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### xtable package
###
### Produce LaTeX and HTML tables from R objects.
###
### Copyright 2000-2013 David B. Dahl <dahl@stat.byu.edu>
###
### 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
xtable <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
UseMethod("xtable")
}
## data.frame and matrix objects
xtable.data.frame <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
logicals <- unlist(lapply(x, is.logical))
##x[, logicals] <- lapply(x[, logicals], as.character)
## Patch for logicals bug, no 1911
## David Scott, <d.scott@auckland.ac.nz>, 2012-08-10
x[, logicals] <- lapply(x[, logicals, drop = FALSE], as.character)
characters <- unlist(lapply(x, is.character))
factors <- unlist(lapply(x, is.factor))
ints <- sapply(x, is.integer)
class(x) <- c("xtable","data.frame")
caption(x) <- caption
label(x) <- label
align(x) <- switch(1+is.null(align), align,
c("r",c("r","l")[(characters|factors)+1]))
digits(x) <- switch(1+is.null(digits), digits, c(0,rep(2,ncol(x))))
## Patch from Seth Falcon <sfalcon@fhcrc.org>, 18-May-2007
if (is.null(display)) {
display <- rep("f", ncol(x))
display[ints] <- "d"
display[characters | factors] <- "s"
display <- c("s", display)
}
display(x) <- display
return(x)
}
xtable.matrix <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
return(xtable.data.frame(data.frame(x, check.names = FALSE),
caption = caption, label = label, align = align,
digits = digits, display = display))
}
### table objects (of 1 or 2 dimensions) by Guido Gay, 9 Feb 2007
### Fixed to pass R checks by DBD, 9 May 2007
xtable.table <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
if (length(dim(x)) == 1) {
return(xtable.matrix(matrix(x,
dimnames = list(rownames(x),
names(dimnames(x)))),
caption = caption, label = label,
align = align, digits = digits, display = display))
} else if (length(dim(x))==2) {
return(xtable.matrix(matrix(x, ncol = dim(x)[2], nrow = dim(x)[1],
dimnames = list(rownames(x), colnames(x))),
caption = caption, label = label,
align = align, digits = digits, display = display))
} else {
stop("xtable.table is not implemented for tables of > 2 dimensions")
}
}
## anova objects
xtable.anova <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
suggested.digits <- c(0,rep(2, ncol(x)))
suggested.digits[grep("Pr\\(>", names(x))+1] <- 4
suggested.digits[grep("P\\(>", names(x))+1] <- 4
suggested.digits[grep("Df", names(x))+1] <- 0
class(x) <- c("xtable","data.frame")
caption(x) <- caption
label(x) <- label
align(x) <- switch(1+is.null(align), align, c("l",rep("r", ncol(x))))
digits(x) <- switch(1+is.null(digits), digits, suggested.digits)
display(x) <- switch(1+is.null(display), display, c("s",rep("f", ncol(x))))
return(x)
}
## aov objects
xtable.aov <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
return(xtable.anova(anova(x, ...), caption = caption, label = label,
align = align, digits = digits, display = display))
}
xtable.summary.aov <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
return(xtable.anova(x[[1]], caption = caption, label = label,
align = align, digits = digits, display = display))
}
xtable.summary.aovlist <- function(x, caption = NULL, label = NULL,
align = NULL,
digits = NULL, display = NULL, ...) {
for (i in 1:length(x)) {
if (i == 1) {
result <- xtable.summary.aov(x[[i]], caption = caption,
label = label,
align = align, digits = digits,
display = display)
} else {
result <- rbind(result,
xtable.anova(x[[i]][[1]], caption = caption,
label = label, align = align,
digits = digits, display = display))
}
}
return(result)
}
xtable.aovlist <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
return(xtable.summary.aovlist(summary(x), caption = caption, label = label,
align = align, digits = digits,
display = display))
}
## lm objects
xtable.lm <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
return(xtable.summary.lm(summary(x), caption = caption, label = label,
align = align, digits = digits, display = display))
