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{Horizontal lines}
 392 <<results=tex>>=
 393 print(xtable(anova(glm.D93)),hline.after=c(1),floating=FALSE)
 394 @
 395
 396 \subsection{Table-level \LaTeX}
 397 <<results=tex>>=
 398 print(xtable(anova(glm.D93)),size="small",floating=FALSE)
 399 @
 400
 401
 402 \subsection{Long tables}
 403 Remember to insert \verb|\usepackage{longtable}| in your LaTeX preamble.
 404 See Table \ref{tabbig}.
 405
 406 <<longtable>>=
 407
 408 ## Demonstration of longtable support.
 409 x <- matrix(rnorm(1000), ncol = 10)
 410 x.big <- xtable(x,label='tabbig',
 411         caption='Example of longtable spanning several pages')
 412 @
 413 <<results=tex>>=
 414 print(x.big,tabular.environment='longtable',floating=FALSE)
 415 @
 416
 417
 418 \subsection{Sideways tables}
 419 Remember to insert \verb|\usepackage{rotating}| in your LaTeX preamble.
 420 Sideways tables can't be forced in place with the `H' specifier, but you can
 421 use the \verb|\clearpage| command to get them fairly nearby.
 422 See Table \ref{tabsmall}.
 423
 424 <<>>=
 425 x <- x[1:30,]
 426 x.small <- xtable(x,label='tabsmall',caption='A sideways table')
 427 @
 428
 429 <<results=tex>>=
 430 print(x.small,floating.environment='sidewaystable')
 431 @
 432 \clearpage
 433
 434 \section{Suppressing Printing}
 435 By default the {\tt print} method will print the LaTeX or HTML to standard
 436 output and also return the character strings invisibly.  The printing to
 437 standard output can be supproessed by specifying {\tt print.result = FALSE}.
 438
 439 <<>>=
 440 # This will print the output and store it.
 441 x.out <- print(tli.table)
 442
 443 # This will just store the value.
 444 x.out2 <- print(tli.table, print.results = FALSE)
 445 @
 446
 447 Formatted output can also be captured without the printing with the
 448 {\tt toLatex} method.
 449
 450 <<>>=
 451 x.ltx <- toLatex(tli.table)
 452 class(x.ltx)
 453 x.ltx
 454 @
 455
 456 \section{Acknowledgements}
 457 Most of the examples in this gallery are taken from the {\tt xtable} documentation.
 458 \section{R Session information}
 459 <<results=tex>>=
 460 toLatex(sessionInfo())
 461 @
 462 \end{document}