pkg/inst/doc/xtableGallery.snw

   1 %\VignetteIndexEntry{xtable Gallery}
   2 %\VignetteDepends{xtable}
   3 %\VignetteKeywords{LaTeX,HTML,table}
   4 %\VignettePackage{xtable}
   5
   6 %**************************************************************************
   7 %
   8 % # $Id:$
   9
  10 % $Revision:  $
  11 % $Author: $
  12 % $Date:  $
  13
  14 <<echo=FALSE,eval=FALSE>>=
  15 makeme <- function() {
  16         # I am a convenience function for debugging and can be ignored
  17         setwd("C:/JonathanSwinton/PathwayModeling/src/R/SourcePackages/xtable/inst/doc")
  18         Sweave("xtableGallery.RnW",stylepath=FALSE)
  19 }
  20 makeme()
  21 @
  22
  23 \documentclass[letterpaper]{article}
  24
  25 \title{
  26 The xtable gallery
  27 }
  28 \author{Jonathan Swinton <jonathan@swintons.net>\\ with small contributions from others}
  29
  30 \usepackage{Sweave}
  31 \SweaveOpts{prefix.string=figdir/fig,debug=TRUE,eps=FALSE,echo=TRUE}
  32 \usepackage{rotating}
  33 \usepackage{longtable}
  34 \usepackage{booktabs}
  35 \usepackage{tabularx}
  36 %\usepackage{hyperref}
  37 \begin{document}
  38
  39 \maketitle
  40 \section{Summary}
  41 This document gives a gallery of tables which can be made
  42 by using the {\tt xtable} package to create \LaTeX\ output.
  43 It doubles as a regression check for the package.
  44
  45 <<>>=
  46 library(xtable)
  47 @
  48
  49 \section{Gallery}
  50 \subsection{Data frame}
  51 Load example dataset
  52 <<>>=
  53 data(tli)
  54
  55 ## Demonstrate data.frame
  56 tli.table <- xtable(tli[1:10,])
  57 digits(tli.table)[c(2,6)] <- 0
  58 @
  59 <<results=tex>>=
  60 print(tli.table,floating=FALSE)
  61 @
  62
  63 \subsection{Matrix}
  64 <<>>=
  65 design.matrix <- model.matrix(~ sex*grade, data=tli[1:10,])
  66 design.table <- xtable(design.matrix)
  67 @
  68 <<results=tex>>=
  69 print(design.table,floating=FALSE)
  70 @
  71
  72 \subsection{aov}
  73 <<>>=
  74 fm1 <- aov(tlimth ~ sex + ethnicty + grade + disadvg, data=tli)
  75 fm1.table <- xtable(fm1)
  76 @
  77 <<results=tex>>=
  78 print(fm1.table,floating=FALSE)
  79 @
  80 \subsection{lm}
  81 <<>>=
  82 fm2 <- lm(tlimth ~ sex*ethnicty, data=tli)
  83 fm2.table <- xtable(fm2)
  84 @
  85 <<results=tex>>=
  86 print(fm2.table,floating=FALSE)
  87 @
  88 \subsubsection{anova object}
  89
  90 <<results=tex>>=
  91 print(xtable(anova(fm2)),floating=FALSE)
  92 @
  93 \subsubsection{Another anova object}
  94 <<>>=
  95 fm2b <- lm(tlimth ~ ethnicty, data=tli)
  96 @
  97 <<results=tex>>=
  98 print(xtable(anova(fm2b,fm2)),floating=FALSE)
  99 @
 100
 101
 102 \subsection{glm}
 103
 104 <<>>=
 105
 106 ## Demonstrate glm
 107 fm3 <- glm(disadvg ~ ethnicty*grade, data=tli, family=binomial())
 108 fm3.table <- xtable(fm3)
 109 @
 110 <<results=tex>>=
 111 print(fm3.table,floating=FALSE)
 112 @
 113
 114 \subsubsection{anova object}
 115 @
 116 <<results=tex>>=
 117 print(xtable(anova(fm3)),floating=FALSE)
 118 @
 119
 120
 121 \subsection{More aov}
 122 <<>>=
 123
 124 ## Demonstrate aov
 125 ## Taken from help(aov) in R 1.1.1
 126 ## From Venables and Ripley (1997) p.210.