}
xtable.summary.lm <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
x <- data.frame(x$coef, check.names = FALSE)
class(x) <- c("xtable","data.frame")
caption(x) <- caption
label(x) <- label
align(x) <- switch(1+is.null(align), align, c("r","r","r","r","r"))
digits(x) <- switch(1+is.null(digits), digits, c(0,4,4,2,4))
display(x) <- switch(1+is.null(display), display, c("s","f","f","f","f"))
return(x)
}
## glm objects
xtable.glm <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
return(xtable.summary.glm(summary(x), caption = caption,
label = label, align = align,
digits = digits, display = display))
}
xtable.summary.glm <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
return(xtable.summary.lm(x, caption = caption, label = label,
align = align, digits = digits, display = display))
}
## prcomp objects
xtable.prcomp <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
x <- data.frame(x$rotation, check.names = FALSE)
class(x) <- c("xtable","data.frame")
caption(x) <- caption
label(x) <- label
align(x) <- switch(1+is.null(align), align, c("r",rep("r", ncol(x))))
digits(x) <- switch(1+is.null(digits), digits, c(0,rep(4, ncol(x))))
display(x) <- switch(1+is.null(display), display, c("s",rep("f", ncol(x))))
return(x)
}
xtable.summary.prcomp <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
x <- data.frame(x$importance, check.names = FALSE)
class(x) <- c("xtable","data.frame")
caption(x) <- caption
label(x) <- label
align(x) <- switch(1+is.null(align), align, c("r",rep("r", ncol(x))))
digits(x) <- switch(1+is.null(digits), digits, c(0,rep(4, ncol(x))))
display(x) <- switch(1+is.null(display), display, c("s",rep("f", ncol(x))))
return(x)
}
# Slightly modified version of xtable.coxph contributed on r-help by
# Date: Wed, 2 Oct 2002 17:47:56 -0500 (CDT)
# From: Jun Yan <jyan@stat.wisc.edu>
# Subject: Re: [R] xtable for Cox model output
xtable.coxph <- function (x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...)
{
cox <- x
beta <- cox$coef
se <- sqrt(diag(cox$var))
if (is.null(cox$naive.var)) {
tmp <- cbind(beta, exp(beta), se, beta/se, 1 - pchisq((beta/se)^2, 1))
dimnames(tmp) <- list(names(beta),
c("coef", "exp(coef)", "se(coef)", "z", "p"))
}
else {
tmp <- cbind( beta, exp(beta), se, beta/se,
signif(1 - pchisq((beta/se)^2, 1), digits - 1))
dimnames(tmp) <- list(names(beta),
c("coef", "exp(coef)", "robust se", "z", "p"))
}
return(xtable(tmp, caption = caption, label = label, align = align,
digits = digits, display = display))
}
# Additional method: xtable.ts
# Contributed by David Mitchell (davidm@netspeed.com.au)
# Date: July 2003
xtable.ts <- function(x, caption = NULL, label = NULL, align = NULL,
digits = NULL, display = NULL, ...) {
if (inherits(x, "ts") && !is.null(ncol(x))) {
# COLNAMES <- paste(colnames(x));
tp.1 <- trunc(time(x))
tp.2 <- trunc(cycle(x))
day.abb <- c("Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat")
ROWNAMES <- switch(frequency(x),
tp.1,
"Arg2", "Arg3", # Dummy arguments
paste(tp.1, c("Q1", "Q2", "Q3", "Q4")[tp.2], sep = " "),
"Arg5", "Arg6",
paste("Wk.", tp.1, " ", day.abb[tp.2], sep = ""),
"Arg8", "Arg9", "Arg10", "Arg11",
paste(tp.1, month.abb[tp.2], sep = " "))
tmp <- data.frame(x, row.names = ROWNAMES);
}
else if (inherits(x, "ts") && is.null(ncol(x))) {
COLNAMES <- switch(frequency(x),
"Value",
"Arg2", "Arg3", # Dummy arguments
c("Q1", "Q2", "Q3", "Q4"),
"Arg5", "Arg6",
day.abb,
"Arg8", "Arg9", "Arg10", "Arg11",
month.abb)
ROWNAMES <- seq(from = start(x)[1], to = end(x)[1])
tmp <- data.frame(matrix(c(rep(NA, start(x)[2] - 1), x,
rep(NA, frequency(x) - end(x)[2])),
ncol = frequency(x), byrow = TRUE),
row.names = ROWNAMES)
names(tmp) <- COLNAMES
}
return(xtable(tmp, caption = caption, label = label, align = align,
digits = digits, display = display))
}
# Suggested by Ajay Narottam Shah <ajayshah@mayin.org> in e-mail 2006/07/22
xtable.zoo <- function(x, ...) {
return(xtable(as.ts(x), ...))
}
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