sdaza/create_descriptive_tables.R

## create_descriptive_tables.R
# author: sebastian daza
# web: sdaza.com


# libraries
library(data.table)
library(xtable)


# create descriptive tables
#' @title Latex descriptive stats table
#' @description Generate a Latex table with descriptive custom stats
#' @param datlist List of data.tables
#' @param summary_function Function for creating summaary tats
#' @param column_names Names of columns
#' @param variable_names List of vectors with variable name by dataset
#' @param variable_labels List of vectors with variable labels by dataset
#' @param group_variable Character with the name of a grouping column
#' @param align Character with table alignment, e.g., "lrrrr"
#' @param digits Vector with number of digits per column (length should be
#' number of columns 1 + )
#' @param title Title of the table
#' @param label Label of the table
#' @param fontsize Text defining the font size of the table, e.g., "\\fontsize{9pt}{10pt}\\selectfont"
#' @param note Note to be addded at the bottomm of the table
#' @param notesize Font size of note, e.g., "scriptsize"
#' @param arraystretch Number to control space between rows
#' @param tabcolsep Number to contrl space between columns
#' @param file Path to save table
#' @examples
#' library(data.table)
#' library(xtable)
#' n = 100
#' dat = data.table(
#'     var1 = runif(n),
#'     var2 = sample(0:1, n, prob = c(0.8, 0.2), replace = TRUE),
#'     var3 = sample(1:4, n, replace = TRUE),
#'     var4 = rnorm(n, 1000, 100),
#'     var5 = factor(sample(1:4, n, prob = c(0.1, 0.4, 0.3, 0.2), replace = TRUE),
#'         labels = c("Low", "Medium", "High", "Very high"), ordered = TRUE)
#' )
#' variables = paste0("var", 1:5)
#' labels = paste0("Variable ", 1:5)
#' createDescriptiveTable(dat,
#'     summary_function = getDescriptives,
#'     variable_names = variables,
#'     variable_labels = labels,
#'     title = "Descriptive statistics",
#'     label = "tab:descriptive",
#'     file = "example.tex")
createDescriptiveTable = function(datasets,
    summary_function,
    column_names = NULL,
    variable_names,
    variable_labels = NULL,
    group_variable = NULL,
    align = NULL,
    digits = NULL,
    title = "Descriptive statistics",
    label = "tab:descriptive",
    fontsize = "\\fontsize{9pt}{10pt}\\selectfont",
    note = NULL,
    notesize = "footnotesize",
    arraystretch = 1.5,
    tabcolsep = 10,
    file = "descriptive_table.tex") {

    # initial checks
    if (is.list(datasets)) {
        for (i in seq_along(datasets)) {
            if (!is.data.table(datasets[[i]])) {
                datasets[[i]] = as.data.table(datasets[[i]])
            }
        }
    }
    else  {
        if (!is.data.table(datasets)) {
            datasets = as.data.table(datasets)
        }
    }

    if (any(class(datasets) %in% "data.table")) { datasets = list(datasets) }
    if (!is.list(variable_names)) { variable_names = list(variable_names) }
    if (!is.list(variable_labels)) { variable_labels = list(variable_labels) }
    if (is.null(variable_labels)) { variables_labels = variable_names }
    length_lists = unique(length(datasets),
        length(variable_names),
        length(variable_labels)
    )
    if (length(length_lists) > 1) {
        stop("Datasets, column names, and variable_labels should be lists of same length")
    }

    org_column_names = column_names

    # list to save tabs
    tabs = list()
    factor_header = list()
    sumrows = 0

    for (i in seq_along(datasets)) {

        if (i > 1) { sumrows = sumrows + nrow(tabs[[i-1]]) }

        if (is.null(group_variable)) { vars = variable_names[[i]] }
        else { vars = c(group_variable, variable_names[[i]]) }
        tabs[[i]] = data.table::copy(datasets[[i]][, ..vars])

        factor_dataset_list = list()
        if (length(variable_names[[i]]) != length(variable_labels[[i]])) {
            stop("Length of variable is different from length of labels!")
        }
        factor_names = names(tabs[[i]])[sapply(tabs[[i]], is.factor)]

