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### xtable package
###
### Produce LaTeX and HTML tables from R objects.
###
### Copyright 2000-2013 David B. Dahl <dahl@stat.byu.edu>
###
### Maintained by David Scott <d.scott@auckland.ac.nz>
###
### This file is part of the `xtable' library for R and related languages.
### It is made available under the terms of the GNU General Public
### License, version 2, or at your option, any later version,
### incorporated herein by reference.
###
### This program is distributed in the hope that it will be
### useful, but WITHOUT ANY WARRANTY; without even the implied
### warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
### PURPOSE. See the GNU General Public License for more
### details.
###
### You should have received a copy of the GNU General Public
### License along with this program; if not, write to the Free
### Software Foundation, Inc., 59 Temple Place - Suite 330, Boston,
### MA 02111-1307, USA
print.xtable <- function(x,
type = getOption("xtable.type", "latex"),
file = getOption("xtable.file", ""),
append = getOption("xtable.append", FALSE),
floating = getOption("xtable.floating", TRUE),
floating.environment = getOption("xtable.floating.environment", "table"),
table.placement = getOption("xtable.table.placement", "ht"),
caption.placement = getOption("xtable.caption.placement", "bottom"),
caption.width = getOption("xtable.caption.width", NULL),
latex.environments = getOption("xtable.latex.environments", c("center")),
tabular.environment = getOption("xtable.tabular.environment", "tabular"),
size = getOption("xtable.size", NULL),
hline.after = getOption("xtable.hline.after", c(-1,0,nrow(x))),
NA.string = getOption("xtable.NA.string", ""),
include.rownames = getOption("xtable.include.rownames", TRUE),
include.colnames = getOption("xtable.include.colnames", TRUE),
only.contents = getOption("xtable.only.contents", FALSE),
add.to.row = getOption("xtable.add.to.row", NULL),
sanitize.text.function = getOption("xtable.sanitize.text.function", NULL),
sanitize.rownames.function = getOption("xtable.sanitize.rownames.function",
sanitize.text.function),
sanitize.colnames.function = getOption("xtable.sanitize.colnames.function",
sanitize.text.function),
math.style.negative = getOption("xtable.math.style.negative", FALSE),
math.style.exponents = getOption("xtable.math.style.exponents", FALSE),
html.table.attributes = getOption("xtable.html.table.attributes", "border=1"),
print.results = getOption("xtable.print.results", TRUE),
format.args = getOption("xtable.format.args", NULL),
rotate.rownames = getOption("xtable.rotate.rownames", FALSE),
rotate.colnames = getOption("xtable.rotate.colnames", FALSE),
booktabs = getOption("xtable.booktabs", FALSE),
scalebox = getOption("xtable.scalebox", NULL),
width = getOption("xtable.width", NULL),
comment = getOption("xtable.comment", TRUE),
timestamp = getOption("xtable.timestamp", date()),
...)
{
## If caption is length 2, treat the second value as the "short caption"
caption <- attr(x,"caption",exact = TRUE)
short.caption <- NULL
if (!is.null(caption) && length(caption) > 1){
short.caption <- caption[2]
caption <- caption[1]
