[xtable.git] / pkg / man / xtable.Rd

\name{xtable}
\alias{xtable}
\alias{xtable.anova}
\alias{xtable.aov}
\alias{xtable.aovlist}
\alias{xtable.data.frame}
\alias{xtable.glm}
\alias{xtable.lm}
\alias{xtable.matrix}
\alias{xtable.prcomp}
\alias{xtable.coxph}
\alias{xtable.summary.aov}
\alias{xtable.summary.aovlist}
\alias{xtable.summary.glm}
\alias{xtable.summary.lm}
\alias{xtable.summary.prcomp}
\alias{xtable.ts}
\alias{xtable.table}
\alias{xtable.zoo}
\title{Create Export Tables}
\description{Function converting an R object to an \code{xtable} object, which can then be printed as a LaTeX or HTML table.}
\usage{
xtable(x, caption=NULL, label=NULL, align=NULL, digits=NULL,
       display=NULL, ...)
}
\arguments{
  \item{x}{An R object of class found among \code{methods(xtable)}.  See below on how to write additional method functions
           for \code{xtable}.}
  \item{caption}{Character vector of length 1 containing the table's caption or title.
                 Set to \code{NULL} to suppress the caption.  Default value is \code{NULL}.}
  \item{label}{Character vector of length 1 containing the LaTeX label or HTML anchor.
               Set to \code{NULL} to suppress the label.  Default value is \code{NULL}.}
  \item{align}{Character vector of length equal to the number of columns of the resulting
               table indicating the alignment of the corresponding columns.  Also, \code{"|"} may be used
               to produce vertical lines between columns in LaTeX tables, but these are effectively ignored
               when considering the required length of the supplied vector.  If a character vector of length one
               is supplied, it is split as \code{strsplit(align,"")[[1]]} before processing.
               Since the row names are printed in the first column, the length of \code{align}
               is one greater than \code{ncol(x)} if \code{x} is a \code{data.frame}.
               Use \code{"l"}, \code{"r"}, and \code{"c"} to denote left, right, and
               center alignment, respectively.  Use \code{"p\{3cm\}"} etc for a LaTeX column of the specified width.
               For HTML output the \code{"p"} alignment is interpreted as \code{"l"}, ignoring
               the width request. Default depends on the class of \code{x}.}
  \item{digits}{Numeric vector of length equal to one (in which case it will be replicated as necessary)
                or to the number of columns of the resulting
                table \bold{or} matrix of the same size as the resulting table 
                indicating the number of digits to display in the corresponding columns.
                Since the row names are printed in the first column, the length of the 
                vector \code{digits} or the number of columns of the matrix \code{digits}
                is one greater than \code{ncol(x)} if \code{x} is a \code{data.frame}.
                Default depends of class of \code{x}.
                If values of \code{digits} are negative, the corresponding values 
                of \code{x} are displayed in scientific format with \code{abs(digits)}
                digits.}
  \item{display}{Character vector of length equal to the number of columns of the resulting
                 table indicating the format for the corresponding columns.
                 Since the row names are printed in the first column, the length of \code{display}
                 is one greater than \code{ncol(x)} if \code{x} is a \code{data.frame}.
                 These values are passed to the \code{formatC} function.  Use \code{"d"} (for integers),
                 \code{"f"}, \code{"e"}, \code{"E"}, \code{"g"}, \code{"G"}, \code{"fg"} (for
                 reals), or \code{"s"} (for strings).
                 \code{"f"} gives numbers in the usual \code{xxx.xxx} format;  \code{"e"} and
                 \code{"E"} give \code{n.ddde+nn} or \code{n.dddE+nn} (scientific format);
                 \code{"g"} and \code{"G"} put \code{x[i]} into scientific format only if it saves
                 space to do so.  \code{"fg"} uses fixed format as \code{"f"}, but \code{digits} as
                 number of \emph{significant} digits.  Note that this can lead to
                 quite long result strings.  Default depends on the class of \code{x}.}
  \item{...}{Additional arguments.  (Currently ignored.)}
}
\details{
  This function extracts tabular information from \code{x} and returns an object of class \code{"xtable"}.
  The nature of the table generated depends on the class of \code{x}.
  For example, \code{aov} objects produce
  ANOVA tables while \code{data.frame} objects produce a table of the entire data.frame.  One can optionally provide a
  caption (called a title in HTML) or label (called an anchor in HTML),
  as well as formatting specifications.  Default
  values for \code{align}, \code{digits}, and \code{display} are
  class dependent.