        # create dummy variables
        for (h in seq_along(factor_names)) {
            categories = as.vector(na.omit(sort(unique(tabs[[i]][[factor_names[h]]]))))
            for (j in seq_along(categories)) {
                tabs[[i]][, (paste0(factor_names[h], "_", j)) :=
                    ifelse(get(factor_names[h]) == categories[j], 1, 0)]
            }

            # position and variable name
            position = which(variable_names[[i]] == factor_names[h])
            if (i == 1) {
                adj_position = ifelse(position == 1, 1, position - 1)
            } else {
                adj_position = sumrows - 1 + position
            }

            variable_names[[i]] = variable_names[[i]][-position]
            temp_position = ifelse(i == 1, adj_position, position - 1)
            variable_names[[i]] = append(variable_names[[i]], paste0(factor_names[h], "_",
                1:length(categories)), after =  temp_position)
            lname = variable_labels[[i]][position]
            factor_dataset_list[[lname]] = c(adj_position, adj_position + length(categories))
            variable_labels[[i]] = variable_labels[[i]][-position]
            variable_labels[[i]] = append(variable_labels[[i]], paste0("\\quad ", categories),
                after = temp_position)

        }

        factor_header[[i]] = factor_dataset_list
        factor_data_list = list()

        # descriptive estimation
        if (is.null(group_variable)) {
            tabs[[i]] = transpose(tabs[[i]][, lapply(.SD, summary_function),
                .SDcols = variable_names[[i]]], keep.names = "variables")
            if (is.null(column_names) & i == 1) {
                column_names = paste0("C", 1:(dim(tabs[[i]])[2]-1))
            }
        } else if (length(group_variable) == 1) {
            group_variable_values = sort(na.omit(unique(tabs[[i]][[group_variable]])))
            setorderv(tabs[[i]], group_variable)
            tabs[[i]] = tabs[[i]][, lapply(.SD, summary_function), group_variable,
                .SDcols = variable_names[[i]]]
            num_cols = tabs[[i]][, .N, group_variable]$N[1]

            if (is.null(column_names) & i == 1) {
                if (num_cols != length(column_names)) {
                    stop("Number of column names is not the same as outputs of the summary function!")
                }
                column_names = paste0("C", 1:num_cols)
                org_column_names = column_names
            }
            tabs[[i]][, summary := rep(org_column_names, length(group_variable_values))]
            column_names = as.vector(outer(org_column_names, group_variable_values, paste))
            tabs[[i]] = dcast(
                melt(tabs[[i]], id.vars = c(group_variable, "summary"), variable.name = "variables"),
                variables ~ get(group_variable) + summary
                )
        } else {
            stop("Group variable should have length 1!")
        }

        if (dim(tabs[[i]])[2] != (length(column_names) + 1)) {
            stop("Descriptive function values are not equal to the number of column names")
        }
        colnames(tabs[[i]]) = c("Variables", column_names)
        tabs[[i]][["Variables"]] = variable_labels[[i]]
    }

    if (length(tabs) == 1) { ftabs = tabs[[1]] }
    else { ftabs = rbindlist(tabs) }

    total_rows = dim(ftabs)[1]
    total_columns = dim(ftabs)[2]

    if (is.null(align)) {
        align = paste0(c("l", "l", rep("r", total_columns - 1)), collapse  = "")
    }
    if (is.null(digits)) {
        digits = rep(2, total_columns + 1)
    }
    if (!is.null(digits) & length(digits) < (total_columns + 1)) {
        digits = c(rep(0, (total_columns + 1) - length(digits)), digits)
    }