 127 N <- c(0,1,0,1,1,1,0,0,0,1,1,0,1,1,0,0,1,0,1,0,1,1,0,0)
 128 P <- c(1,1,0,0,0,1,0,1,1,1,0,0,0,1,0,1,1,0,0,1,0,1,1,0)
 129 K <- c(1,0,0,1,0,1,1,0,0,1,0,1,0,1,1,0,0,0,1,1,1,0,1,0)
 130 yield <- c(49.5,62.8,46.8,57.0,59.8,58.5,55.5,56.0,62.8,55.8,69.5,55.0,
 131            62.0,48.8,45.5,44.2,52.0,51.5,49.8,48.8,57.2,59.0,53.2,56.0)
 132 npk <- data.frame(block=gl(6,4), N=factor(N), P=factor(P), K=factor(K), yield=yield)
 133 npk.aov <- aov(yield ~ block + N*P*K, npk)
 134 op <- options(contrasts=c("contr.helmert", "contr.treatment"))
 135 npk.aovE <- aov(yield ~  N*P*K + Error(block), npk)
 136 options(op)
 137 #summary(npk.aov)
 138 @
 139 <<results=tex>>=
 140 print(xtable(npk.aov),floating=FALSE)
 141 @
 142
 143 \subsubsection{anova object}
 144 <<results=tex>>=
 145 print(xtable(anova(npk.aov)),floating=FALSE)
 146 @
 147
 148 \subsubsection{Another anova object}
 149 <<results=tex>>=
 150 print(xtable(summary(npk.aov)),floating=FALSE)
 151 @
 152
 153 <<>>=
 154 #summary(npk.aovE)
 155 @
 156 <<results=tex>>=
 157 print(xtable(npk.aovE),floating=FALSE)
 158 @
 159
 160
 161 <<results=tex>>=
 162 print(xtable(summary(npk.aovE)),floating=FALSE)
 163 @
 164
 165 \subsection{More lm}
 166 <<>>=
 167
 168 ## Demonstrate lm
 169 ## Taken from help(lm) in R 1.1.1
 170 ## Annette Dobson (1990) "An Introduction to Generalized Linear Models".
 171 ## Page 9: Plant Weight Data.
 172 ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
 173 trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
 174 group <- gl(2,10,20, labels=c("Ctl","Trt"))
 175 weight <- c(ctl, trt)
 176 lm.D9 <- lm(weight ~ group)
 177 @
 178 <<results=tex>>=
 179 print(xtable(lm.D9),floating=FALSE)
 180 @
 181
 182
 183 <<results=tex>>=
 184 print(xtable(anova(lm.D9)),floating=FALSE)
 185 @
 186
 187 \subsection{More glm}
 188 <<>>=
 189
 190 ## Demonstrate glm
 191 ## Taken from help(glm) in R 1.1.1
 192 ## Annette Dobson (1990) "An Introduction to Generalized Linear Models".
 193 ## Page 93: Randomized Controlled Trial :
 194 counts <- c(18,17,15,20,10,20,25,13,12)
 195 outcome <- gl(3,1,9)
 196 treatment <- gl(3,3)
 197 d.AD <- data.frame(treatment, outcome, counts)
 198 glm.D93 <- glm(counts ~ outcome + treatment, family=poisson())
 199 @
 200 <<results=tex>>=
 201 print(xtable(glm.D93,align="r|llrc"),floating=FALSE)
 202 @
 203
 204 \subsection{prcomp}
 205 <<prcomp>>=
 206 if(require(stats,quietly=TRUE)) {
 207   ## Demonstrate prcomp
 208   ## Taken from help(prcomp) in mva package of R 1.1.1
 209   data(USArrests)
 210   pr1 <- prcomp(USArrests)
 211 }
 212 @
 213 <<results=tex>>=
 214 if(require(stats,quietly=TRUE)) {
 215   print(xtable(pr1),floating=FALSE)
 216 }
 217 @
 218
 219
 220 @
 221 <<results=tex>>=
 222   print(xtable(summary(pr1)),floating=FALSE)
 223 @
 224
 225
 226
 227 <<>>=
 228 #  ## Demonstrate princomp
 229 #  ## Taken from help(princomp) in mva package of R 1.1.1
 230 #  pr2 <- princomp(USArrests)
 231 #  print(xtable(pr2))
 232 @
 233 \subsection{Time series}
 234
 235 <<>>=
 236 temp.ts <- ts(cumsum(1+round(rnorm(100), 0)), start = c(1954, 7), frequency=12)
 237    temp.table <- xtable(temp.ts,digits=0)
 238     caption(temp.table) <- "Time series example"
 239 @
 240 <<results=tex>>=