}
## Claudio Agostinelli <claudio@unive.it> dated 2006-07-28 hline.after
## By default it print an \hline before and after the columns names
## independently they are printed or not and at the end of the table
## Old code that set hline.after should include c(-1, 0, nrow(x)) in the
## hline.after vector
## If you do not want any \hline inside the data, set hline.after to NULL
## PHEADER instead the string '\\hline\n' is used in the code
## Now hline.after counts how many time a position appear
## I left an automatic PHEADER in the longtable is this correct?
## Claudio Agostinelli <claudio@unive.it> dated 2006-07-28 include.rownames,
## include.colnames
pos <- 0
if (include.rownames) pos <- 1
## Claudio Agostinelli <claudio@unive.it> dated 2006-07-28
## hline.after checks
if (any(hline.after < -1) | any(hline.after > nrow(x))) {
stop("'hline.after' must be inside [-1, ", nrow(x), "]")
}
## Claudio Agostinelli <claudio@unive.it> dated 2006-07-28
## add.to.row checks
if (!is.null(add.to.row)) {
if (is.list(add.to.row) && length(add.to.row) == 2) {
if (is.null(names(add.to.row))) {
names(add.to.row) <- c('pos', 'command')
} else if (any(sort(names(add.to.row))!= c('command', 'pos'))) {
stop("the names of the elements of 'add.to.row' must be 'pos' and 'command'")
}
if (is.list(add.to.row$pos) && is.vector(add.to.row$command,
mode = 'character')) {
if ((npos <- length(add.to.row$pos)) !=
length(add.to.row$command)) {
stop("the length of 'add.to.row$pos' must be equal to the length of 'add.to.row$command'")
}
if (any(unlist(add.to.row$pos) < -1) |
any(unlist(add.to.row$pos) > nrow(x))) {
stop("the values in add.to.row$pos must be inside the interval [-1, ", nrow(x), "]")
}
} else {
stop("the first argument ('pos') of 'add.to.row' must be a list, the second argument ('command') must be a vector of mode character")
}
} else {
stop("'add.to.row' argument must be a list of length 2")
}
} else {
add.to.row <- list(pos = list(),
command = vector(length = 0, mode = "character"))
npos <- 0
}
## Claudio Agostinelli <claudio@unive.it> dated 2006-07-28 add.to.row
## Add further commands at the end of rows
if (type == "latex") {
## Original code before changes in version 1.6-1
## PHEADER <- "\\hline\n"
## booktabs code from Matthieu Stigler <matthieu.stigler@gmail.com>,
## 1 Feb 2012
if(!booktabs){
PHEADER <- "\\hline\n"
} else {
## This code replaced to fix bug #2309, David Scott, 8 Jan 2014
## PHEADER <- ifelse(-1%in%hline.after, "\\toprule\n", "")
## if(0%in%hline.after) {
## PHEADER <- c(PHEADER, "\\midrule\n")
## }
## if(nrow(x)%in%hline.after) {
## PHEADER <- c(PHEADER, "\\bottomrule\n")
## }
if (is.null(hline.after)){
PHEADER <- ""
} else {
hline.after <- sort(hline.after)
PHEADER <- rep("\\midrule\n", length(hline.after))
if (hline.after[1] == -1) {
PHEADER[1] <- "\\toprule\n"
}
if (hline.after[length(hline.after)] == nrow(x)) {
PHEADER[length(hline.after)] <- "\\bottomrule\n"
}
}
}
} else {
PHEADER <- ""
}
lastcol <- rep(" ", nrow(x)+2)
if (!is.null(hline.after)) {
## booktabs change - Matthieu Stigler: fill the hline arguments
## separately, 1 Feb 2012
##
## Code before booktabs change was:
## add.to.row$pos[[npos+1]] <- hline.after
if (!booktabs){
add.to.row$pos[[npos+1]] <- hline.after
} else {
for(i in 1:length(hline.after)) {
add.to.row$pos[[npos+i]] <- hline.after[i]
}
}
add.to.row$command <- c(add.to.row$command, PHEADER)
}
if ( length(add.to.row$command) > 0 ) {
for (i in 1:length(add.to.row$command)) {
addpos <- add.to.row$pos[[i]]
freq <- table(addpos)
addpos <- unique(addpos)
for (j in 1:length(addpos)) {
lastcol[addpos[j]+2] <- paste(lastcol[addpos[j]+2],
paste(rep(add.to.row$command[i],
freq[j]),
sep = "", collapse = ""),
sep = " ")
}
}
}
if (length(type)>1) stop("\"type\" must have length 1")
type <- tolower(type)
if (!all(!is.na(match(type, c("latex","html"))))) {
stop("\"type\" must be in {\"latex\", \"html\"}")