    # create headers
    addtorow = list()
    positions = -1
    command = list()
    new_columns = c(" ", column_names)
    command[[1]]  = paste0(
        "\\hline\n\\addlinespace\n", paste0(new_columns, collapse = " & "), " \\\\\n\\addlinespace\n")

    name_datasets = names(datasets)
    if (is.null(name_datasets)) { name_datasets = rep("", length(datasets)) }
    sumrows = 0

    for (i in seq_along(datasets)) {

        if (i > 1) { sumrows = sumrows + nrow(tabs[[i-1]]) }
        # conditions for dataset position
        if (i == 1 & name_datasets[i] != "") {
            positions = append(positions, tail(positions, 1) + 1)
        }
        else if (i > 1 & name_datasets[i] != "") {
            positions = append(positions, sumrows)
        }
        if (name_datasets[i] != "") {
            command[[length(command) + 1]] = paste0(
                "\\addlinespace\n\\multicolumn{", total_columns, "}{l}{\\textbf{\\textit{", name_datasets[i], "}}} \\\\\n\\addlinespace\n"
            )
        }

        if (length(factor_header[[i]]) > 0) {

            for (h in seq_along(factor_header[[i]])) {
                factor_position = factor_header[[i]][[h]][1]
                factor_end_position = factor_header[[i]][[h]][2]
                text = paste0(
                    "\\addlinespace\n\\multicolumn{", total_columns, "}{l}{\\textit{", names(factor_header[[i]])[h], "}} \\\\\n")
                text_end = "\\addlinespace\n"
                if (factor_position == 0 & !is.null(name_datasets)) {
                    command[[2]] = paste0(command[[2]], text)
                } else {
                    positions = append(positions, factor_position)
                    command[[length(command) + 1]] = text
                    positions = append(positions, factor_end_position)
                    command[[length(command) + 1]] = text_end
                }
            }
        }
    }

    positions = append(positions, total_rows)
    command[[length(command) + 1]] = "\\addlinespace\n\\hline\n\\addlinespace\n"

    addtorow$command = unlist(command)
    addtorow$pos = as.list(positions)

    # create latex table
    latex_table = xtable(ftabs,
        caption = title,
        label= label,
        align = align,
        digits = digits)

    output = print(latex_table,
        hline.after = c(-1),
        table.placement = 'htp',
        caption.placement = 'top',
        add.to.row = addtorow,
        include.rownames = FALSE,
        include.colnames = FALSE,
        type = 'latex',
        sanitize.text.function = identity,
        size = fontsize,
    )

    # create header
    if (!is.null(group_variable)) {

        group_length = rep(length(org_column_names), length(group_variable_values))

        # simple header
        table_header = paste0("& ", column_names[1], ".+", column_names[length(column_names)], " \\\\")
        print(table_header)
        # nested header
        table_header_line1 = paste0(paste0("& \\\\multicolumn\\{", group_length, "\\}\\{c\\}\\{",
            as.character(group_variable_values), "\\}"), collapse = " ")

        # positions
        rule_position = NULL
        for (i in seq(group_variable_values)) {
            stat_number = length(org_column_names)
            if (i == 1) {
                last_value = 2 + stat_number - 1
                rule_position[i] = paste0("2", "-", last_value)
            } else {
                rule_position[i] = paste0(last_value + 1, "-", last_value + stat_number)
                last_value = last_value + stat_number
            }
        }

        # rule
        table_header_line2 = paste0(paste0("\\\\cmidrule(lr)\\{", rule_position, "\\}"), collapse = " ")
        # stats
        table_header_line3 = paste0("& ", rep(org_column_names, length(group_variable_values)),
            collapse = " ")

        header_replacement = paste0(table_header_line1, " \\\\\\\\ \\\n", table_header_line2,
            " \\\n", table_header_line3, " \\\\")
        output = gsub(table_header, header_replacement, output)
        print(output)
    }