 241     print(temp.table,floating=FALSE)
 242 @
 243 <<savetofile,echo=FALSE>>=
 244 if (FALSE) {
 245   for(i in c("latex","html")) {
 246     outFileName <- paste("xtable.",ifelse(i=="latex","tex",i),sep="")
 247     print(xtable(lm.D9),type=i,file=outFileName,append=TRUE,latex.environment=NULL)
 248     print(xtable(lm.D9),type=i,file=outFileName,append=TRUE,latex.environment="")
 249     print(xtable(lm.D9),type=i,file=outFileName,append=TRUE,latex.environment="center")
 250     print(xtable(anova(glm.D93,test="Chisq")),type=i,file=outFileName,append=TRUE)
 251     print(xtable(anova(glm.D93)),hline.after=c(1),size="small",type=i,file=outFileName,append=TRUE)
 252       # print(xtable(pr2),type=i,file=outFileName,append=TRUE)
 253          }
 254 }
 255 @
 256
 257 \section{Sanitization}
 258 <<>>=
 259 insane <- data.frame(Name=c("Ampersand","Greater than","Less than","Underscore","Per cent","Dollar","Backslash","Hash", "Caret", "Tilde","Left brace","Right brace"),
 260                                 Character = I(c("&",">",                "<",            "_",            "%",            "$",            "\\", "#",      "^",            "~","{","}")))
 261 colnames(insane)[2] <- paste(insane[,2],collapse="")
 262 @
 263
 264 <<pxti,results=tex>>=
 265 print( xtable(insane))
 266 @
 267 Sometimes you might want to have your own sanitization function
 268 <<>>=
 269 wanttex <- xtable(data.frame( label=paste("Value_is $10^{-",1:3,"}$",sep="")))
 270 @
 271 <<results=tex>>=
 272 print(wanttex,sanitize.text.function=function(str)gsub("_","\\_",str,fixed=TRUE))
 273 @
 274
 275 \subsection{Markup in tables}
 276
 277 Markup can be kept in tables, including column and row names, by using a custom sanitize.text.function:
 278
 279 <<>>=
 280 mat <- round(matrix(c(0.9, 0.89, 200, 0.045, 2.0), c(1, 5)), 4)
 281 rownames(mat) <- "$y_{t-1}$"
 282 colnames(mat) <- c("$R^2$", "$\\bar{R}^2$", "F-stat", "S.E.E", "DW")
 283 mat <- xtable(mat)
 284 @
 285 <<results=tex>>=
 286 print(mat, sanitize.text.function = function(x){x})
 287 @
 288
 289 % By David Dahl to demonstrate contribution from David Whitting, 2007-10-09.
 290 You can also have sanitize functions that are specific to column or row names.  In the table below, the row name is not sanitized but column names and table elements are:
 291 <<>>=
 292 money <- matrix(c("$1,000","$900","$100"),ncol=3,dimnames=list("$\\alpha$",c("Income (US$)","Expenses (US$)","Profit (US$)")))
 293 @
 294 <<results=tex>>=
 295 print(xtable(money),sanitize.rownames.function=function(x) {x})
 296 @
 297
 298 \section{Format examples}
 299 \subsection{Adding a centering environment }
 300 <<results=tex>>=
 301    print(xtable(lm.D9,caption="\\tt latex.environment=NULL"),latex.environment=NULL)
 302     print(xtable(lm.D9,caption="\\tt latex.environment=\"\""),latex.environment="")
 303     print(xtable(lm.D9,caption="\\tt latex.environment=\"center\""),latex.environment="center")
 304 @
 305 \subsection{Column alignment}
 306
 307 <<>>=
 308 tli.table <- xtable(tli[1:10,])
 309 @
 310 <<>>=
 311 align(tli.table) <- rep("r",6)
 312 @
 313 <<results=tex>>=
 314 print(tli.table,floating=FALSE)
 315 @
 316 \subsubsection{Single string and column lines}
 317 <<>>=
