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table.R
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table.R
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#' Create tables in LaTeX, HTML, Markdown and reStructuredText
#'
#' This is a very simple table generator. It is simple by design. It is not
#' intended to replace any other R packages for making tables.
#'
#' Missing values (\code{NA}) in the table are displayed as \code{NA} by
#' default. If you want to display them with other characters, you can set the
#' option \code{knitr.kable.NA}, e.g. \code{options(knitr.kable.NA = '')} to
#' hide \code{NA} values.
#' @param x an R object (typically a matrix or data frame)
#' @param format a character string; possible values are \code{latex},
#' \code{html}, \code{markdown}, \code{pandoc}, and \code{rst}; this will be
#' automatically determined if the function is called within \pkg{knitr}; it
#' can also be set in the global option \code{knitr.table.format}; if
#' \code{format} is a function, it must return a character string
#' @param digits the maximum number of digits for numeric columns (passed to
#' \code{round()}); it can also be a vector of length \code{ncol(x)} to set
#' the number of digits for individual columns
#' @param row.names a logical value indicating whether to include row names; by
#' default, row names are included if \code{rownames(x)} is neither
#' \code{NULL} nor identical to \code{1:nrow(x)}
#' @param col.names a character vector of column names to be used in the table
#' @param align the alignment of columns: a character vector consisting of
#' \code{'l'} (left), \code{'c'} (center) and/or \code{'r'} (right); by
#' default, numeric columns are right-aligned, and other columns are
#' left-aligned; if \code{align = NULL}, the default alignment is used;
#' alternatively, if \code{length(align) == 1L}, the string will be expanded
#' to a vector of individual letters unless the output format is LaTeX; for
#' example, \code{'clc'} will be converted to \code{c('c', 'l', 'c')}
#' @param caption the table caption
#' @param format.args a list of arguments to be passed to \code{\link{format}()}
#' to format table values, e.g. \code{list(big.mark = ',')}
#' @param escape escape special characters when producing HTML or LaTeX tables
#' @param ... other arguments (see examples)
#' @return A character vector of the table source code.
#' @seealso Other R packages such as \pkg{huxtable}, \pkg{xtable},
#' \pkg{kableExtra}, and \pkg{tables} for HTML and LaTeX tables, and
#' \pkg{ascii} and \pkg{pander} for different flavors of markdown output and
#' some advanced features and table styles.
#' @note The tables for \code{format = 'markdown'} also work for Pandoc when the
#' \code{pipe_tables} extension is enabled (this is the default behavior for
#' Pandoc >= 1.10).
#'
#' When using \code{kable()} as a \emph{top-level} expression, you do not need
#' to explicitly \code{print()} it due to R's automatic implicit printing.
#' When it is wrapped inside other expressions (such as a \code{\link{for}}
#' loop), you must explicitly \code{print(kable(...))}.
#' @references See
#' \url{https://github.com/yihui/knitr-examples/blob/master/091-knitr-table.Rnw}
#' for some examples in LaTeX, but they also apply to other document formats.
#' @export
#' @examples kable(head(iris), format = 'latex')
#' kable(head(iris), format = 'html')
#' kable(head(iris), format = 'latex', caption = 'Title of the table')
#' kable(head(iris), format = 'html', caption = 'Title of the table')
#' # use the booktabs package
#' kable(mtcars, format = 'latex', booktabs = TRUE)
#' # use the longtable package
#' kable(matrix(1000, ncol=5), format = 'latex', digits = 2, longtable = TRUE)
#' # add some table attributes
#' kable(head(iris), format = 'html', table.attr = 'id="mytable"')
#' # reST output
#' kable(head(mtcars), format = 'rst')
#' # no row names
#' kable(head(mtcars), format = 'rst', row.names = FALSE)
#' # R Markdown/Github Markdown tables
#' kable(head(mtcars[, 1:5]), format = 'markdown')
#' # no inner padding
#' kable(head(mtcars), format = 'markdown', padding = 0)
#' # more padding
#' kable(head(mtcars), format = 'markdown', padding = 2)
#' # Pandoc tables
#' kable(head(mtcars), format = 'pandoc', caption = 'Title of the table')
#' # format numbers using , as decimal point, and ' as thousands separator
#' x = as.data.frame(matrix(rnorm(60, 1e6, 1e4), 10))
#' kable(x, format.args = list(decimal.mark = ',', big.mark = "'"))
#' # save the value
#' x = kable(mtcars, format = 'html')
#' cat(x, sep = '\n')
#' # can also set options(knitr.table.format = 'html') so that the output is HTML
kable = function(
x, format, digits = getOption('digits'), row.names = NA, col.names = NA,
align, caption = NULL, format.args = list(), escape = TRUE, ...
