with its factor loadings
for (i in seq_len(nrow(dataframe))) {
# get factor loadings for each item
rowval <- as.numeric(abs(df[i, ]))
# retrieve highest loading
maxload <- max(rowval)
# retrieve 2. highest loading
max2load <- sort(rowval, TRUE)[2]
# check difference between both
if (abs(maxload - max2load) < fctr.load.tlrn) {
# if difference is below the tolerance,
# remeber row-ID so we can remove that items
# for further PCA with updated data frame
removers <- c(removers, i)
}
}
# return a vector with index numbers indicating which items
# have unclear loadings
return(removers)
}
# --------------------------------------------------------
# this function retrieves a list with the column index ("factor" index)
# where each case of the data frame has its highedt factor loading.
# So we know to which "group" (factor dimension) each case of the
# data frame belongs to according to the pca results
# --------------------------------------------------------
getItemLoadings <- function(dataframe) {
# return a vector with index numbers indicating which items
# loads the highest on which factor
return(apply(dataframe, 1, function(x) which.max(abs(x))))
}
# --------------------------------------------------------
# this function calculates the cronbach's alpha value for
# each factor scale, i.e. all variables with the highest loading
# for a factor are taken for the reliability test. The result is
# an alpha value for each factor dimension
# --------------------------------------------------------
getCronbach <- function(dataframe, itemloadings) {
# clear vector
cbv <- c()
# iterate all highest factor loadings of items
for (n in seq_len(length(unique(itemloadings)))) {
# calculate cronbach's alpha for those cases that all have the
# highest loading on the same factor
cbv <- c(cbv, performance::cronbachs_alpha(stats::na.omit(dataframe[, which(itemloadings == n)])))
}
# cbv now contains the factor numbers and the related alpha values
# for each "factor dimension scale"
return(cbv)
}
# ----------------------------------
# Cronbach's Alpha can only be calculated when having a data frame
# with each component / variable as column
# ----------------------------------
if (dataframeparam) {
# get alpha values
alphaValues <- getCronbach(data, getItemLoadings(df))
} else {
message("Cronbach's Alpha can only be calculated when having a data frame with each component / variable as column.")
alphaValues <- NULL
show.cronb <- FALSE
}
# -------------------------------------
# retrieve those items that have unclear factor loadings, i.e.
# which almost load equally on several factors. The tolerance
# that indicates which difference between factor loadings is
# considered as "equally" is defined via fctr.load.tlrn
# -------------------------------------
removableItems <- getRemovableItems(df)
# -------------------------------------
# retrieve kmo and msa for data set
# -------------------------------------
#kmo <- NULL # not implemented at the moment
#if (show.msa) kmo <- psych::KMO(data)
# -------------------------------------
# convert data frame, add label names
# -------------------------------------
maxdf <- apply(df, 1, function(x) max(abs(x)))
# -------------------------------------
# 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 seq_len(ncol(df))) {
page.content <- paste0(page.content, sprintf(" <th class=\"thead\">Factor %i</th>\n", i))
}
# check if communality column should be shown
if (show.comm) page.content <- paste0(page.content, " <th class=\"thead comm\">Communality</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(df))) {
# start table row
rowcss <- ""
# check for removable items in first row
if (i %in% removableItems && i == 1) rowcss <- " firsttablerow removable"
# check for removable items in other rows
if (i %in% removableItems && i != 1) rowcss <- " removable"
# check for non-removable items in first row
if (is.na(match(i, removableItems)) && i == 1) rowcss <- " firsttablerow"
# 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 with class-attributes
page.content <- paste0(page.content, " <tr>\n")
# print first table cell
page.content <- paste0(page.content, sprintf(" <td class=\"firsttablecol%s%s\">%s</td>\n",
arcstring, rowcss, var.labels[i]))
# iterate all columns
for (j in seq_len(ncol(df))) {
# start table column
colcss <- sprintf(" class=\"tdata centeralign%s%s\"", arcstring, rowcss)
if (maxdf[[i]] != max(abs(df[i, j])))
colcss <- sprintf(" class=\"tdata centeralign minval%s%s\"", arcstring, rowcss)
page.content <- paste0(page.content, sprintf(" <td%s>%.*f</td>\n",
colcss, digits, df[i, j]))
}
# check if comm column should be shown
if (show.comm) page.content <- paste0(page.content, sprintf(" <td class=\"tdata comm centeralign%s%s\">%.*f</td>\n",
arcstring,
rowcss,
digits,
fadata$communalities[[i]]))
# close row
page.content <- paste0(page.content, " </tr>\n")
}
#
#
# # -------------------------------------
# # Total Communalities # not implemented at the moment
# # -------------------------------------
if (show.comm) {
# write tr-tag with class-attributes
page.content <- paste0(page.content, " <tr>\n")
page.content <- paste0(page.content, " <td class=\"tdata kmo\">Total Communalities</td>\n")
page.content <- paste0(page.content, sprintf(" <td class=\"tdata centeralign kmo\" colspan=\"%i\"></td>\n", ncol(df)))
page.content <- paste0(page.content, sprintf(" <td class=\"tdata centeralign kmo\">%.*f</td>\n", digits, sum(fadata$communalities)))
page.content <- paste0(page.content, " </tr>\n")
}
# -------------------------------------
# cronbach's alpha
# -------------------------------------
if (show.cronb && !is.null(alphaValues)) {
# write tr-tag with class-attributes
page.content <- paste0(page.content, " <tr>\n")
# first column
page.content <- paste0(page.content, " <td class=\"tdata cronbach\">Cronbach's α</td>\n")
# iterate alpha-values
for (i in seq_len(length(alphaValues))) {
page.content <- paste0(page.content, sprintf(" <td class=\"tdata centeralign cronbach\">%.*f</td>\n",
digits,
alphaValues[i]))
}
# check if comm column should be shown
if (show.comm) page.content <- paste0(page.content, " <td class=\"tdata centeralign cronbach\"></td>\n")
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>")
# -------------------------------------
# create list with factor loadings that indicate
# on which column inside the data frame the highest
# loading is
# -------------------------------------
factorindex <- apply(df, 1, function(x) which.max(abs(x)))
# -------------------------------------
# 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.rightalign, css.rightalign, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.cronbach, css.cronbach, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.comm, css.comm, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.arc, css.arc, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.kmo, css.kmo, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.rotation, css.rotation, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.minval, css.minval, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.removable, css.removable, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.firsttablerow, css.firsttablerow, knitr, fixed = TRUE, useBytes = TRUE)
knitr <- gsub(tag.firsttablecol, css.firsttablecol, 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", "sjtfa"),
list(
page.style = page.style,
page.content = page.content,
page.complete = toWrite,
knitr = knitr,
factor.index = factorindex,
removed.items = removableItems,
file = file,
viewer = use.viewer
)
)
}
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