 318 align(tli.table) <- "|rrl|l|lr|"
 319 @
 320 <<results=tex>>=
 321 print(tli.table,floating=FALSE)
 322 @
 323 \subsubsection{Fixed width columns}
 324 <<>>=
 325 align(tli.table) <- "|rr|lp{3cm}l|r|"
 326 @
 327 <<results=tex>>=
 328 print(tli.table,floating=FALSE)
 329 @
 330
 331 \subsection{Significant digits}
 332
 333
 334 Specify with a single argument
 335 <<>>=
 336 digits(tli.table) <- 3
 337 @
 338 <<results=tex>>=
 339 print(tli.table,floating=FALSE,)
 340 @
 341
 342
 343 or one for each column, counting the row names
 344 <<>>=
 345 digits(tli.table) <- 1:(ncol(tli)+1)
 346 @
 347 <<results=tex>>=
 348 print(tli.table,floating=FALSE,)
 349 @
 350
 351
 352 or as a full matrix
 353 <<>>=
 354 digits(tli.table) <- matrix( 0:4, nrow = 10, ncol = ncol(tli)+1 )
 355 @
 356 <<results=tex>>=
 357 print(tli.table,floating=FALSE,)
 358 @
 359
 360 \subsection{Suppress row names}
 361 <<results=tex>>=
 362 print((tli.table),include.rownames=FALSE,floating=FALSE)
 363 @
 364
 365 If you want a vertical line on the left, you need to change the align attribute.
 366 <<>>=
 367 align(tli.table) <- "|r|r|lp{3cm}l|r|"
 368 @
 369 <<results=tex>>=
 370 print((tli.table),include.rownames=FALSE,floating=FALSE)
 371 @
 372
 373 Revert the alignment to what is was before.
 374 <<>>=
 375 align(tli.table) <- "|rr|lp{3cm}l|r|"
 376 @
 377
 378 \subsection{Suppress column names}
 379 <<results=tex>>=
 380 print((tli.table),include.colnames=FALSE,floating=FALSE)
 381 @
 382 \\
 383 Note the doubled header lines which can be suppressed with, eg,
 384 <<results=tex>>=
 385 print(tli.table,include.colnames=FALSE,floating=FALSE,hline.after=c(0,nrow(tli.table)))
 386 @
 387
 388 \subsection{Suppress row and column names}
 389 <<results=tex>>=
 390 print((tli.table),include.colnames=FALSE,include.rownames=FALSE,floating=FALSE)
 391 @
 392
 393 \subsection{Rotate row and column names}
 394 The {\tt rotate.rownames } and {\tt rotate.colnames} arguments can be
 395 used to rotate the row and/or column names.
 396
 397 <<results=tex>>=
 398 print((tli.table),rotate.rownames=TRUE,rotate.colnames=TRUE)
 399 @
 400
 401 \subsection{Horizontal lines}
 402
 403 \subsubsection{Line locations}
 404
 405 Use the {\tt hline.after} argument to specify the position of the horizontal lines.
 406
 407 <<results=tex>>=
 408 print(xtable(anova(glm.D93)),hline.after=c(1),floating=FALSE)
 409 @
 410
 411 \subsubsection{Line styles}
 412
 413 The \LaTeX package {\tt booktabs} can be used to specify different
 414 line style tags for top, middle, and bottom lines.  Specifying
 415 {\tt booktabs = TRUE} will lead to separate tags being generated
 416 for the three line types.
 417
 418 Insert \verb|\usepackage{booktabs}| in your \LaTeX preamble and
 419 define the {\tt toprule}, {\tt midrule}, and {\tt bottomrule}
 420 tags to specify the line styles.
 421
 422 <<results=tex>>=
 423 print(tli.table , booktabs=TRUE)
 424 @
 425
 426 \subsection{Table-level \LaTeX}
 427 <<results=tex>>=
 428 print(xtable(anova(glm.D93)),size="small",floating=FALSE)
 429 @
 430
 431
 432 \subsection{Long tables}
 433 Remember to insert \verb|\usepackage{longtable}| in your \LaTeX preamble.
 434
 435 <<longtable>>=
 436
 437 ## Demonstration of longtable support.
