dlatex: Dieter Menne's Latex Related Functions

#' @title LaTeX ANOVA table for lme
#'
#' @description Generates LaTeX code for an ANOVA table from \code{lme}.  Number of
#' significant digits depends on standard deviation of the results. Significant
#' p-values are shaded.  The \code{(Intercept)} term is not printed.
#'
#' @method latex anova.lme
#' @param object a fitted model object inheriting from class \code{anova.lme},
#' representing ANOVA of a mixed-effects model.
#' @param title to be printed in upper left corner
#' @param parameter label of the estimated parameter (required), used for
#' caption and label of the table. Can have spaces. See also
#' \code{\link{lmeLabel}}
#' @param file output file name; default prints output to the standard output,
#' which is the choice for Sweave.
#' @param shadep table cells for p-values lower than this will be shaded;
#' p-values for \code{(Intercept)} are never shaded.
#' @param caption caption used for table; default caption is: \emph{Contrast
#' table for <parameter> (model <formula>).  Value in row (Intercept) gives
#' base value for <reference values of variables>}.
#' @param ctable Uses \code{ctable}-formatting of LaTeX.
#' @param where positioning parameter for LaTeX
#' @param \dots Additional parameters passed to \code{latex} in \code{Hmisc}.
#' @return Returns the result of the call to \code{latex} in \code{Hmisc}.
#' @note The function is modelled after \code{print.anova.lme} from package
#' \code{nlme}. Requires \code{ctable} and
#' \code{colortable} in your Snw/tex file.
#' @author Dieter Menne, \email{dieter.menne@@menne-biomed.de}
#' @seealso \code{\link[Hmisc]{latex}}, \code{\link{latex.lme}},
#' \code{\link[nlme]{lme}}
#' @keywords print models
#' @import Hmisc
#' @examples
#'
#' # Pinheiro/Bates page 47
#' library(nlme)
#' library(Hmisc)
#' fm1Oats <- lme(yield~ordered(nitro)*Variety, data=Oats,
#'   random = ~1|Block/Variety)
#' latex(anova(fm1Oats),parameter="Yield",file ="")
#'
#' @export
"latex.anova.lme" <-
  function(object, title = "", parameter, file = "",
            shadep = 0.05, caption = NULL, ctable = FALSE, where = "!htbp", ...)
  {
    options(Hverbose = FALSE)
    if (attr(object, "rt") == 1) {
      # don't show intercept
      object <- object[-1,]
      # background shading; use shadep = 0 for no shading
      sigp <- object[,"p-value"] < shadep
      pval <- format(signif(object[, "p-value"], 2))
      pval[as.double(pval) == 0] <- "\\textless .0001"
      object[, "p-value"] <- pval
      object[,"F-value"] <- round(object[,"F-value"],1)
      cellTex <-
        matrix(rep("", NROW(object) * NCOL(object)), nrow = NROW(object))
      cellTex[sigp,4] <- "cellcolor[gray]{0.9}"
      if (is.null(caption))
        caption = paste("ANOVA for ",parameter,'.',sep = "")
      label <- lmeLabel("anova",parameter)
      rowlabel <- ifelse(nchar(parameter) > 9,"",parameter)
      names(object) <- c("numDF","denDF","F","p")
      latex(
        as.data.frame(object),title = title,rowlabel = rowlabel,
        cellTexCmds = cellTex,file = file,where = where,
        label = label, caption = caption,caption.loc = "bottom",
        booktabs = !ctable,
        numeric.dollar = FALSE,col.just = rep("r",5),ctable = ctable,...
      )
    }
    else {
      stop("latex output of anova.lme with multiple arguments not handled")
    }
  }