3 ### Produce LaTeX and HTML tables from R objects.
5 ### Copyright 2000-2013 David B. Dahl <dahl@stat.byu.edu>
7 ### This file is part of the `xtable' library for R and related languages.
8 ### It is made available under the terms of the GNU General Public
9 ### License, version 2, or at your option, any later version,
10 ### incorporated herein by reference.
12 ### This program is distributed in the hope that it will be
13 ### useful, but WITHOUT ANY WARRANTY; without even the implied
14 ### warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 ### PURPOSE. See the GNU General Public License for more
18 ### You should have received a copy of the GNU General Public
19 ### License along with this program; if not, write to the Free
20 ### Software Foundation, Inc., 59 Temple Place - Suite 330, Boston,
21 ### MA 02111-1307, USA
23 xtable <- function(x, caption = NULL, label = NULL, align = NULL,
24 digits = NULL, display = NULL, auto = FALSE, ...) {
29 ## data.frame and matrix objects
31 xtable.data.frame <- function(x, caption = NULL, label = NULL, align = NULL,
32 digits = NULL, display = NULL, auto = FALSE,
34 logicals <- unlist(lapply(x, is.logical))
35 ##x[, logicals] <- lapply(x[, logicals], as.character)
36 ## Patch for logicals bug, no 1911
37 ## David Scott, <d.scott@auckland.ac.nz>, 2012-08-10
38 x[, logicals] <- lapply(x[, logicals, drop = FALSE], as.character)
39 characters <- unlist(lapply(x, is.character))
40 factors <- unlist(lapply(x, is.factor))
41 ints <- sapply(x, is.integer)
42 class(x) <- c("xtable","data.frame")
45 if(auto && is.null(align)) align <- xalign(x)
46 if(auto && is.null(digits)) digits <- xdigits(x)
47 if(auto && is.null(display)) display <- xdisplay(x)
48 align(x) <- switch(1+is.null(align), align,
49 c("r",c("r","l")[(characters|factors)+1]))
50 digits(x) <- switch(1+is.null(digits), digits, c(0,rep(2,ncol(x))))
51 ## Patch from Seth Falcon <sfalcon@fhcrc.org>, 18-May-2007
52 if (is.null(display)) {
53 display <- rep("f", ncol(x))
55 display[characters | factors] <- "s"
56 display <- c("s", display)
62 xtable.matrix <- function(x, caption = NULL, label = NULL, align = NULL,
63 digits = NULL, display = NULL, auto = FALSE, ...) {
64 return(xtable.data.frame(data.frame(x, check.names = FALSE),
65 caption = caption, label = label, align = align,
66 digits = digits, display = display, auto = auto))
70 ### table objects (of 1 or 2 dimensions) by Guido Gay, 9 Feb 2007
71 ### Fixed to pass R checks by DBD, 9 May 2007
72 xtable.table <- function(x, caption = NULL, label = NULL, align = NULL,
73 digits = NULL, display = NULL, auto = FALSE, ...) {
74 if (length(dim(x)) == 1) {
75 return(xtable.matrix(matrix(x,
76 dimnames = list(rownames(x),
78 caption = caption, label = label, align = align,
79 digits = digits, display = display, auto = auto))
80 } else if (length(dim(x))==2) {
81 return(xtable.matrix(matrix(x, ncol = dim(x)[2], nrow = dim(x)[1],
82 dimnames = list(rownames(x), colnames(x))),
83 caption = caption, label = label, align = align,
84 digits = digits, display = display, auto = auto))
86 stop("xtable.table is not implemented for tables of > 2 dimensions")
93 xtable.anova <- function(x, caption = NULL, label = NULL, align = NULL,
94 digits = NULL, display = NULL, auto = FALSE, ...) {
95 suggested.digits <- c(0,rep(2, ncol(x)))
96 suggested.digits[grep("Pr\\(>", names(x))+1] <- 4
97 suggested.digits[grep("P\\(>", names(x))+1] <- 4