  The available method functions for \code{xtable} are given by \code{methods(xtable)}.
  Users can extend the list of available classes by writing methods for the generic function \code{xtable}.
  These methods functions should have \code{x} as their first argument
  with additional arguments to
  specify \code{caption}, \code{label}, \code{align},
  \code{digits}, and
  \code{display}.  Optionally, other arguments
  may be present to specify how the object \code{x} should be manipulated.
  All method functions should return an object whose class if given by \code{c("xtable","data.frame")}.
  The resulting object can have attributes \code{caption} and
  \code{label}, but must have attributes \code{align},
  \code{digits}, and \code{display}.  It is strongly recommened that you set these attributes through the 
  provided replacement functions as they perform validity checks.
}
\value{
  An object of class \code{"xtable"} which inherits the \code{data.frame} class and contains several additional attributes
  specifying the table formatting options.
}
\author{David Dahl \email{dahl@stat.tamu.edu} with contributions and suggestions from many others (see source code).}
\seealso{\code{\link{print.xtable}}, \code{\link{caption}}, \code{\link{label}},
         \code{\link{align}}, \code{\link{digits}}, \code{\link{display}}, \code{\link{formatC}}, \code{\link{methods}}}
\examples{

## Load example dataset
data(tli)

## Demonstrate data.frame
tli.table <- xtable(tli[1:20,])
digits(tli.table)[c(2,6)] <- 0
print(tli.table)
print(tli.table,type="html")

## Demonstrate data.frame with different digits in cells
tli.table <- xtable(tli[1:20,])
digits(tli.table) <- matrix( 0:4, nrow = 20, ncol = ncol(tli)+1 )
print(tli.table)
print(tli.table,type="html")

## Demonstrate matrix
design.matrix <- model.matrix(~ sex*grade, data=tli[1:20,])
design.table <- xtable(design.matrix)
print(design.table)
print(design.table,type="html")

## Demonstrate aov
fm1 <- aov(tlimth ~ sex + ethnicty + grade + disadvg, data=tli)
fm1.table <- xtable(fm1)
print(fm1.table)
print(fm1.table,type="html")

## Demonstrate lm
fm2 <- lm(tlimth ~ sex*ethnicty, data=tli)
fm2.table <- xtable(fm2)
print(fm2.table)
print(fm2.table,type="html")
print(xtable(anova(fm2)))
print(xtable(anova(fm2)),type="html")
fm2b <- lm(tlimth ~ ethnicty, data=tli)
print(xtable(anova(fm2b,fm2)))
print(xtable(anova(fm2b,fm2)),type="html")

## Demonstrate glm
fm3 <- glm(disadvg ~ ethnicty*grade, data=tli, family=binomial())
fm3.table <- xtable(fm3)
print(fm3.table)
print(fm3.table,type="html")
print(xtable(anova(fm3)))
print(xtable(anova(fm3)),type="html")

## Demonstrate aov
## Taken from help(aov) in R 1.1.1
## From Venables and Ripley (1997) p.210.
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)
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)
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)
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,
           62.0,48.8,45.5,44.2,52.0,51.5,49.8,48.8,57.2,59.0,53.2,56.0)
npk <- data.frame(block=gl(6,4), N=factor(N), P=factor(P), K=factor(K), yield=yield)
npk.aov <- aov(yield ~ block + N*P*K, npk)
op <- options(contrasts=c("contr.helmert", "contr.treatment"))
npk.aovE <- aov(yield ~  N*P*K + Error(block), npk)
options(op)

summary(npk.aov)
print(xtable(npk.aov))
print(xtable(anova(npk.aov)))
print(xtable(summary(npk.aov)))

summary(npk.aovE)
print(xtable(npk.aovE),type="html")
print(xtable(summary(npk.aovE)),type="html")

## Demonstrate lm
## Taken from help(lm) in R 1.1.1
## Annette Dobson (1990) "An Introduction to Generalized Linear Models".
## Page 9: Plant Weight Data.
ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
group <- gl(2,10,20, labels=c("Ctl","Trt"))
weight <- c(ctl, trt)
lm.D9 <- lm(weight ~ group)
print(xtable(lm.D9))
print(xtable(anova(lm.D9)))

