### xtable package
###
### Produce LaTeX and HTML tables from R objects.
###
### Copyright 2000-2007 David B. Dahl <dahl@stat.tamu.edu>
###
### This file is part of the `xtable' library for R and related languages.
### It is made available under the terms of the GNU General Public
### License, version 2, or at your option, any later version,
### incorporated herein by reference.
###
### This program is distributed in the hope that it will be
### useful, but WITHOUT ANY WARRANTY; without even the implied
### warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
### PURPOSE.  See the GNU General Public License for more
### details.
###
### You should have received a copy of the GNU General Public
### License along with this program; if not, write to the Free
### Software Foundation, Inc., 59 Temple Place - Suite 330, Boston,
### MA 02111-1307, USA

xtable <- function(x,caption=NULL,label=NULL,align=NULL,
                   digits=NULL,display=NULL,...) {
  UseMethod("xtable")
}


## data.frame and matrix objects

xtable.data.frame <- function(x,caption=NULL,label=NULL,align=NULL,
                              digits=NULL,display=NULL,...) {
  logicals <- unlist(lapply(x,is.logical))
  x[,logicals] <- lapply(x[,logicals], as.character)
  characters <- unlist(lapply(x,is.character))
  factors <- unlist(lapply(x,is.factor))
  ints <- sapply(x, is.integer)
  class(x) <- c("xtable","data.frame")
  caption(x) <- caption
  label(x) <- label
  align(x) <- switch(1+is.null(align), align,
                     c("r",c("r","l")[(characters|factors)+1]))
  digits(x) <- switch(1+is.null(digits),digits,c(0,rep(2,ncol(x))))
  # Patch from Seth Falcon <sfalcon@fhcrc.org>, 18-May-2007
  if (is.null(display)) {
      display <- rep("f", ncol(x))
      display[ints] <- "d"
      display[characters | factors] <- "s"
      display <- c("s", display)
  }
  display(x) <- display
  return(x)
}

xtable.matrix <- function(x,caption=NULL,label=NULL,align=NULL,
                          digits=NULL,display=NULL,...) {
  return(xtable.data.frame(data.frame(x,check.names=FALSE),
                           caption=caption,label=label,align=align,
                           digits=digits,display=display))
}


## table objects (of 1 or 2 dimensions) by Guido Gay, 9 Feb 2007
## Fixed to pass R checks by DBD, 9 May 2007
xtable.table<-function(x,caption=NULL,label=NULL,align=NULL, digits=NULL,display=NULL,...) {
  if (length(dim(x))==1) {
    return(xtable.matrix(matrix(x,dimnames=list(rownames(x),names(dimnames(x)))),caption=caption,label=label,align=align,digits=digits,display=display))
  } else if (length(dim(x))==2) {
    return(xtable.matrix(matrix(x,ncol=dim(x)[2],nrow=dim(x)[1],dimnames=list(rownames(x),colnames(x))),caption=caption,label=label,align=align,digits=digits,display=display))
  } else {
    stop("xtable.table is not implemented for tables of > 2 dimensions")
  }
}


## anova objects

xtable.anova <- function(x,caption=NULL,label=NULL,align=NULL,
                         digits=NULL,display=NULL,...) {
  suggested.digits <- c(0,rep(2,ncol(x)))
  suggested.digits[grep("Pr\\(>",names(x))+1] <- 4
  suggested.digits[grep("P\\(>",names(x))+1] <- 4
  suggested.digits[grep("Df",names(x))+1] <- 0

  class(x) <- c("xtable","data.frame")
  caption(x) <- caption
  label(x) <- label
  align(x) <- switch(1+is.null(align),align,c("l",rep("r",ncol(x))))
  digits(x) <- switch(1+is.null(digits),digits,suggested.digits)
  display(x) <- switch(1+is.null(display),display,c("s",rep("f",ncol(x))))
  return(x)
}


## aov objects

xtable.aov <- function(x,caption=NULL,label=NULL,align=NULL,
                       digits=NULL,display=NULL,...) {
  return(xtable.anova(anova(x,...),caption=caption,label=label,
                      align=align, digits=digits,display=display))
}

xtable.summary.aov <- function(x,caption=NULL,label=NULL,align=NULL,
                               digits=NULL,display=NULL,...) {
  return(xtable.anova(x[[1]],caption=caption,label=label,
                      align=align, digits=digits,display=display))
}

xtable.summary.aovlist <- function(x,caption=NULL,label=NULL,align=NULL,
                                   digits=NULL,display=NULL,...) {
  for(i in 1:length(x)) {
    if (i==1) result <- xtable.summary.aov(x[[i]],caption=caption,label=label,
          align=align, digits=digits,display=display)
    else result <- rbind(result,xtable.anova(x[[i]][[1]],caption=caption,
                                             label=label, align=align,
                                             digits=digits,display=display))
  }
  return(result)
}

xtable.aovlist <- function(x,caption=NULL,label=NULL,align=NULL,
                           digits=NULL,display=NULL,...) {
  return(xtable.summary.aovlist(summary(x),caption=caption,label=label,
                                align=align, digits=digits,display=display))
}