) {
# determine the table format
if (missing(format) || is.null(format)) format = getOption('knitr.table.format')
if (is.null(format)) format = if (is.null(pandoc_to())) switch(
out_format() %n% 'markdown',
latex = 'latex', listings = 'latex', sweave = 'latex',
html = 'html', markdown = 'markdown', rst = 'rst',
stop('table format not implemented yet!')
) else if (isTRUE(opts_knit$get('kable.force.latex')) && is_latex_output()) {
# force LaTeX table because Pandoc's longtable may not work well with floats
# http://tex.stackexchange.com/q/276699/9128
'latex'
} else 'pandoc'
if (is.function(format)) format = format()
# expand align if applicable
if (format != 'latex' && !missing(align) && length(align) == 1L)
align = strsplit(align, '')[[1]]
# create a label for bookdown if applicable
if (!is.null(caption) && !is.na(caption)) caption = paste0(
create_label('tab:', opts_current$get('label'), latex = (format == 'latex')),
caption
)
if (inherits(x, 'list')) {
# if the output is for Pandoc and we want multiple tabular in one table, we
# should use the latex format instead, because Pandoc does not support
# Markdown in LaTeX yet https://github.com/jgm/pandoc/issues/2453
if (format == 'pandoc' && is_latex_output()) format = 'latex'
res = lapply(
x, kable, format = format, digits = digits, row.names = row.names,
col.names = col.names, align = align, caption = NA,
format.args = format.args, escape = escape, ...
)
res = unlist(lapply(res, paste, collapse = '\n'))
res = if (format == 'latex') {
kable_latex_caption(res, caption)
} else if (format == 'html' || (format == 'pandoc' && is_html_output())) kable_html(
matrix(paste0('\n\n', res, '\n\n'), 1), caption = caption, escape = FALSE,
table.attr = 'class="kable_wrapper"'
) else {
res = paste(res, collapse = '\n\n')
if (format == 'pandoc') kable_pandoc_caption(res, caption) else res
}
return(structure(res, format = format, class = 'knitr_kable'))
}
if (identical(col.names, NA)) col.names = colnames(x)
if (!is.matrix(x)) x = as.data.frame(x)
m = ncol(x)
# numeric columns
isn = if (is.matrix(x)) rep(is.numeric(x), m) else sapply(x, is.numeric)
if (missing(align) || (format == 'latex' && is.null(align)))
align = ifelse(isn, 'r', 'l')
# rounding
digits = rep(digits, length.out = m)
for (j in seq_len(m)) {
if (is_numeric(x[, j])) x[, j] = round(x[, j], digits[j])
}
if (any(isn)) {
if (is.matrix(x)) {
if (is.table(x) && length(dim(x)) == 2) class(x) = 'matrix'
x = format_matrix(x, format.args)
} else x[, isn] = format_args(x[, isn], format.args)
}
if (is.na(row.names)) row.names = has_rownames(x)
if (!is.null(align)) align = rep(align, length.out = m)
if (row.names) {
x = cbind(' ' = rownames(x), x)
if (!is.null(col.names)) col.names = c(' ', col.names)
if (!is.null(align)) align = c('l', align) # left align row names
}
n = nrow(x)
x = replace_na(base::format(as.matrix(x), trim = TRUE, justify = 'none'), is.na(x))
if (!is.matrix(x)) x = matrix(x, nrow = n)
if (ncol(x) == 1 && format == 'pandoc') format = 'markdown'
x = trimws(x)
colnames(x) = col.names
if (format != 'latex' && length(align) && !all(align %in% c('l', 'r', 'c')))
stop("'align' must be a character vector of possible values 'l', 'r', and 'c'")
attr(x, 'align') = align
res = do.call(
paste('kable', format, sep = '_'),
list(x = x, caption = caption, escape = escape, ...)