}
## Disabling the check on known floating environments as many users
## want to use additional environments.
## if (!all(!is.na(match(floating.environment,
## c("table","table*","sidewaystable",
## "margintable"))))) {
## stop("\"type\" must be in {\"table\", \"table*\", \"sidewaystable\", \"margintable\"}")
## }
if (("margintable" %in% floating.environment)
& (!is.null(table.placement))) {
warning("margintable does not allow for table placement; setting table.placement to NULL")
table.placement <- NULL
}
if (!is.null(table.placement) &&
!all(!is.na(match(unlist(strsplit(table.placement, split = "")),
c("H","h","t","b","p","!"))))) {
stop("\"table.placement\" must contain only elements of {\"h\",\"t\",\"b\",\"p\",\"!\"}")
}
if (!all(!is.na(match(caption.placement, c("bottom","top"))))) {
stop("\"caption.placement\" must be either {\"bottom\",\"top\"}")
}
if (type == "latex") {
BCOMMENT <- "% "
ECOMMENT <- "\n"
## See e-mail from "John S. Walker <jsw9c@uic.edu>" dated 5-19-2003
## regarding "texfloat"
## See e-mail form "Fernando Henrique Ferraz P. da Rosa"
## <academic@feferraz.net>" dated 10-28-2005 regarding "longtable"
if ( tabular.environment == "longtable" & floating == TRUE ) {
warning("Attempt to use \"longtable\" with floating = TRUE. Changing to FALSE.")
floating <- FALSE
}
if ( floating == TRUE ) {
## See e-mail from "Pfaff, Bernhard <Bernhard.Pfaff@drkw.com>"
## dated 7-09-2003 regarding "suggestion for an amendment of
## the source"
## See e-mail from "Mitchell, David"
## <David.Mitchell@dotars.gov.au>" dated 2003-07-09 regarding
## "Additions to R xtable package"
## See e-mail from "Garbade, Sven"
## <Sven.Garbade@med.uni-heidelberg.de> dated 2006-05-22
## regarding the floating environment.
BTABLE <- paste("\\begin{", floating.environment, "}",
ifelse(!is.null(table.placement),
paste("[", table.placement, "]", sep = ""),
""), "\n", sep = "")
if ( is.null(latex.environments) ||
(length(latex.environments) == 0) ) {
BENVIRONMENT <- ""
EENVIRONMENT <- ""
} else {
BENVIRONMENT <- ""
EENVIRONMENT <- ""
if ("center" %in% latex.environments){
BENVIRONMENT <- paste(BENVIRONMENT, "\\centering\n",
sep = "")
}
for (i in 1:length(latex.environments)) {
if (latex.environments[i] == "") next
if (latex.environments[i] != "center"){
BENVIRONMENT <- paste(BENVIRONMENT,
"\\begin{", latex.environments[i],
"}\n", sep = "")
EENVIRONMENT <- paste("\\end{", latex.environments[i],
"}\n", EENVIRONMENT, sep = "")
}
}
}
ETABLE <- paste("\\end{", floating.environment, "}\n", sep = "")
} else {
BTABLE <- ""
ETABLE <- ""
BENVIRONMENT <- ""
EENVIRONMENT <- ""
}
tmp.index.start <- 1
if ( ! include.rownames ) {
while ( attr(x, "align", exact = TRUE)[tmp.index.start] == '|' )
tmp.index.start <- tmp.index.start + 1
tmp.index.start <- tmp.index.start + 1
}
## Added "width" argument for use with "tabular*" or
## "tabularx" environments - CR, 7/2/12
if (is.null(width)){
WIDTH <-""
} else if (is.element(tabular.environment,
c("tabular", "longtable"))){
warning("Ignoring 'width' argument. The 'tabular' and 'longtable' environments do not support a width specification. Use another environment such as 'tabular*' or 'tabularx' to specify the width.")
