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{hyperref}
  35 \begin{document}
  36
  37 \maketitle
  38 \section{Summary}
  39 This document gives a gallery of tables which can be made
  40 by using the {\tt xtable} package to create \LaTeX\ output.
  41 It doubles as a regression check for the package.
  42
  43 <<>>=
  44 library(xtable)
  45 @
  46
  47 \section{Gallery}
  48 \subsection{Data frame}
  49 Load example dataset
  50 <<>>=
  51 data(tli)
  52
  53 ## Demonstrate data.frame
  54 tli.table <- xtable(tli[1:10,])
  55 digits(tli.table)[c(2,6)] <- 0
  56 @
  57 <<results=tex>>=
  58 print(tli.table,floating=FALSE)
  59 @
  60
  61 \subsection{Matrix}
  62 <<>>=
  63 design.matrix <- model.matrix(~ sex*grade, data=tli[1:10,])
  64 design.table <- xtable(design.matrix)
  65 @
  66 <<results=tex>>=
  67 print(design.table,floating=FALSE)
  68 @
  69
  70 \subsection{aov}
  71 <<>>=
  72 fm1 <- aov(tlimth ~ sex + ethnicty + grade + disadvg, data=tli)
  73 fm1.table <- xtable(fm1)
  74 @
  75 <<results=tex>>=
  76 print(fm1.table,floating=FALSE)
  77 @
  78 \subsection{lm}
  79 <<>>=
  80 fm2 <- lm(tlimth ~ sex*ethnicty, data=tli)
  81 fm2.table <- xtable(fm2)
  82 @
  83 <<results=tex>>=
  84 print(fm2.table,floating=FALSE)
  85 @
  86 \subsubsection{anova object}
  87
  88 <<results=tex>>=
  89 print(xtable(anova(fm2)),floating=FALSE)
  90 @
  91 \subsubsection{Another anova object}
  92 <<>>=
  93 fm2b <- lm(tlimth ~ ethnicty, data=tli)
  94 @
  95 <<results=tex>>=
  96 print(xtable(anova(fm2b,fm2)),floating=FALSE)
  97 @
  98
  99
 100 \subsection{glm}
 101
 102 <<>>=
 103
 104 ## Demonstrate glm
 105 fm3 <- glm(disadvg ~ ethnicty*grade, data=tli, family=binomial())
 106 fm3.table <- xtable(fm3)
 107 @
 108 <<results=tex>>=
 109 print(fm3.table,floating=FALSE)
 110 @
 111
 112 \subsubsection{anova object}
 113 @
 114 <<results=tex>>=
 115 print(xtable(anova(fm3)),floating=FALSE)
 116 @
 117
 118
 119 \subsection{More aov}
 120 <<>>=
 121
 122 ## Demonstrate aov
 123 ## Taken from help(aov) in R 1.1.1
 124 ## From Venables and Ripley (1997) p.210.
 125 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)
 126 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)
 127 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)
 128 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,
 129            62.0,48.8,45.5,44.2,52.0,51.5,49.8,48.8,57.2,59.0,53.2,56.0)
 130 npk <- data.frame(block=gl(6,4), N=factor(N), P=factor(P), K=factor(K), yield=yield)
 131 npk.aov <- aov(yield ~ block + N*P*K, npk)
 132 op <- options(contrasts=c("contr.helmert", "contr.treatment"))
 133 npk.aovE <- aov(yield ~  N*P*K + Error(block), npk)
 134 options(op)
 135 #summary(npk.aov)
 136 @
 137 <<results=tex>>=
 138 print(xtable(npk.aov),floating=FALSE)
 139 @
 140
 141 \subsubsection{anova object}
 142 <<results=tex>>=
 143 print(xtable(anova(npk.aov)),floating=FALSE)
 144 @
 145
 146 \subsubsection{Another anova object}
 147 <<results=tex>>=
 148 print(xtable(summary(npk.aov)),floating=FALSE)
 149 @
 150
 151 <<>>=
 152 #summary(npk.aovE)
 153 @
 154 <<results=tex>>=
 155 print(xtable(npk.aovE),floating=FALSE)
 156 @
 157
 158
 159 <<results=tex>>=
 160 print(xtable(summary(npk.aovE)),floating=FALSE)
 161 @
 162
 163 \subsection{More lm}
 164 <<>>=
 165
 166 ## Demonstrate lm
 167 ## Taken from help(lm) in R 1.1.1
 168 ## Annette Dobson (1990) "An Introduction to Generalized Linear Models".