## Demonstrate glm
## Taken from help(glm) in R 1.1.1
## Annette Dobson (1990) "An Introduction to Generalized Linear Models".
## Page 93: Randomized Controlled Trial :
counts <- c(18,17,15,20,10,20,25,13,12)
outcome <- gl(3,1,9)
treatment <- gl(3,3)
d.AD <- data.frame(treatment, outcome, counts)
glm.D93 <- glm(counts ~ outcome + treatment, family=poisson())
print(xtable(glm.D93,align="r|llrc"))
print(xtable(anova(glm.D93)),hline.after=c(1),size="small")

## Demonstration of additional formatC() arguments.
print(fm1.table, format.args=list(big.mark = "'", decimal.mark = ","))

## Demonstration of short caption support.
fm1sc <- aov(tlimth ~ sex + ethnicty + grade, data=tli)
fm1sc.table <- xtable(fm1sc, 
  caption="ANOVA Model with Predictors Sex, Ethnicity, and Grade")
print(fm1sc.table,
  short.caption="ANOVA: Sex, Ethnicity, Grade")

## Demonstration of longtable support.
## Remember to insert \usepackage{longtable} on your LaTeX preamble
x <- matrix(rnorm(1000), ncol = 10)
x.big <- xtable(x,label='tabbig',caption='Example of longtable spanning several pages')
print(x.big,tabular.environment='longtable',floating=FALSE) 
x <- x[1:30,]
x.small <- xtable(x,label='tabsmall',caption='regular table env')
print(x.small)  # default, no longtable 

## Demonstration of sidewaystable support.
## Remember to insert \usepackage{rotating} on your LaTeX preamble
print(x.small,floating.environment='sidewaystable') 

if(require(stats,quietly=TRUE)) {
  ## Demonstrate prcomp
  ## Taken from help(prcomp) in mva package of R 1.1.1
  data(USArrests)
  pr1 <- prcomp(USArrests)
  print(xtable(pr1))
  print(xtable(summary(pr1)))

#  ## Demonstrate princomp
#  ## Taken from help(princomp) in mva package of R 1.1.1
#  pr2 <- princomp(USArrests)
#  print(xtable(pr2))
}

## Demonstrate include.rownames, include.colnames, 
## only.contents and add.to.row arguments
set.seed(2345)
res <- matrix(sample(0:9, size=6*9, replace=TRUE), ncol=6, nrow=9)
xres <- xtable(res)
digits(xres) <- rep(0, 7)
addtorow <- list()
addtorow$pos <- list()
addtorow$pos[[1]] <- c(0, 2)
addtorow$pos[[2]] <- 4
addtorow$command <- c('\\vspace{2mm} \n', '\\vspace{10mm} \n')
print(xres, add.to.row=addtorow, include.rownames=FALSE, include.colnames=TRUE, 
  only.contents=TRUE, hline.after=c(0, 0, 9, 9))

## Demostrate include.rownames, include.colnames, 
## only.contents and add.to.row arguments in Rweave files

\dontrun{
 \begin{small}
 \setlongtables % For longtable version 3.x or less
 \begin{longtable}{
 <<results=tex,fig=FALSE>>=
 cat(paste(c('c', rep('cc', 34/2-1), 'c'), collapse='@{\\hspace{2pt}}'))
 @ 
 }
 \hline
 \endhead
 \hline
 \endfoot
 <<results=tex,fig=FALSE>>=
 library(xtable)
 set.seed(2345)
 res <- matrix(sample(0:9, size=34*90, replace=TRUE), ncol=34, nrow=90)
 xres <- xtable(res)
 digits(xres) <- rep(0, 35)
 addtorow <- list()
 addtorow$pos <- list()
 addtorow$pos[[1]] <- c(seq(4, 40, 5), seq(49, 85, 5))
 addtorow$pos[[2]] <- 45
 addtorow$command <- c('\\vspace{2mm} \n', '\\newpage \n')
 print(xres, add.to.row=addtorow, include.rownames=FALSE, include.colnames=FALSE, 
   only.contents=TRUE, hline.after=NULL)
 @
 \end{longtable}
 \end{small}
}

## Demonstrate sanitization
mat <- round(matrix(c(0.9, 0.89, 200, 0.045, 2.0), c(1, 5)), 4)
rownames(mat) <- "$y_{t-1}$"
colnames(mat) <- c("$R^2$", "$\\\bar{R}^2$", "F-stat", "S.E.E", "DW")
print(xtable(mat), type="latex", sanitize.text.function = function(x){x})

