R/table2tex.R

In export: Streamlined Export of Graphs and Data Tables

#' Export statistical output to HTML or Latex table
#' 
#' Export currently showing R stats object or stats object obj to a
#' HTML or Latex table
#' @import stats
#' @importFrom utils capture.output
#' @import stargazer
#' @aliases table2tex table2html 
#' @param x given R stats object or list of stats objects to export; if set to \code{NULL} 
#' the output of the previous R command will be exported.
#' @param file name of output file. The appropriate extension is added automatically.
#' @param type desired output type - \code{"TEX"} for Latex and \code{"HTML"} for HTML.
#' @param digits number of significant digits to show for all columns except
#' for the column with p values.
#' @param digitspvals number of significant digits to show for columns with p
#' values.
#' @param trim.pval a threshold below which the p-values are trimmed as 
#' "< \code{trim.pval}".
#' @param summary logical indicating whether or not to summarize data files.
#' @param standAlone logical indicating whether exported Latex code should be
#' standalone compilable, or whether it will be pasted into another document.
#' @param add.rownames logical indicating whether the names of the rows should be added
#' to the table (inserting a column before first column).
#' @param \dots extra options are passed on to stargazer.
#' @return No return value
#' @details Objects that can be exported are all those supported by \code{\link[xtable]{xtable}}, 
#' \code{\link{tidy}} (see \code{\link{table2office}} for an extensive list of supported 
#' methods), or \code{\link[stargazer]{stargazer}}. The models supported by 
#' \code{\link[stargazer]{stargazer}} are:
#' \itemize{
#' \item \code{aftreg} (\code{eha})
#' \item \code{anova} (\code{stats})
#' \item \code{aov} (\code{stats})
#' \item \code{aovlist} (\code{stats})
#' \item \code{arima} (\code{stats}) 
#' \item \code{betareg} (\code{betareg})
#' \item \code{binaryChoice} (\code{sampleSelection})
#' \item \code{bj} (\code{rms})
#' \item \code{brglm} (\code{brglm}) 
#' \item \code{censReg} (\code{censReg})
#' \item \code{coeftest} (\code{lmtest})
#' \item \code{coxph} (\code{survival})
#' \item \code{coxreg} (\code{eha}) 
#' \item \code{clm} (\code{ordinal})
#' \item \code{clogit} (\code{survival})
#' \item \code{cph} (\code{rms})
#' \item \code{dynlm} (\code{dynlm})
#' \item \code{ergm} (\code{ergm})
#' \item \code{errorsarlm} (\code{spdev})
#' \item \code{felm} (\code{lfe})
#' \item \code{gam} (\code{mgcv})
#' \item \code{garchFit} (\code{fGarch})
#' \item \code{gee} (\code{gee})
#' \item \code{glm} (\code{stats})
#' \item \code{Glm} (\code{rms})
#' \item \code{glmer} (\code{lme4})
#' \item \code{glmrob} (\code{robustbase})
#' \item \code{gls} (\code{nlme})
#' \item \code{Gls} (\code{rms})
#' \item \code{gmm} (\code{gmm})
#' \item \code{heckit} (\code{sampleSelection})
#' \item \code{hetglm} (\code{glmx})
#' \item \code{hurdle} (\code{pscl})
#' \item \code{ivreg} (\code{AER})
#' \item \code{lagarlm} (\code{spdep})
#' \item \code{lm} (\code{stats})
#' \item \code{lme} (\code{nlme})
#' \item \code{lmer} (\code{lme4})
#' \item \code{lmrob} (\code{robustbase})
#' \item \code{lrm} (\code{rms})
#' \item \code{maBina} (\code{erer})
#' \item \code{mclogit} (\code{mclogit})
#' \item \code{mlogit} (\code{mlogit})
#' \item \code{mnlogit} (\code{mnlogit})
#' \item \code{mlreg} (\code{eha})
#' \item \code{multinom} (\code{nnet})
#' \item \code{nlme} (\code{nlme})
#' \item \code{nlmer} (\code{lme4})
#' \item \code{ols} (\code{rms})
#' \item \code{pgmm} (\code{plm})
#' \item \code{phreg} (\code{eha})
#' \item \code{plm} (\code{plm})
#' \item \code{pmg} (\code{plm})
#' \item \code{polr} (\code{MASS})
#' \item \code{psm} (\code{rms})
#' \item \code{rem.dyad} (\code{relevent})
#' \item \code{rlm} (\code{MASS})
#' \item \code{rq} (\code{quantreg})
#' \item \code{Rq} (\code{rms})
#' \item \code{selection} (\code{sampleSelection})
#' \item \code{svyglm} (\code{survey})
#' \item \code{survreg} (\code{survival})
#' \item \code{tobit} (\code{AER})
#' \item \code{weibreg} (\code{eha})
#' \item \code{zeroin} (\code{pscl})
#' \item \code{relogit} (\code{zelig})
#' \item \code{cloglog.net} (\code{zelig})
#' \item \code{gamma.net} (\code{zelig})
#' \item \code{probit.net} (\code{zelig}) 
#' \item \code{logit.net} (\code{zelig})
#' }
#' @author Tom Wenseleers, Christophe Vanderaa
#' @example examples/table2tex.R
#' @seealso \code{\link{table2office}} ,\code{\link{table2ppt}}, \code{\link{table2doc}}, 
#' \code{\link[stargazer]{stargazer}}
#' @export
#' 
table2tex = function(x = NULL, file = "Rtable", type="TEX", digits = 2, digitspvals = 2, 
                     trim.pval = 1e-16, summary=FALSE, standAlone=TRUE, add.rownames = FALSE,...) {
  # Get the data that will be exported
  obj=x
  if (is.null(obj)) 
    outp = .Last.value else outp = obj  # capture previously shown output or use passed object
  if (is.null(outp)) 
    stop("no R stats object available to export")
  obj=outp