 169 ## Page 9: Plant Weight Data.
 170 ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
 171 trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
 172 group <- gl(2,10,20, labels=c("Ctl","Trt"))
 173 weight <- c(ctl, trt)
 174 lm.D9 <- lm(weight ~ group)
 175 @
 176 <<results=tex>>=
 177 print(xtable(lm.D9),floating=FALSE)
 178 @
 179
 180
 181 <<results=tex>>=
 182 print(xtable(anova(lm.D9)),floating=FALSE)
 183 @
 184
 185 \subsection{More glm}
 186 <<>>=
 187
 188 ## Demonstrate glm
 189 ## Taken from help(glm) in R 1.1.1
 190 ## Annette Dobson (1990) "An Introduction to Generalized Linear Models".
 191 ## Page 93: Randomized Controlled Trial :
 192 counts <- c(18,17,15,20,10,20,25,13,12)
 193 outcome <- gl(3,1,9)
 194 treatment <- gl(3,3)
 195 d.AD <- data.frame(treatment, outcome, counts)
 196 glm.D93 <- glm(counts ~ outcome + treatment, family=poisson())
 197 @
 198 <<results=tex>>=
 199 print(xtable(glm.D93,align="r|llrc"),floating=FALSE)
 200 @
 201
 202 \subsection{prcomp}
 203 <<prcomp>>=
 204 if(require(stats,quietly=TRUE)) {
 205   ## Demonstrate prcomp
 206   ## Taken from help(prcomp) in mva package of R 1.1.1
 207   data(USArrests)
 208   pr1 <- prcomp(USArrests)
 209 }
 210 @
 211 <<results=tex>>=
 212 if(require(stats,quietly=TRUE)) {
 213   print(xtable(pr1),floating=FALSE)
 214 }
 215 @
 216
 217
 218 @
 219 <<results=tex>>=
 220   print(xtable(summary(pr1)),floating=FALSE)
 221 @
 222
 223
 224
 225 <<>>=
 226 #  ## Demonstrate princomp
 227 #  ## Taken from help(princomp) in mva package of R 1.1.1
 228 #  pr2 <- princomp(USArrests)
 229 #  print(xtable(pr2))
 230 @
 231 \subsection{Time series}
 232
 233 <<>>=
 234 temp.ts <- ts(cumsum(1+round(rnorm(100), 0)), start = c(1954, 7), frequency=12)
 235    temp.table <- xtable(temp.ts,digits=0)
 236     caption(temp.table) <- "Time series example"
 237 @
 238 <<results=tex>>=
 239     print(temp.table,floating=FALSE)
 240 @
 241 <<savetofile,echo=FALSE>>=
 242 if (FALSE) {
 243   for(i in c("latex","html")) {
 244     outFileName <- paste("xtable.",ifelse(i=="latex","tex",i),sep="")
 245     print(xtable(lm.D9),type=i,file=outFileName,append=TRUE,latex.environment=NULL)
 246     print(xtable(lm.D9),type=i,file=outFileName,append=TRUE,latex.environment="")
 247     print(xtable(lm.D9),type=i,file=outFileName,append=TRUE,latex.environment="center")
 248     print(xtable(anova(glm.D93,test="Chisq")),type=i,file=outFileName,append=TRUE)
 249     print(xtable(anova(glm.D93)),hline.after=c(1),size="small",type=i,file=outFileName,append=TRUE)
 250       # print(xtable(pr2),type=i,file=outFileName,append=TRUE)
 251          }
 252 }
 253 @
 254
 255 \section{Sanitization}
 256 <<>>=
 257 insane <- data.frame(Name=c("Ampersand","Greater than","Less than","Underscore","Per cent","Dollar","Backslash","Hash", "Caret", "Tilde","Left brace","Right brace"),
 258                                 Character = I(c("&",">",                "<",            "_",            "%",            "$",            "\\", "#",      "^",            "~","{","}")))
 259 colnames(insane)[2] <- paste(insane[,2],collapse="")
 260 @
 261
 262 <<pxti,results=tex>>=
 263 print( xtable(insane))
 264 @
 265 Sometimes you might want to have your own sanitization function
 266 <<>>=
 267 wanttex <- xtable(data.frame( label=paste("Value_is $10^{-",1:3,"}$",sep="")))
 268 @
 269 <<results=tex>>=
 270 print(wanttex,sanitize.text.function=function(str)gsub("_","\\_",str,fixed=TRUE))
 271 @
 272
 273 \subsection{Markup in tables}
 274
 275 Markup can be kept in tables, including column and row names, by using a custom sanitize.text.function:
 276
 277 <<>>=
 278 mat <- round(matrix(c(0.9, 0.89, 200, 0.045, 2.0), c(1, 5)), 4)
 279 rownames(mat) <- "$y_{t-1}$"
 280 colnames(mat) <- c("$R^2$", "$\\bar{R}^2$", "F-stat", "S.E.E", "DW")
 281 mat <- xtable(mat)
 282 @
 283 <<results=tex>>=
 284 print(mat, sanitize.text.function = function(x){x})
 285 @
 286
 287 % By David Dahl to demonstrate contribution from David Whitting, 2007-10-09.