 438 x <- matrix(rnorm(1000), ncol = 10)
 439 x.big <- xtable(x,label='tabbig',
 440         caption='Example of longtable spanning several pages')
 441 @
 442 <<results=tex>>=
 443 print(x.big,tabular.environment='longtable',floating=FALSE)
 444 @
 445
 446 %%
 447 %% The column name alignment is off in the following example.
 448 %% It needs some revision before exposing it. - CR, 7/2/2012
 449 %%
 450 %
 451 %\subsubsection{Long tables with the header on each page}
 452 %
 453 %The {\tt add.to.row} argument can be used to display the header
 454 %for a long table on each page, and to add a "continued" footer
 455 %on all pages except the last page.
 456 %
 457 %<<results=tex>>=
 458 %library(xtable)
 459 %x<-matrix(rnorm(1000), ncol = 10)
 460 %addtorow<-list()
 461 %addtorow$pos<-list()
 462 %addtorow$pos[[1]]<-c(0)
 463 %addtorow$command<-c(paste(
 464 %    "\\hline \n",
 465 %    "  \\endhead \n",
 466 %    "  \\hline \n",
 467 %    "  {\\footnotesize Continued on next page} \n",
 468 %    "  \\endfoot \n",
 469 %    "  \\endlastfoot \n",sep=""))
 470 %x.big2 <- xtable(x, label = "tabbig2",
 471 %    caption = "Example of longtable with the header on each page")
 472 %print(x.big2, tabular.environment = "longtable", floating = FALSE,
 473 %include.rownames=FALSE, add.to.row=addtorow, hline.after=c(-1) )
 474 %@
 475
 476 \subsection{Sideways tables}
 477 Remember to insert \verb|\usepackage{rotating}| in your LaTeX preamble.
 478 Sideways tables can't be forced in place with the `H' specifier, but you can
 479 use the \verb|\clearpage| command to get them fairly nearby.
 480
 481 <<>>=
 482 x <- x[1:30,]
 483 x.small <- xtable(x,label='tabsmall',caption='A sideways table')
 484 @
 485
 486 <<results=tex>>=
 487 print(x.small,floating.environment='sidewaystable')
 488 @
 489 \clearpage
 490
 491 \subsection{Rescaled tables}
 492 Specify a \code{scalebox} value to rescale the table.
 493
 494 <<>>=
 495 x <- x[1:20,]
 496 x.rescale <- xtable(x,label='tabrescaled',caption='A rescaled table')
 497 @
 498
 499 <<results=tex>>=
 500 print(x.rescale, scalebox=0.7)
 501 @
 502
 503 \subsection{Table Width}
 504 The {\tt tabularx} tabular environment provides more alignment options,
 505 and has a \code{width} argument to specify the table width.
 506
 507 Remember to insert \verb|\usepackage{tabularx}| in your \LaTeX preamble.
 508
 509 <<>>=
 510 df.width <- data.frame(
 511   "label 1 with much more text than is needed" = c("item 1", "A"),
 512   "label 2 is also very long" = c("item 2","B"),
 513   "label 3" = c("item 3","C"),
 514   "label 4" = c("item 4 but again with too much text","D"),
 515   check.names = FALSE)
 516
 517 x.width <- xtable(df.width,
 518   caption="Using the 'tabularx' environment")
 519 align(x.width) <- "|l|X|X|l|X|"
 520 @
 521
 522 <<results=tex>>=
 523 print(x.width, tabular.environment="tabularx",
 524   width="\\textwidth")
 525 @
 526
 527 \section{Suppressing Printing}
 528 By default the {\tt print} method will print the LaTeX or HTML to standard
 529 output and also return the character strings invisibly.  The printing to
 530 standard output can be suppressed by specifying {\tt print.results = FALSE}.
 531
 532 <<>>=
 533 x.out <- print(tli.table, print.results = FALSE)
 534 @
 535
 536 Formatted output can also be captured without printing with the
 537 {\tt toLatex} method.  This function returns an object of class
 538 {\tt "Latex"}.
 539
 540 <<>>=
 541 x.ltx <- toLatex(tli.table)
 542 class(x.ltx)
 543 x.ltx
 544 @
 545
 546 \section{Acknowledgements}
 547 Most of the examples in this gallery are taken from the {\tt xtable} documentation.
 548 \section{R Session information}
 549 <<results=tex>>=
 550 toLatex(sessionInfo())
 551 @
 552 \end{document}