98 suggested.digits[grep("Df", names(x))+1] <- 0
100 class(x) <- c("xtable","data.frame")
101 caption(x) <- caption
103 if(auto && is.null(align)) align <- xalign(x)
104 if(auto && is.null(digits)) digits <- xdigits(x)
105 if(auto && is.null(display)) display <- xdisplay(x)
106 align(x) <- switch(1+is.null(align), align, c("l",rep("r", ncol(x))))
107 digits(x) <- switch(1+is.null(digits), digits, suggested.digits)
108 display(x) <- switch(1+is.null(display), display, c("s",rep("f", ncol(x))))
115 xtable.aov <- function(x, caption = NULL, label = NULL, align = NULL,
116 digits = NULL, display = NULL, auto = FALSE, ...) {
117 return(xtable.anova(anova(x, ...), caption = caption, label = label,
118 align = align, digits = digits, display = display,
122 xtable.summary.aov <- function(x, caption = NULL, label = NULL, align = NULL,
123 digits = NULL, display = NULL, auto = FALSE,
125 return(xtable.anova(x[[1]], caption = caption, label = label, align = align,
126 digits = digits, display = display, auto = auto))
129 xtable.summary.aovlist <- function(x, caption = NULL, label = NULL,
130 align = NULL, digits = NULL, display = NULL,
132 for (i in 1:length(x)) {
134 result <- xtable.summary.aov(x[[i]], caption = caption,
136 align = align, digits = digits,
137 display = display, auto = auto)
139 result <- rbind(result,
140 xtable.anova(x[[i]][[1]], caption = caption,
141 label = label, align = align,
142 digits = digits, display = display,
149 xtable.aovlist <- function(x, caption = NULL, label = NULL, align = NULL,
150 digits = NULL, display = NULL, auto = FALSE, ...) {
151 return(xtable.summary.aovlist(summary(x), caption = caption, label = label,
152 align = align, digits = digits,
153 display = display, auto = auto))
160 xtable.lm <- function(x, caption = NULL, label = NULL, align = NULL,
161 digits = NULL, display = NULL, auto = FALSE, ...) {
162 return(xtable.summary.lm(summary(x), caption = caption, label = label,
163 align = align, digits = digits, display = display,
167 xtable.summary.lm <- function(x, caption = NULL, label = NULL, align = NULL,
168 digits = NULL, display = NULL, auto = FALSE,
170 x <- data.frame(x$coef, check.names = FALSE)
172 class(x) <- c("xtable","data.frame")
173 caption(x) <- caption
175 if(auto && is.null(align)) align <- xalign(x)
176 if(auto && is.null(digits)) digits <- xdigits(x)
177 if(auto && is.null(display)) display <- xdisplay(x)
178 align(x) <- switch(1+is.null(align), align, c("r","r","r","r","r"))
179 digits(x) <- switch(1+is.null(digits), digits, c(0,4,4,2,4))
180 display(x) <- switch(1+is.null(display), display, c("s","f","f","f","f"))
187 xtable.glm <- function(x, caption = NULL, label = NULL, align = NULL,
188 digits = NULL, display = NULL, auto = FALSE, ...) {
189 return(xtable.summary.glm(summary(x), caption = caption,
190 label = label, align = align,
191 digits = digits, display = display, auto = auto))
194 xtable.summary.glm <- function(x, caption = NULL, label = NULL, align = NULL,
195 digits = NULL, display = NULL, auto = FALSE,
197 return(xtable.summary.lm(x, caption = caption, label = label, align = align,
198 digits = digits, display = display, auto = auto))
204 xtable.prcomp <- function(x, caption = NULL, label = NULL, align = NULL,
205 digits = NULL, display = NULL, auto = FALSE, ...) {
206 x <- data.frame(x$rotation, check.names = FALSE)
208 class(x) <- c("xtable","data.frame")
209 caption(x) <- caption