    # adding comment
    if (!is.null(note)) {
        clean_note = longText(note)
        header_replacement = paste0("begin\\{table\\}\\[htp\\]\\\n",
            "\\\\setlength\\{\\\\tabcolsep\\}\\{",
            tabcolsep,
            "pt\\}\\\n\\\\renewcommand\\{\\\\arraystretch\\}\\{",
            arraystretch,
            "\\}\\\n\\\\centering\\\n\\\\begin\\{threeparttable\\}\\\n")
        bottom = "end\\{tabular\\}\\\n\\\\endgroup\\\n"
        bottom_replacement = paste0("end\\{tabular\\}\\\n\\\\endgroup\\\n\\\\begin{tablenotes}\\\n\\\\", notesize, "\\\n\\\\item ",
            note,
        "\\\n\\\\end{tablenotes}")

        add_notes_table(output,
            comment = clean_note,
            header_replacement = header_replacement,
            bottom = bottom,
            bottom_replacement = bottom_replacement,
            closing = "end\\{tablenotes\\}",
            closing_replacement = "end\\{tablenotes\\}\\\n\\\\end{threeparttable}\\\n",
            filename = file)
    } else {
        header = "begin\\{table\\}\\[htp\\]\\\n"
        header_replacement = paste0("begin\\{table\\}\\[htp\\]\\\n",
            "\\\\setlength\\{\\\\tabcolsep\\}\\{",
            tabcolsep,
            "pt\\}\\\n\\\\renewcommand\\{\\\\arraystretch\\}\\{",
            arraystretch, "}\\\n")
        output = gsub(header, header_replacement, output)
        cat(output, file = file)
    }
}


# descriptive function
getDescriptives = function(x) {
    x = as.numeric(x)
    m = mean(x, na.rm = TRUE)
    sd = sd(x, na.rm = TRUE)
    pm = mean(is.na(x))*100
    n = length(x[!is.na(x)])
    return(c(m, sd, pm, n))
}


# clean long text
longText = function(text) {
    dtext = gsub("\n", "", text)
    dtext = gsub("\\s+", " ", dtext)
    return(dtext)
}


# add note to table
add_notes_table = function(tab,
    comment = "",
    arraystretch = 0.8,
    tabcolsep = 10,
    filename = "",
    header  = NULL,
    header_replacement = NULL,
    bottom = NULL,
    bottom_replacement = NULL ,
    closing = NULL,
    closing_replacement = NULL) {

    if (is.null(header)) {
        header = "begin\\{table\\}\\[htp\\]\\\n\\\\centering\\\n"
    }
    if (is.null(header_replacement)) {
        header_replacement = paste0("begin\\{table\\}\\[htp\\]\\\n",
                                    "\\\\setlength\\{\\\\tabcolsep\\}\\{",
                                    tabcolsep,
                                    "pt\\}\\\n\\\\renewcommand\\{\\\\arraystretch\\}\\{",
                                    arraystretch,
                                    "\\}\\\n",
                                    "\\\\begin\\{center\\}\\\n",
                                    "\\\\scriptsize\\\n",
                                    "\\\\begin\\{threeparttable\\}\\\n")
    }
    tab = gsub(header, header_replacement, tab)

    if (is.null(bottom)) {
        bottom = "end\\{tabular\\}\\n"
    }
    if (is.null(bottom_replacement)) {
        bottom_replacement = paste0("end\\{tabular\\}\\\n\\\\begin{tablenotes}\\\n\\\\scriptsize\\\n\\\\item ",
                                    comment,
                                    "\\\n\\\\end{tablenotes}\\\n")
    }
    tab = gsub(bottom, bottom_replacement, tab)

    if (is.null(closing)) {
        closing = "end\\{table\\}\\n"
    }
    if (is.null(closing_replacement)) {
        closing_replacement = paste0("end{threeparttable}\\\n",
                                     "\\\\end\\{center\\}\\\n",
                                     "\\\\end\\{table\\}\\\n"
                                    )
    }
    tab = gsub(closing, closing_replacement, tab)
    cat(tab, file = filename)
}
	# author: sebastian daza
	# web: sdaza.com