WIDTH <- ""
} else {
WIDTH <- paste("{", width, "}", sep = "")
}
BTABULAR <-
paste("\\begin{", tabular.environment, "}",
WIDTH, "{",
paste(c(attr(x, "align",
exact = TRUE)[
tmp.index.start:length(attr(x, "align",
exact = TRUE))],
"}\n"),
sep = "", collapse = ""),
sep = "")
## fix 10-26-09 (robert.castelo@upf.edu) the following
## 'if' condition is added here to support
## a caption on the top of a longtable
if (tabular.environment == "longtable" && caption.placement == "top") {
if (is.null(short.caption)){
BCAPTION <- "\\caption{"
} else {
BCAPTION <- paste("\\caption[", short.caption, "]{", sep = "")
}
ECAPTION <- "} \\\\ \n"
if ((!is.null(caption)) && (type == "latex")) {
BTABULAR <- paste(BTABULAR, BCAPTION, caption, ECAPTION,
sep = "")
}
}
## Claudio Agostinelli <claudio@unive.it> dated 2006-07-28
## add.to.row position -1
BTABULAR <- paste(BTABULAR, lastcol[1], sep = "")
## the \hline at the end, if present, is set in full matrix
ETABULAR <- paste("\\end{", tabular.environment, "}\n", sep = "")
## Add scalebox - CR, 7/2/12
if (!is.null(scalebox)){
BTABULAR <- paste("\\scalebox{", scalebox, "}{\n", BTABULAR,
sep = "")
ETABULAR <- paste(ETABULAR, "}\n", sep = "")
}
## BSIZE contributed by Benno <puetz@mpipsykl.mpg.de> in e-mail
## dated Wednesday, December 01, 2004
if (is.null(size) || !is.character(size)) {
BSIZE <- ""
ESIZE <- ""
} else {
if(length(grep("^\\\\", size)) == 0){
size <- paste("\\", size, sep = "")
}
## Change suggested by Claudius Loehnert reported in Bug #6260
## BSIZE <- paste("{", size, "\n", sep = "")
## ESIZE <- "{\n"
BSIZE <- paste("\\begingroup", size, "\n", sep = "")
ESIZE <- "\\endgroup\n"
}
BLABEL <- "\\label{"
ELABEL <- "}\n"
## Added caption width (jeff.laake@nooa.gov)
if(!is.null(caption.width)){
BCAPTION <- paste("\\parbox{",caption.width,"}{",sep="")
ECAPTION <- "}"
} else {
BCAPTION <- NULL
ECAPTION <- NULL
}
if (is.null(short.caption)){
BCAPTION <- paste(BCAPTION,"\\caption{",sep="")
} else {
BCAPTION <- paste(BCAPTION,"\\caption[", short.caption, "]{", sep="")
}
ECAPTION <- paste(ECAPTION,"} \n",sep="")
BROW <- ""
EROW <- " \\\\ \n"
BTH <- ""
ETH <- ""
STH <- " & "
BTD1 <- " & "
BTD2 <- ""
BTD3 <- ""
ETD <- ""
} else {
BCOMMENT <- "<!-- "
ECOMMENT <- " -->\n"
BTABLE <- paste("<table ", html.table.attributes, ">\n", sep = "")
ETABLE <- "</table>\n"
BENVIRONMENT <- ""
EENVIRONMENT <- ""
BTABULAR <- ""
ETABULAR <- ""
BSIZE <- ""
ESIZE <- ""
BLABEL <- "<a name="
ELABEL <- "></a>\n"
BCAPTION <- paste("<caption align=\"", caption.placement, "\"> ",
sep = "")
ECAPTION <- " </caption>\n"
BROW <- "<tr>"
EROW <- " </tr>\n"
BTH <- " <th> "
ETH <- " </th> "
STH <- " </th> <th> "
BTD1 <- " <td align=\""
align.tmp <- attr(x, "align", exact = TRUE)
align.tmp <- align.tmp[align.tmp!="|"]