211 if(auto && is.null(align)) align <- xalign(x)
212 if(auto && is.null(digits)) digits <- xdigits(x)
213 if(auto && is.null(display)) display <- xdisplay(x)
214 align(x) <- switch(1+is.null(align), align, c("r",rep("r", ncol(x))))
215 digits(x) <- switch(1+is.null(digits), digits, c(0,rep(4, ncol(x))))
216 display(x) <- switch(1+is.null(display), display, c("s",rep("f", ncol(x))))
220 xtable.summary.prcomp <- function(x, caption = NULL, label = NULL, align = NULL,
221 digits = NULL, display = NULL, auto = FALSE,
223 x <- data.frame(x$importance, check.names = FALSE)
225 class(x) <- c("xtable","data.frame")
226 caption(x) <- caption
228 if(auto && is.null(align)) align <- xalign(x)
229 if(auto && is.null(digits)) digits <- xdigits(x)
230 if(auto && is.null(display)) display <- xdisplay(x)
231 align(x) <- switch(1+is.null(align), align, c("r",rep("r", ncol(x))))
232 digits(x) <- switch(1+is.null(digits), digits, c(0,rep(4, ncol(x))))
233 display(x) <- switch(1+is.null(display), display, c("s",rep("f", ncol(x))))
238 # Slightly modified version of xtable.coxph contributed on r-help by
239 # Date: Wed, 2 Oct 2002 17:47:56 -0500 (CDT)
240 # From: Jun Yan <jyan@stat.wisc.edu>
241 # Subject: Re: [R] xtable for Cox model output
242 xtable.coxph <- function (x, caption = NULL, label = NULL, align = NULL,
243 digits = NULL, display = NULL, auto = FALSE, ...)
247 se <- sqrt(diag(cox$var))
248 if (is.null(cox$naive.var)) {
249 tmp <- cbind(beta, exp(beta), se, beta/se, 1 - pchisq((beta/se)^2, 1))
250 dimnames(tmp) <- list(names(beta),
251 c("coef", "exp(coef)", "se(coef)", "z", "p"))
254 tmp <- cbind( beta, exp(beta), se, beta/se,
255 signif(1 - pchisq((beta/se)^2, 1), digits - 1))
256 dimnames(tmp) <- list(names(beta),
257 c("coef", "exp(coef)", "robust se", "z", "p"))
259 return(xtable(tmp, caption = caption, label = label, align = align,
260 digits = digits, display = display, auto = auto))
263 # Additional method: xtable.ts
264 # Contributed by David Mitchell (davidm@netspeed.com.au)
266 xtable.ts <- function(x, caption = NULL, label = NULL, align = NULL,
267 digits = NULL, display = NULL, auto = FALSE, ...) {
268 if (inherits(x, "ts") && !is.null(ncol(x))) {
269 # COLNAMES <- paste(colnames(x));
270 tp.1 <- trunc(time(x))
271 tp.2 <- trunc(cycle(x))
272 day.abb <- c("Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat")
273 ROWNAMES <- switch(frequency(x),
275 "Arg2", "Arg3", # Dummy arguments
276 paste(tp.1, c("Q1", "Q2", "Q3", "Q4")[tp.2], sep = " "),
278 paste("Wk.", tp.1, " ", day.abb[tp.2], sep = ""),
279 "Arg8", "Arg9", "Arg10", "Arg11",
280 paste(tp.1, month.abb[tp.2], sep = " "))
281 tmp <- data.frame(x, row.names = ROWNAMES);
283 else if (inherits(x, "ts") && is.null(ncol(x))) {
284 COLNAMES <- switch(frequency(x),
286 "Arg2", "Arg3", # Dummy arguments
287 c("Q1", "Q2", "Q3", "Q4"),
290 "Arg8", "Arg9", "Arg10", "Arg11",
292 ROWNAMES <- seq(from = start(x)[1], to = end(x)[1])
293 tmp <- data.frame(matrix(c(rep(NA, start(x)[2] - 1), x,
294 rep(NA, frequency(x) - end(x)[2])),
295 ncol = frequency(x), byrow = TRUE),
296 row.names = ROWNAMES)
297 names(tmp) <- COLNAMES
299 return(xtable(tmp, caption = caption, label = label, align = align,
300 digits = digits, display = display, auto = auto))
303 # Suggested by Ajay Narottam Shah <ajayshah@mayin.org> in e-mail 2006/07/22
304 xtable.zoo <- function(x, ...) {
305 return(xtable(as.ts(x), ...))