 288 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:
 289 <<>>=
 290 money <- matrix(c("$1,000","$900","$100"),ncol=3,dimnames=list("$\\alpha$",c("Income (US$)","Expenses (US$)","Profit (US$)")))
 291 @
 292 <<results=tex>>=
 293 print(xtable(money),sanitize.rownames.function=function(x) {x})
 294 @
 295
 296 \section{Format examples}
 297 \subsection{Adding a centering environment }
 298 <<results=tex>>=
 299    print(xtable(lm.D9,caption="\\tt latex.environment=NULL"),latex.environment=NULL)
 300     print(xtable(lm.D9,caption="\\tt latex.environment=\"\""),latex.environment="")
 301     print(xtable(lm.D9,caption="\\tt latex.environment=\"center\""),latex.environment="center")
 302 @
 303 \subsection{Column alignment}
 304
 305 <<>>=
 306 tli.table <- xtable(tli[1:10,])
 307 @
 308 <<>>=
 309 align(tli.table) <- rep("r",6)
 310 @
 311 <<results=tex>>=
 312 print(tli.table,floating=FALSE)
 313 @
 314 \subsubsection{Single string and column lines}
 315 <<>>=
 316 align(tli.table) <- "|rrl|l|lr|"
 317 @
 318 <<results=tex>>=
 319 print(tli.table,floating=FALSE)
 320 @
 321 \subsubsection{Fixed width columns}
 322 <<>>=
 323 align(tli.table) <- "|rr|lp{3cm}l|r|"
 324 @
 325 <<results=tex>>=
 326 print(tli.table,floating=FALSE)
 327 @
 328
 329 \subsection{Significant digits}
 330
 331
 332 Specify with a single argument
 333 <<>>=
 334 digits(tli.table) <- 3
 335 @
 336 <<results=tex>>=
 337 print(tli.table,floating=FALSE,)
 338 @
 339
 340
 341 or one for each column, counting the row names
 342 <<>>=
 343 digits(tli.table) <- 1:(ncol(tli)+1)
 344 @
 345 <<results=tex>>=
 346 print(tli.table,floating=FALSE,)
 347 @
 348
 349
 350 or as a full matrix
 351 <<>>=
 352 digits(tli.table) <- matrix( 0:4, nrow = 10, ncol = ncol(tli)+1 )
 353 @
 354 <<results=tex>>=
 355 print(tli.table,floating=FALSE,)
 356 @
 357
 358 \subsection{Suppress row names}
 359 <<results=tex>>=
 360 print((tli.table),include.rownames=FALSE,floating=FALSE)
 361 @
 362
 363 If you want a vertical line on the left, you need to change the align attribute.
 364 <<>>=
 365 align(tli.table) <- "|r|r|lp{3cm}l|r|"
 366 @
 367 <<results=tex>>=
 368 print((tli.table),include.rownames=FALSE,floating=FALSE)
 369 @
 370
 371 Revert the alignment to what is was before.
 372 <<>>=
 373 align(tli.table) <- "|rr|lp{3cm}l|r|"
 374 @
 375
 376 \subsection{Suppress column names}
 377 <<results=tex>>=
 378 print((tli.table),include.colnames=FALSE,floating=FALSE)
 379 @
 380 \\
 381 Note the doubled header lines which can be suppressed with, eg,
 382 <<results=tex>>=
 383 print(tli.table,include.colnames=FALSE,floating=FALSE,hline.after=c(0,nrow(tli.table)))
 384 @
 385
 386 \subsection{Suppress row and column names}
 387 <<results=tex>>=
 388 print((tli.table),include.colnames=FALSE,include.rownames=FALSE,floating=FALSE)
 389 @
 390
 391 \subsection{Rotate row and column names}
 392 The {\tt rotate.rownames } and {\tt rotate.colnames} arguments can be
 393 used to rotate the row and/or column names.