)
structure(res, format = format, class = 'knitr_kable')
}
# as.data.frame() does not allow duplicate row names (#898)
format_matrix = function(x, args) {
nms = rownames(x)
rownames(x) = NULL
x = as.matrix(format_args(as.data.frame(x), args))
rownames(x) = nms
x
}
format_args = function(x, args = list()) {
args$x = x
args$trim = TRUE
replace_na(do.call(format, args), is.na(x))
}
replace_na = function(x, which = is.na(x), to = getOption('knitr.kable.NA')) {
if (is.null(to)) return(x)
x[which] = to
x
}
has_rownames = function(x) {
!is.null(rownames(x)) && !identical(rownames(x), as.character(seq_len(NROW(x))))
}
#' @export
print.knitr_kable = function(x, ...) {
if (!(attr(x, 'format') %in% c('html', 'latex'))) cat('\n\n')
cat(x, sep = '\n')
}
#' @export
knit_print.knitr_kable = function(x, ...) {
x = paste(c(
if (!(attr(x, 'format') %in% c('html', 'latex'))) c('', ''), x, '\n'
), collapse = '\n')
asis_output(x)
}
kable_latex = function(
x, booktabs = FALSE, longtable = FALSE, valign = 't', centering = TRUE,
vline = getOption('knitr.table.vline', if (booktabs) '' else '|'),
toprule = getOption('knitr.table.toprule', if (booktabs) '\\toprule' else '\\hline'),
bottomrule = getOption('knitr.table.bottomrule', if (booktabs) '\\bottomrule' else '\\hline'),
midrule = getOption('knitr.table.midrule', if (booktabs) '\\midrule' else '\\hline'),
linesep = if (booktabs) c('', '', '', '', '\\addlinespace') else '\\hline',
caption = NULL, caption.short = '', table.envir = if (!is.null(caption)) 'table',
escape = TRUE
) {
if (!is.null(align <- attr(x, 'align'))) {
align = paste(align, collapse = vline)
align = paste0('{', align, '}')
}
centering = if (centering && !is.null(caption)) '\n\\centering'
# vertical align only if 'caption' is not NULL (may be NA) or 'valign' has
# been explicitly specified
valign = if ((!is.null(caption) || !missing(valign)) && valign != '') {
sprintf('[%s]', valign)
} else ''
if (identical(caption, NA)) caption = NULL
env1 = sprintf('\\begin{%s}\n', table.envir)
env2 = sprintf('\n\\end{%s}', table.envir)
if (caption.short != '') caption.short = paste0('[', caption.short, ']')
cap = if (is.null(caption)) '' else sprintf('\n\\caption%s{%s}', caption.short, caption)
if (nrow(x) == 0) midrule = ""
linesep = if (nrow(x) > 1) {
c(rep(linesep, length.out = nrow(x) - 2), linesep[[1L]], '')
} else rep('', nrow(x))
linesep = ifelse(linesep == "", linesep, paste0('\n', linesep))
if (escape) x = escape_latex(x)
if (!is.character(toprule)) toprule = NULL
if (!is.character(bottomrule)) bottomrule = NULL
tabular = if (longtable) 'longtable' else 'tabular'
paste(c(
if (!longtable) c(env1, cap, centering),
sprintf('\n\\begin{%s}%s', tabular, valign), align,
if (longtable && cap != '') c(cap, '\\\\'),
sprintf('\n%s', toprule), '\n',
if (!is.null(cn <- colnames(x))) {
if (escape) cn = escape_latex(cn)
paste0(paste(cn, collapse = ' & '), sprintf('\\\\\n%s\n', midrule))
},
paste0(apply(x, 1, paste, collapse = ' & '), sprintf('\\\\%s', linesep),
collapse = '\n'),
sprintf('\n%s', bottomrule),
sprintf('\n\\end{%s}', tabular),
if (!longtable) env2
), collapse = '')
}
kable_latex_caption = function(x, caption) {
paste(c(
'\\begin{table}\n', sprintf('\\caption{%s}\n', caption), x, '\n\\end{table}'
), collapse = '')
}
kable_html = function(x, table.attr = '', caption = NULL, escape = TRUE, ...) {
table.attr = trimws(table.attr)
# need a space between <table and attributes
if (nzchar(table.attr)) table.attr = paste('', table.attr)
align = if (is.null(align <- attr(x, 'align'))) '' else {
sprintf(' style="text-align:%s;"', c(l = 'left', c = 'center', r = 'right')[align])
}
if (identical(caption, NA)) caption = NULL
cap = if (length(caption)) sprintf('\n<caption>%s</caption>', caption) else ''
if (escape) x = escape_html(x)
paste0(c(
sprintf('<table%s>%s', table.attr, cap),
if (!is.null(cn <- colnames(x))) {
if (escape) cn = escape_html(cn)
c(' <thead>', ' <tr>', sprintf(' <th%s> %s </th>', align, cn), ' </tr>', ' </thead>')
},
'<tbody>',
paste(
' <tr>',
apply(x, 1, function(z) paste(sprintf(' <td%s> %s </td>', align, z), collapse = '\n')),
' </tr>', sep = '\n'
),
'</tbody>',
'</table>'
), collapse = '\n')
}
#' Generate tables for Markdown and reST
#'
#' This function provides the basis for Markdown and reST tables.