	# libraries
	library(data.table)
	library(xtable)


	# create descriptive tables
	#' @title Latex descriptive stats table
	#' @description Generate a Latex table with descriptive custom stats
	#' @param datlist List of data.tables
	#' @param summary_function Function for creating summaary tats
	#' @param column_names Names of columns
	#' @param variable_names List of vectors with variable name by dataset
	#' @param variable_labels List of vectors with variable labels by dataset
	#' @param group_variable Character with the name of a grouping column
	#' @param align Character with table alignment, e.g., "lrrrr"
	#' @param digits Vector with number of digits per column (length should be
	#' number of columns 1 + )
	#' @param title Title of the table
	#' @param label Label of the table
	#' @param fontsize Text defining the font size of the table, e.g., "\\fontsize{9pt}{10pt}\\selectfont"
	#' @param note Note to be addded at the bottomm of the table
	#' @param notesize Font size of note, e.g., "scriptsize"
	#' @param arraystretch Number to control space between rows
	#' @param tabcolsep Number to contrl space between columns
	#' @param file Path to save table
	#' @examples
	#' library(data.table)
	#' library(xtable)
	#' n = 100
	#' dat = data.table(
	#' var1 = runif(n),
	#' var2 = sample(0:1, n, prob = c(0.8, 0.2), replace = TRUE),
	#' var3 = sample(1:4, n, replace = TRUE),
	#' var4 = rnorm(n, 1000, 100),
	#' var5 = factor(sample(1:4, n, prob = c(0.1, 0.4, 0.3, 0.2), replace = TRUE),
	#' labels = c("Low", "Medium", "High", "Very high"), ordered = TRUE)
	#' )
	#' variables = paste0("var", 1:5)
	#' labels = paste0("Variable ", 1:5)
	#' createDescriptiveTable(dat,
	#' summary_function = getDescriptives,
	#' variable_names = variables,
	#' variable_labels = labels,
	#' title = "Descriptive statistics",
	#' label = "tab:descriptive",
	#' file = "example.tex")
	createDescriptiveTable = function(datasets,
	summary_function,
	column_names = NULL,
	variable_names,
	variable_labels = NULL,
	group_variable = NULL,
	align = NULL,
	digits = NULL,
	title = "Descriptive statistics",
	label = "tab:descriptive",
	fontsize = "\\fontsize{9pt}{10pt}\\selectfont",
	note = NULL,
	notesize = "footnotesize",
	arraystretch = 1.5,
	tabcolsep = 10,
	file = "descriptive_table.tex") {

	# initial checks
	if (is.list(datasets)) {
	for (i in seq_along(datasets)) {
	if (!is.data.table(datasets[[i]])) {
	datasets[[i]] = as.data.table(datasets[[i]])
	}
	}
	}
	else {
	if (!is.data.table(datasets)) {
	datasets = as.data.table(datasets)
	}
	}

	if (any(class(datasets) %in% "data.table")) { datasets = list(datasets) }
	if (!is.list(variable_names)) { variable_names = list(variable_names) }
	if (!is.list(variable_labels)) { variable_labels = list(variable_labels) }
	if (is.null(variable_labels)) { variables_labels = variable_names }
	length_lists = unique(length(datasets),
	length(variable_names),
	length(variable_labels)
	)
	if (length(length_lists) > 1) {
	stop("Datasets, column names, and variable_labels should be lists of same length")
	}

	org_column_names = column_names

	# list to save tabs
	tabs = list()
	factor_header = list()
	sumrows = 0

	for (i in seq_along(datasets)) {

	if (i > 1) { sumrows = sumrows + nrow(tabs[[i-1]]) }

	if (is.null(group_variable)) { vars = variable_names[[i]] }
	else { vars = c(group_variable, variable_names[[i]]) }
	tabs[[i]] = data.table::copy(datasets[[i]][, ..vars])

	factor_dataset_list = list()
	if (length(variable_names[[i]]) != length(variable_labels[[i]])) {
	stop("Length of variable is different from length of labels!")
	}
	factor_names = names(tabs[[i]])[sapply(tabs[[i]], is.factor)]