## lm objects

xtable.lm <- function(x,caption=NULL,label=NULL,align=NULL,
                      digits=NULL,display=NULL,...) {
  return(xtable.summary.lm(summary(x),caption=caption,label=label,
                           align=align, digits=digits,display=display))
}

xtable.summary.lm <- function(x,caption=NULL,label=NULL,align=NULL,
                              digits=NULL,display=NULL,...) {
  x <- data.frame(x$coef,check.names=FALSE)

  class(x) <- c("xtable","data.frame")
  caption(x) <- caption
  label(x) <- label
  align(x) <- switch(1+is.null(align),align,c("r","r","r","r","r"))
  digits(x) <- switch(1+is.null(digits),digits,c(0,4,4,2,4))
  display(x) <- switch(1+is.null(display),display,c("s","f","f","f","f"))
  return(x)
}


## glm objects

xtable.glm <- function(x,caption=NULL,label=NULL,align=NULL,
                       digits=NULL,display=NULL,...) {
  return(xtable.summary.glm(summary(x),caption=caption,label=label,align=align,
                            digits=digits,display=display))
}

xtable.summary.glm <- function(x,caption=NULL,label=NULL,align=NULL,
                               digits=NULL,display=NULL,...) {
  return(xtable.summary.lm(x,caption=caption,label=label,
                           align=align, digits=digits,display=display))
}


## prcomp objects

xtable.prcomp <- function(x,caption=NULL,label=NULL,align=NULL,
                          digits=NULL,display=NULL,...) {
  x <- data.frame(x$rotation,check.names=FALSE)

  class(x) <- c("xtable","data.frame")
  caption(x) <- caption
  label(x) <- label
  align(x) <- switch(1+is.null(align),align,c("r",rep("r",ncol(x))))
  digits(x) <- switch(1+is.null(digits),digits,c(0,rep(4,ncol(x))))
  display(x) <- switch(1+is.null(display),display,c("s",rep("f",ncol(x))))
  return(x)
}

xtable.summary.prcomp <- function(x,caption=NULL,label=NULL,align=NULL,
                                  digits=NULL,display=NULL,...) {
  x <- data.frame(x$importance,check.names=FALSE)

  class(x) <- c("xtable","data.frame")
  caption(x) <- caption
  label(x) <- label
  align(x) <- switch(1+is.null(align),align,c("r",rep("r",ncol(x))))
  digits(x) <- switch(1+is.null(digits),digits,c(0,rep(4,ncol(x))))
  display(x) <- switch(1+is.null(display),display,c("s",rep("f",ncol(x))))
  return(x)
}


# Slightly modified version of xtable.coxph contributed on r-help by
#   Date: Wed, 2 Oct 2002 17:47:56 -0500 (CDT)
#   From: Jun Yan <jyan@stat.wisc.edu>
#   Subject: Re: [R] xtable for Cox model output
xtable.coxph <- function (x,caption=NULL,label=NULL,align=NULL,
                          digits=NULL,display=NULL,...)
{
  cox <- x
  beta <- cox$coef
  se <- sqrt(diag(cox$var))
  if (is.null(cox$naive.var)) {
    tmp <- cbind(beta, exp(beta), se, beta/se, 1 - pchisq((beta/se)^2, 1))
    dimnames(tmp) <- list(names(beta),
      c("coef", "exp(coef)", "se(coef)", "z", "p"))
  }
  else {
    tmp <- cbind( beta, exp(beta), se, beta/se,
      signif(1 - pchisq((beta/se)^2, 1), digits - 1))
    dimnames(tmp) <- list(names(beta),
      c("coef", "exp(coef)", "robust se", "z", "p"))
  }
  return(xtable(tmp, caption = caption, label = label, align = align,
                digits = digits, display = display))
}

# Additional method: xtable.ts
# Contributed by David Mitchell (davidm@netspeed.com.au)
# Date: July 2003
xtable.ts <- function(x,caption=NULL,label=NULL,align=NULL,
                      digits=NULL,display=NULL,...) {
  if (inherits(x, "ts") && !is.null(ncol(x))) {
    # COLNAMES <- paste(colnames(x));
    tp.1 <- trunc(time(x))
    tp.2 <- trunc(cycle(x))
    day.abb <- c("Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat")
    ROWNAMES <- switch(frequency(x),
                       tp.1,
                       "Arg2", "Arg3",              ## Dummy arguments
                       paste(tp.1, c("Q1", "Q2", "Q3", "Q4")[tp.2], sep=" "),
                       "Arg5", "Arg6",
                       paste("Wk.", tp.1, " ", day.abb[tp.2], sep=""),
                       "Arg8", "Arg9", "Arg10", "Arg11",
                       paste(tp.1, month.abb[tp.2], sep=" "))
    tmp <- data.frame(x, row.names=ROWNAMES);
  }
  else if (inherits(x, "ts") && is.null(ncol(x))) {
    COLNAMES <- switch(frequency(x),
                       "Value",
                       "Arg2", "Arg3",              ## Dummy arguments
                       c("Q1", "Q2", "Q3", "Q4"),
                       "Arg5", "Arg6",
                       day.abb,
                       "Arg8", "Arg9", "Arg10", "Arg11",
                       month.abb)
    ROWNAMES <- seq(from=start(x)[1], to=end(x)[1])
    tmp <- data.frame(matrix(c(rep(NA, start(x)[2] - 1), x,
                               rep(NA, frequency(x) - end(x)[2])),
                             ncol=frequency(x), byrow=TRUE), row.names=ROWNAMES)
    names(tmp) <- COLNAMES
  }
  return(xtable(tmp, caption = caption, label = label, align = align,
                digits = digits, display = display))
}

# Suggested by Ajay Narottam Shah <ajayshah@mayin.org> in e-mail 2006/07/22
xtable.zoo <- function(x,...) {
  return(xtable(as.ts(x),...))
}