if (nrow(x) == 0) {
BTD2 <- matrix(nrow = 0, ncol = ncol(x)+pos)
} else {
BTD2 <- matrix(align.tmp[(2-pos):(ncol(x)+1)],
nrow = nrow(x), ncol = ncol(x)+pos, byrow = TRUE)
}
## Based on contribution from Jonathan Swinton <jonathan@swintons.net>
## in e-mail dated Wednesday, January 17, 2007
BTD2[regexpr("^p", BTD2)>0] <- "left"
BTD2[BTD2 == "r"] <- "right"
BTD2[BTD2 == "l"] <- "left"
BTD2[BTD2 == "c"] <- "center"
BTD3 <- "\"> "
ETD <- " </td>"
}
result <- string("", file = file, append = append)
info <- R.Version()
## modified Claudio Agostinelli <claudio@unive.it> dated 2006-07-28
## to set automatically the package version
if (comment){
result <- result + BCOMMENT + type + " table generated in " +
info$language + " " + info$major + "." + info$minor +
" by xtable " + packageDescription('xtable')$Version +
" package" + ECOMMENT
if (!is.null(timestamp)){
result <- result + BCOMMENT + timestamp + ECOMMENT
}
}
## Claudio Agostinelli <claudio@unive.it> dated 2006-07-28 only.contents
if (!only.contents) {
result <- result + BTABLE
result <- result + BENVIRONMENT
if ( floating == TRUE ) {
if ((!is.null(caption)) &&
(type == "html" ||caption.placement == "top")) {
result <- result + BCAPTION + caption + ECAPTION
}
if (!is.null(attr(x, "label", exact = TRUE)) &&
(type == "latex" && caption.placement == "top")) {
result <- result + BLABEL +
attr(x, "label", exact = TRUE) + ELABEL
}
}
result <- result + BSIZE
result <- result + BTABULAR
}
## Claudio Agostinelli <claudio@unive.it> dated 2006-07-28
## include.colnames, include.rownames
if (include.colnames) {
result <- result + BROW + BTH
if (include.rownames) {
result <- result + STH
}
## David G. Whiting in e-mail 2007-10-09
if (is.null(sanitize.colnames.function)) {
CNAMES <- sanitize(names(x), type = type)
} else {
CNAMES <- sanitize.colnames.function(names(x))
}
if (rotate.colnames) {
##added by Markus Loecher, 2009-11-16
CNAMES <- paste("\\begin{sideways}", CNAMES, "\\end{sideways}")
}
result <- result + paste(CNAMES, collapse = STH)
result <- result + ETH + EROW
}
cols <- matrix("", nrow = nrow(x), ncol = ncol(x)+pos)
if (include.rownames) {
## David G. Whiting in e-mail 2007-10-09
if (is.null(sanitize.rownames.function)) {
RNAMES <- sanitize(row.names(x), type = type)
} else {
RNAMES <- sanitize.rownames.function(row.names(x))
}
if (rotate.rownames) {
##added by Markus Loecher, 2009-11-16
RNAMES <- paste("\\begin{sideways}", RNAMES, "\\end{sideways}")
}
cols[, 1] <- RNAMES
}
## Begin vectorizing the formatting code by Ian Fellows [ian@fellstat.com]
## 06 Dec 2011
##
## disp <- function(y) {
## if (is.factor(y)) {
## y <- levels(y)[y]
## }
## if (is.list(y)) {
## y <- unlist(y)
## }
## return(y)
## }
varying.digits <- is.matrix( attr( x, "digits", exact = TRUE ) )