	# create dummy variables
	for (h in seq_along(factor_names)) {
	categories = as.vector(na.omit(sort(unique(tabs[[i]][[factor_names[h]]]))))
	for (j in seq_along(categories)) {
	tabs[[i]][, (paste0(factor_names[h], "_", j)) :=
	ifelse(get(factor_names[h]) == categories[j], 1, 0)]
	}

	# position and variable name
	position = which(variable_names[[i]] == factor_names[h])
	if (i == 1) {
	adj_position = ifelse(position == 1, 1, position - 1)
	} else {
	adj_position = sumrows - 1 + position
	}

	variable_names[[i]] = variable_names[[i]][-position]
	temp_position = ifelse(i == 1, adj_position, position - 1)
	variable_names[[i]] = append(variable_names[[i]], paste0(factor_names[h], "_",
	1:length(categories)), after = temp_position)
	lname = variable_labels[[i]][position]
	factor_dataset_list[[lname]] = c(adj_position, adj_position + length(categories))
	variable_labels[[i]] = variable_labels[[i]][-position]
	variable_labels[[i]] = append(variable_labels[[i]], paste0("\\quad ", categories),
	after = temp_position)

	}

	factor_header[[i]] = factor_dataset_list
	factor_data_list = list()

	# descriptive estimation
	if (is.null(group_variable)) {
	tabs[[i]] = transpose(tabs[[i]][, lapply(.SD, summary_function),
	.SDcols = variable_names[[i]]], keep.names = "variables")
	if (is.null(column_names) & i == 1) {
	column_names = paste0("C", 1:(dim(tabs[[i]])[2]-1))
	}
	} else if (length(group_variable) == 1) {
	group_variable_values = sort(na.omit(unique(tabs[[i]][[group_variable]])))
	setorderv(tabs[[i]], group_variable)
	tabs[[i]] = tabs[[i]][, lapply(.SD, summary_function), group_variable,
	.SDcols = variable_names[[i]]]
	num_cols = tabs[[i]][, .N, group_variable]$N[1]

	if (is.null(column_names) & i == 1) {
	if (num_cols != length(column_names)) {
	stop("Number of column names is not the same as outputs of the summary function!")
	}
	column_names = paste0("C", 1:num_cols)
	org_column_names = column_names
	}
	tabs[[i]][, summary := rep(org_column_names, length(group_variable_values))]
	column_names = as.vector(outer(org_column_names, group_variable_values, paste))
	tabs[[i]] = dcast(
	melt(tabs[[i]], id.vars = c(group_variable, "summary"), variable.name = "variables"),
	variables ~ get(group_variable) + summary
	)
	} else {
	stop("Group variable should have length 1!")
	}

	if (dim(tabs[[i]])[2] != (length(column_names) + 1)) {
	stop("Descriptive function values are not equal to the number of column names")
	}
	colnames(tabs[[i]]) = c("Variables", column_names)
	tabs[[i]][["Variables"]] = variable_labels[[i]]
	}

	if (length(tabs) == 1) { ftabs = tabs[[1]] }
	else { ftabs = rbindlist(tabs) }

	total_rows = dim(ftabs)[1]
	total_columns = dim(ftabs)[2]

	if (is.null(align)) {
	align = paste0(c("l", "l", rep("r", total_columns - 1)), collapse = "")
	}
	if (is.null(digits)) {
	digits = rep(2, total_columns + 1)
	}
	if (!is.null(digits) & length(digits) < (total_columns + 1)) {
	digits = c(rep(0, (total_columns + 1) - length(digits)), digits)
	}