#' @param x the data matrix
#' @param sep.row a chracter vector of length 3 that specifies the separators
#' before the header, after the header and at the end of the table,
#' respectively
#' @param sep.col the column separator
#' @param padding the number of spaces for the table cell padding
#' @param align.fun a function to process the separator under the header
#' according to alignment
#' @return A character vector of the table content.
#' @noRd
kable_mark = function(x, sep.row = c('=', '=', '='), sep.col = ' ', padding = 0,
align.fun = function(s, a) s, rownames.name = '', ...) {
# when the column separator is |, replace existing | with its HTML entity
if (sep.col == '|') for (j in seq_len(ncol(x))) {
x[, j] = gsub('\\|', '|', x[, j])
}
l = if (prod(dim(x)) > 0) apply(x, 2, function(z) max(nchar(z, type = 'width'), na.rm = TRUE))
cn = colnames(x)
if (length(cn) > 0) {
cn[is.na(cn)] = "NA"
if (sep.col == '|') cn = gsub('\\|', '|', cn)
if (grepl('^\\s*$', cn[1L])) cn[1L] = rownames.name # no empty cells for reST
l = pmax(if (length(l) == 0) 0 else l, nchar(cn, type = 'width'))
}
align = attr(x, 'align')
padding = padding * if (length(align) == 0) 2 else {
ifelse(align == 'c', 2, 1)
}
l = pmax(l + padding, 3) # at least of width 3 for Github Markdown
s = unlist(lapply(l, function(i) paste(rep(sep.row[2], i), collapse = '')))
res = rbind(if (!is.na(sep.row[1])) s, cn, align.fun(s, align),
x, if (!is.na(sep.row[3])) s)
apply(mat_pad(res, l, align), 1, paste, collapse = sep.col)
}
kable_rst = function(x, rownames.name = '\\', ...) {
kable_mark(x, rownames.name = rownames.name)
}
# actually R Markdown
kable_markdown = function(x, padding = 1, ...) {
if (is.null(colnames(x))) {
warning('The table should have a header (column names)')
colnames(x) = rep('', ncol(x))
}
res = kable_mark(x, c(NA, '-', NA), '|', padding, align.fun = function(s, a) {
if (is.null(a)) return(s)
r = c(l = '^.', c = '^.|.$', r = '.$')
for (i in seq_along(s)) {
s[i] = gsub(r[a[i]], ':', s[i])
}
s
}, ...)
sprintf('|%s|', res)
}
kable_pandoc = function(x, caption = NULL, padding = 1, ...) {
tab = kable_mark(
x, c(NA, '-', if (is_blank(colnames(x))) '-' else NA),
padding = padding, ...
)
kable_pandoc_caption(tab, caption)
}
kable_pandoc_caption = function(x, caption) {
if (identical(caption, NA)) caption = NULL
if (length(caption)) c(paste('Table:', caption), "", x) else x
}
# pad a matrix
mat_pad = function(m, width, align = NULL) {
n = nrow(m); p = ncol(m)
res = matrix('', nrow = n, ncol = p)
if (n * p == 0) return(res)
stopifnot(p == length(width))
side = rep('both', p)
if (!is.null(align)) side = c(l = 'right', c = 'both', r = 'left')[align]
apply(m, 2, function(x) max(nchar(x, 'width') - nchar(x, 'chars')))
matrix(pad_width(c(m), rep(width, each = n), rep(side, each = n)), ncol = p)
}
# pad a character vector to width (instead of number of chars), considering the
# case of width > chars (e.g. CJK chars)
pad_width = function(x, width, side) {
if (!all(side %in% c('left', 'right', 'both')))
stop("'side' must be 'left', 'right', or 'both'")
w = width - nchar(x, 'width')
w1 = floor(w / 2) # the left half of spaces when side = 'both'
s1 = v_spaces(w * (side == 'left') + w1 * (side == 'both'))
s2 = v_spaces(w * (side == 'right') + (w - w1) * (side == 'both'))
paste0(s1, x, s2)
}
# vectorized over n to generate sequences of spaces
v_spaces = function(n) {
unlist(lapply(n, highr:::spaces))
}