## Code for letting "digits" be a matrix was provided by
## Arne Henningsen <ahenningsen@agric-econ.uni-kiel.de>
## in e-mail dated 2005-06-04.
##if( !varying.digits ) {
## modified Claudio Agostinelli <claudio@unive.it> dated 2006-07-28
## attr(x,"digits") <- matrix( attr( x, "digits",exact=TRUE ),
## nrow = nrow(x), ncol = ncol(x)+1, byrow = TRUE )
##}
for(i in 1:ncol(x)) {
xcol <- x[, i]
if(is.factor(xcol))
xcol <- as.character(xcol)
if(is.list(xcol))
xcol <- sapply(xcol, unlist)
ina <- is.na(xcol)
is.numeric.column <- is.numeric(xcol)
if(is.character(xcol)) {
cols[, i+pos] <- xcol
} else {
if (is.null(format.args)){
format.args <- list()
}
if (is.null(format.args$decimal.mark)){
format.args$decimal.mark <- options()$OutDec
}
if(!varying.digits){
curFormatArgs <-
c(list(
x = xcol,
format =
ifelse(attr(x, "digits", exact = TRUE )[i+1] < 0, "E",
attr(x, "display", exact = TRUE )[i+1]),
digits = abs(attr(x, "digits", exact = TRUE )[i+1])),
format.args)
cols[, i+pos] <- do.call("formatC", curFormatArgs)
}else{
for( j in 1:nrow( cols ) ) {
curFormatArgs <-
c(list(
x = xcol[j],
format =
ifelse(attr(x, "digits", exact = TRUE )[j, i+1] < 0,
"E", attr(x, "display", exact = TRUE )[i+1]),
digits =
abs(attr(x, "digits", exact = TRUE )[j, i+1])),
format.args)
cols[j, i+pos] <- do.call("formatC", curFormatArgs)
}
}
}
## End Ian Fellows changes
if ( any(ina) ) cols[ina, i+pos] <- NA.string
## Based on contribution from Jonathan Swinton <jonathan@swintons.net>
## in e-mail dated Wednesday, January 17, 2007
if ( is.numeric.column ) {
cols[, i+pos] <-
sanitize.numbers(cols[, i+pos], type = type,
math.style.negative = math.style.negative,
math.style.exponents = math.style.exponents)
} else {
if (is.null(sanitize.text.function)) {
cols[, i+pos] <- sanitize(cols[, i+pos], type = type)
} else {
cols[, i+pos] <- sanitize.text.function(cols[, i+pos])
}
}
}
multiplier <- 5
full <- matrix("", nrow = nrow(x), ncol = multiplier*(ncol(x)+pos)+2)
full[, 1] <- BROW
full[, multiplier*(0:(ncol(x)+pos-1))+2] <- BTD1
full[, multiplier*(0:(ncol(x)+pos-1))+3] <- BTD2
full[, multiplier*(0:(ncol(x)+pos-1))+4] <- BTD3
full[, multiplier*(0:(ncol(x)+pos-1))+5] <- cols
full[, multiplier*(0:(ncol(x)+pos-1))+6] <- ETD
full[, multiplier*(ncol(x)+pos)+2] <- paste(EROW, lastcol[-(1:2)],
sep = " ")
if (type == "latex") full[, 2] <- ""
result <- result + lastcol[2] + paste(t(full), collapse = "")
if (!only.contents) {
if (tabular.environment == "longtable") {
## booktabs change added the if() - 1 Feb 2012
if(!booktabs) {
result <- result + PHEADER
}
## fix 10-27-09 Liviu Andronic (landronimirc@gmail.com) the
## following 'if' condition is inserted in order to avoid
## that bottom caption interferes with a top caption of a longtable
if(caption.placement == "bottom"){
if ((!is.null(caption)) && (type == "latex")) {
result <- result + BCAPTION + caption + ECAPTION
}
}
if (!is.null(attr(x, "label", exact = TRUE))) {
result <- result + BLABEL + attr(x, "label", exact = TRUE) +
ELABEL
}
ETABULAR <- "\\end{longtable}\n"
}
result <- result + ETABULAR
result <- result + ESIZE
if ( floating == TRUE ) {
if ((!is.null(caption)) &&
(type == "latex" && caption.placement == "bottom")) {
result <- result + BCAPTION + caption + ECAPTION
}
if (!is.null(attr(x, "label", exact = TRUE)) &&
caption.placement == "bottom") {
result <- result + BLABEL + attr(x, "label", exact = TRUE) +
ELABEL
}
}
result <- result + EENVIRONMENT
result <- result + ETABLE
}
result <- sanitize.final(result, type = type)
if (print.results){
print(result)
}
return(invisible(result$text))
}
"+.string" <- function(x, y) {
x$text <- paste(x$text, as.string(y)$text, sep = "")
return(x)
}
print.string <- function(x, ...) {
cat(x$text, file = x$file, append = x$append)
return(invisible())
}
string <- function(text, file = "", append = FALSE) {
x <- list(text = text, file = file, append = append)
class(x) <- "string"
return(x)
}
as.string <- function(x, file = "", append = FALSE) {
if (is.null(attr(x, "class", exact = TRUE)))
switch(data.class(x),
character = return(string(x, file, append)),
numeric = return(string(as.character(x), file, append)),
stop("Cannot coerce argument to a string"))
if (class(x) == "string")
return(x)
stop("Cannot coerce argument to a string")
}
is.string <- function(x) {
return(class(x) == "string")
}
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