	# create headers
	addtorow = list()
	positions = -1
	command = list()
	new_columns = c(" ", column_names)
	command[[1]] = paste0(
	"\\hline\n\\addlinespace\n", paste0(new_columns, collapse = " & "), " \\\\\n\\addlinespace\n")

	name_datasets = names(datasets)
	if (is.null(name_datasets)) { name_datasets = rep("", length(datasets)) }
	sumrows = 0

	for (i in seq_along(datasets)) {

	if (i > 1) { sumrows = sumrows + nrow(tabs[[i-1]]) }
	# conditions for dataset position
	if (i == 1 & name_datasets[i] != "") {
	positions = append(positions, tail(positions, 1) + 1)
	}
	else if (i > 1 & name_datasets[i] != "") {
	positions = append(positions, sumrows)
	}
	if (name_datasets[i] != "") {
	command[[length(command) + 1]] = paste0(
	"\\addlinespace\n\\multicolumn{", total_columns, "}{l}{\\textbf{\\textit{", name_datasets[i], "}}} \\\\\n\\addlinespace\n"
	)
	}

	if (length(factor_header[[i]]) > 0) {

	for (h in seq_along(factor_header[[i]])) {
	factor_position = factor_header[[i]][[h]][1]
	factor_end_position = factor_header[[i]][[h]][2]
	text = paste0(
	"\\addlinespace\n\\multicolumn{", total_columns, "}{l}{\\textit{", names(factor_header[[i]])[h], "}} \\\\\n")
	text_end = "\\addlinespace\n"
	if (factor_position == 0 & !is.null(name_datasets)) {
	command[[2]] = paste0(command[[2]], text)
	} else {
	positions = append(positions, factor_position)
	command[[length(command) + 1]] = text
	positions = append(positions, factor_end_position)
	command[[length(command) + 1]] = text_end
	}
	}
	}
	}

	positions = append(positions, total_rows)
	command[[length(command) + 1]] = "\\addlinespace\n\\hline\n\\addlinespace\n"

	addtorow$command = unlist(command)
	addtorow$pos = as.list(positions)

	# create latex table
	latex_table = xtable(ftabs,
	caption = title,
	label= label,
	align = align,
	digits = digits)

	output = print(latex_table,
	hline.after = c(-1),
	table.placement = 'htp',
	caption.placement = 'top',
	add.to.row = addtorow,
	include.rownames = FALSE,
	include.colnames = FALSE,
	type = 'latex',
	sanitize.text.function = identity,
	size = fontsize,
	)

	# create header
	if (!is.null(group_variable)) {

	group_length = rep(length(org_column_names), length(group_variable_values))

	# simple header
	table_header = paste0("& ", column_names[1], ".+", column_names[length(column_names)], " \\\\")
	print(table_header)
	# nested header
	table_header_line1 = paste0(paste0("& \\\\multicolumn\\{", group_length, "\\}\\{c\\}\\{",
	as.character(group_variable_values), "\\}"), collapse = " ")

	# positions
	rule_position = NULL
	for (i in seq(group_variable_values)) {
	stat_number = length(org_column_names)
	if (i == 1) {
	last_value = 2 + stat_number - 1
	rule_position[i] = paste0("2", "-", last_value)
	} else {
	rule_position[i] = paste0(last_value + 1, "-", last_value + stat_number)
	last_value = last_value + stat_number
	}
	}

	# rule
	table_header_line2 = paste0(paste0("\\\\cmidrule(lr)\\{", rule_position, "\\}"), collapse = " ")
	# stats
	table_header_line3 = paste0("& ", rep(org_column_names, length(group_variable_values)),
	collapse = " ")

	header_replacement = paste0(table_header_line1, " \\\\\\\\ \\\n", table_header_line2,
	" \\\n", table_header_line3, " \\\\")
	output = gsub(table_header, header_replacement, output)
	print(output)
	}