 394
 395 <<results=tex>>=
 396 print((tli.table),rotate.rownames=TRUE,rotate.colnames=TRUE)
 397 @
 398
 399 \subsection{Horizontal lines}
 400 <<results=tex>>=
 401 print(xtable(anova(glm.D93)),hline.after=c(1),floating=FALSE)
 402 @
 403
 404 \subsection{Table-level \LaTeX}
 405 <<results=tex>>=
 406 print(xtable(anova(glm.D93)),size="small",floating=FALSE)
 407 @
 408
 409
 410 \subsection{Long tables}
 411 Remember to insert \verb|\usepackage{longtable}| in your LaTeX preamble.
 412 See Table \ref{tabbig}.
 413
 414 <<longtable>>=
 415
 416 ## Demonstration of longtable support.
 417 x <- matrix(rnorm(1000), ncol = 10)
 418 x.big <- xtable(x,label='tabbig',
 419         caption='Example of longtable spanning several pages')
 420 @
 421 <<results=tex>>=
 422 print(x.big,tabular.environment='longtable',floating=FALSE)
 423 @
 424
 425 \subsubsection{Long tables with headers on each page}
 426
 427 The {\tt add.to.row} argument can be used to display the header
 428 for a long table on each page, and to add a "continued" footer
 429 on all pages except the last page.
 430
 431 <<results=tex>>=
 432 library(xtable)
 433 x<-matrix(rnorm(1000), ncol = 10)
 434
 435 addtorow<-list()
 436 addtorow$pos<-list()
 437 addtorow$pos[[1]]<-c(0)
 438 addtorow$command<-c(paste(
 439     "\\hline \n",
 440     "  \\endhead \n",
 441     "  \\hline \n",
 442     "  {\\footnotesize Continued on next page} \n",
 443     "  \\endfoot \n",
 444     "  \\endlastfoot \n",sep=""))
 445 x.big <- xtable(x, label = "tabbig",
 446     caption = "Example of longtable spanning several pages")
 447 print(x.big, tabular.environment = "longtable", floating = FALSE,
 448 include.rownames=FALSE,add.to.row=addtorow,hline.after=c(-1) )
 449 @
 450
 451 \subsection{Sideways tables}
 452 Remember to insert \verb|\usepackage{rotating}| in your LaTeX preamble.
 453 Sideways tables can't be forced in place with the `H' specifier, but you can
 454 use the \verb|\clearpage| command to get them fairly nearby.
 455 See Table \ref{tabsmall}.
 456
 457 <<>>=
 458 x <- x[1:30,]
 459 x.small <- xtable(x,label='tabsmall',caption='A sideways table')
 460 @
 461
 462 <<results=tex>>=
 463 print(x.small,floating.environment='sidewaystable')
 464 @
 465 \clearpage
 466
 467 \section{Suppressing Printing}
 468 By default the {\tt print} method will print the LaTeX or HTML to standard
 469 output and also return the character strings invisibly.  The printing to
 470 standard output can be suppressed by specifying {\tt print.results = FALSE}.
 471
 472 <<>>=
 473 # This will print the output and store it.
 474 x.out <- print(tli.table)
 475
 476 # This will just store the value.
 477 x.out2 <- print(tli.table, print.results = FALSE)
 478 @
 479
 480 Formatted output can also be captured without printing with the
 481 {\tt toLatex} method.  This function returns an object of class
 482 {\tt "Latex"}.
 483
 484 <<>>=
 485 x.ltx <- toLatex(tli.table)
 486 class(x.ltx)
 487 x.ltx
 488 @
 489
 490 \section{Acknowledgements}
 491 Most of the examples in this gallery are taken from the {\tt xtable} documentation.
 492 \section{R Session information}
 493 <<results=tex>>=
 494 toLatex(sessionInfo())
 495 @
 496 \end{document}