  # Match the requested file type
  type=toupper(type)
  type=match.arg(type,c("TEX","HTML"))
  if (type=="HTML") { ext=".html" }
  if (type=="TEX") { ext=".tex" }
  file = sub("^(.*)[.].*", "\\1", file)  # remove extension if given
  file = paste0(file, ext)  # add extension
  
  # Depending on the class of the data call the formating function
  if (length(intersect(class(obj), as.character(gsub("xtable.", "", methods(xtable))))) >= 1) {
    obj <- xtable2(x=obj, ndigits = digits, ndigitspvals = digitspvals, trim.pval=trim.pval)
    obj <- as.data.frame(obj)
  } else if (length(intersect(class(obj), as.character(gsub("tidy.", "", methods(tidy))))) >= 1) {
    obj <- tidy2(x=obj, ndigits = digits, ndigitspvals = digitspvals, trim.pval=trim.pval)
    obj <- as.data.frame(obj)
  } 
  # Else supported objects that should be supported by stargazer
  
  if ("aov" %in% class(obj)) {obj=as.data.frame(anova(obj));summary=FALSE}
  if ("summary.aov" %in% class(obj)) {obj=as.data.frame(obj);summary=FALSE}
  # object supported by stargazer?
  supported=!grepl("Unrecognized object type",paste(capture.output(stargazer(obj)),collapse=""))
  if (!supported) stop(paste0("Object of class ",class(obj)," is not supported by stargazer."))
  
  # preview table in viewer or browser
  htmlout = capture.output(stargazer(obj, type="html", summary=summary, rownames = add.rownames, digits = digits,...)) 
  texout = capture.output(stargazer(obj, type="latex", summary=summary, rownames = add.rownames, digits = digits,...))
  outp = preview(htmlout)
    
  # export to HTML/Latex
  if (standAlone) {
    texheader=c("\\documentclass[10pt]{article}","\\begin{document}")
    texfooter=c("\\end{document}")
    texout=c(texout[1:3],texheader,texout[4:length(texout)],texfooter)
  }
  if (type=="HTML") { fileConn = file(file)
                      writeLines(htmlout,file)
                      close(fileConn) }
  
  if (type=="TEX") { fileConn = file(file)
                     writeLines(texout,file)
                     close(fileConn) }
  
  message(paste0("Exported table as ",file))
  
}

#' @describeIn table2tex
#' Export statistical output to HTML table
#' @export
table2html = function(...) table2tex(type = "HTML", ...)