	# adding comment
	if (!is.null(note)) {
	clean_note = longText(note)
	header_replacement = paste0("begin\\{table\\}\\[htp\\]\\\n",
	"\\\\setlength\\{\\\\tabcolsep\\}\\{",
	tabcolsep,
	"pt\\}\\\n\\\\renewcommand\\{\\\\arraystretch\\}\\{",
	arraystretch,
	"\\}\\\n\\\\centering\\\n\\\\begin\\{threeparttable\\}\\\n")
	bottom = "end\\{tabular\\}\\\n\\\\endgroup\\\n"
	bottom_replacement = paste0("end\\{tabular\\}\\\n\\\\endgroup\\\n\\\\begin{tablenotes}\\\n\\\\", notesize, "\\\n\\\\item ",
	note,
	"\\\n\\\\end{tablenotes}")

	add_notes_table(output,
	comment = clean_note,
	header_replacement = header_replacement,
	bottom = bottom,
	bottom_replacement = bottom_replacement,
	closing = "end\\{tablenotes\\}",
	closing_replacement = "end\\{tablenotes\\}\\\n\\\\end{threeparttable}\\\n",
	filename = file)
	} else {
	header = "begin\\{table\\}\\[htp\\]\\\n"
	header_replacement = paste0("begin\\{table\\}\\[htp\\]\\\n",
	"\\\\setlength\\{\\\\tabcolsep\\}\\{",
	tabcolsep,
	"pt\\}\\\n\\\\renewcommand\\{\\\\arraystretch\\}\\{",
	arraystretch, "}\\\n")
	output = gsub(header, header_replacement, output)
	cat(output, file = file)
	}
	}


	# descriptive function
	getDescriptives = function(x) {
	x = as.numeric(x)
	m = mean(x, na.rm = TRUE)
	sd = sd(x, na.rm = TRUE)
	pm = mean(is.na(x))*100
	n = length(x[!is.na(x)])
	return(c(m, sd, pm, n))
	}


	# clean long text
	longText = function(text) {
	dtext = gsub("\n", "", text)
	dtext = gsub("\\s+", " ", dtext)
	return(dtext)
	}


	# add note to table
	add_notes_table = function(tab,
	comment = "",
	arraystretch = 0.8,
	tabcolsep = 10,
	filename = "",
	header = NULL,
	header_replacement = NULL,
	bottom = NULL,
	bottom_replacement = NULL ,
	closing = NULL,
	closing_replacement = NULL) {

	if (is.null(header)) {
	header = "begin\\{table\\}\\[htp\\]\\\n\\\\centering\\\n"
	}
	if (is.null(header_replacement)) {
	header_replacement = paste0("begin\\{table\\}\\[htp\\]\\\n",
	"\\\\setlength\\{\\\\tabcolsep\\}\\{",
	tabcolsep,
	"pt\\}\\\n\\\\renewcommand\\{\\\\arraystretch\\}\\{",
	arraystretch,
	"\\}\\\n",
	"\\\\begin\\{center\\}\\\n",
	"\\\\scriptsize\\\n",
	"\\\\begin\\{threeparttable\\}\\\n")
	}
	tab = gsub(header, header_replacement, tab)

	if (is.null(bottom)) {
	bottom = "end\\{tabular\\}\\n"
	}
	if (is.null(bottom_replacement)) {
	bottom_replacement = paste0("end\\{tabular\\}\\\n\\\\begin{tablenotes}\\\n\\\\scriptsize\\\n\\\\item ",
	comment,
	"\\\n\\\\end{tablenotes}\\\n")
	}
	tab = gsub(bottom, bottom_replacement, tab)

	if (is.null(closing)) {
	closing = "end\\{table\\}\\n"
	}
	if (is.null(closing_replacement)) {
	closing_replacement = paste0("end{threeparttable}\\\n",
	"\\\\end\\{center\\}\\\n",
	"\\\\end\\{table\\}\\\n"
	)
	}
	tab = gsub(closing, closing_replacement, tab)
	cat(tab, file = filename)
	}