## Demonstrate booktabs
print(tli.table)
print(tli.table , hline.after=c(-1,0))
print(tli.table , hline.after=NULL)
print(tli.table ,  add.to.row=list(pos=list(2), command=c("\\vspace{2mm} \n")))

print(tli.table , booktabs=TRUE)
print(tli.table , booktabs=TRUE, hline.after=c(-1,0))
print(tli.table , booktabs=TRUE, hline.after=NULL)
print(tli.table , booktabs=TRUE, 
  add.to.row=list(pos=list(2), command=c("\\vspace{2mm} \n")))
print(tli.table , booktabs=TRUE, add.to.row=list(pos=list(2), 
  command=c("youhou\n")),tabular.environment = "longtable")

\testonly{
  for(i in c("latex","html")) {
    outFileName <- paste("xtable.",ifelse(i=="latex","tex",i),sep="")
    print(tli.table,type=i,file=outFileName,append=FALSE)
    print(design.table,type=i,file=outFileName,append=TRUE)
    print(fm1.table,type=i,file=outFileName,append=TRUE)
    print(fm2.table,type=i,file=outFileName,append=TRUE)
    print(fm2.table,type=i,file=outFileName,append=TRUE,math.style.negative=TRUE)
    print(xtable(anova(fm2)),type=i,file=outFileName,append=TRUE)
    print(xtable(anova(fm2b,fm2)),type=i,file=outFileName,append=TRUE)
    print(fm3.table,type=i,file=outFileName,append=TRUE)
    print(xtable(anova(fm3)),type=i,file=outFileName,append=TRUE)
    print(xtable(npk.aov),type=i,file=outFileName,append=TRUE)
    print(xtable(anova(npk.aov)),type=i,file=outFileName,append=TRUE)
    print(xtable(summary(npk.aov)),type=i,file=outFileName,append=TRUE)
    print(xtable(npk.aovE),type=i,file=outFileName,append=TRUE)
    print(xtable(summary(npk.aovE)),type=i,file=outFileName,append=TRUE)
    if(i=="latex") cat("\\\clearpage\n",file=outFileName,append=TRUE)
    print(xtable(lm.D9),type=i,file=outFileName,append=TRUE,latex.environment=NULL)
    print(xtable(lm.D9),type=i,file=outFileName,append=TRUE,latex.environment="")
    print(xtable(lm.D9),type=i,file=outFileName,append=TRUE,latex.environment="center")
    print(xtable(anova(lm.D9)),type=i,file=outFileName,append=TRUE)
    print(xtable(glm.D93),type=i,file=outFileName,append=TRUE)
    print(xtable(anova(glm.D93,test="Chisq")),type=i,file=outFileName,append=TRUE)
    print(xtable(glm.D93,align="r|llrc"),include.rownames=FALSE,include.colnames=TRUE,
      type=i,file=outFileName,append=TRUE)
    print(xtable(glm.D93,align="r||llrc"),include.rownames=TRUE,include.colnames=FALSE,
      type=i,file=outFileName,append=TRUE)
    print(xtable(glm.D93,align="|r||llrc"),include.rownames=FALSE,include.colnames=FALSE,
      type=i,file=outFileName,append=TRUE)
    print(xtable(glm.D93,align="|r||llrc|"),type=i,file=outFileName,append=TRUE)
    print(xtable(anova(glm.D93)),hline.after=c(1),size="small",type=i,file=outFileName, append=TRUE)
    if(require(stats,quietly=TRUE)) {
      print(xtable(pr1),type=i,file=outFileName,append=TRUE)
      print(xtable(summary(pr1)),type=i,file=outFileName,append=TRUE)
      # print(xtable(pr2),type=i,file=outFileName,append=TRUE)
    }
    temp.table <- xtable(ts(cumsum(1+round(rnorm(100), 2)), start = c(1954, 7), frequency=12))
    caption(temp.table) <- "Time series example"
    print(temp.table,type=i,file=outFileName,append=TRUE,caption.placement="top",
      table.placement="h")
    print(temp.table,type=i,file=outFileName,append=TRUE,caption.placement="bottom",
      table.placement="htb")
  }
} 

}
\keyword{file}