moved from svn to git

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+# Help files (because they will be created automatically by roxygen)
+*.Rd
+# Example code in package build process
+*-Ex.R
+# Output files from R CMD build
+/*.tar.gz
+# Output files from R CMD check
+/*.Rcheck/
+# RStudio files
+.Rproj.user/
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+.Rproj.user
+inst/doc

DESCRIPTION

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+Package: lusweave
+Type: Package
+Title: Landuse Sweave Utilities
+Version: 1.43.4
+Date: 2017-11-29
+Author: Markus Bonsch, Jan Philipp Dietrich, Florian Humpenoeder
+Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
+Description: Set of tools which simplify the usage of SWeave in R and allow to easily create PDF files based on R data.
+Depends: R(>= 2.10.0), methods
+Imports: xtable,  
+	 knitr,
+	 utils
+License: BSD_2_clause + file LICENSE
+LazyData: no
+RoxygenNote: 6.0.1

LICENSE

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+YEAR: 2016
+COPYRIGHT HOLDER: Potsdam Institute for Climate Impact Research (PIK)

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(swR)
+export(swclose)
+export(swfigure)
+export(swlatex)
+export(swopen)
+export(swtable)
+importFrom(methods,is)
+importFrom(methods,new)
+importFrom(utils,Sweave)
+importFrom(utils,data)
+importFrom(xtable,xtable)

R/Sweave.sty

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+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{Sweave}{}
+\RequirePackage{ifthen}
+\newboolean{Sweave@gin}
+\setboolean{Sweave@gin}{true}
+\newboolean{Sweave@ae}
+\setboolean{Sweave@ae}{true}
+\DeclareOption{nogin}{\setboolean{Sweave@gin}{false}}
+\DeclareOption{noae}{\setboolean{Sweave@ae}{false}}
+\ProcessOptions
+\RequirePackage{graphicx,fancyvrb}
+\ifthenelse{\boolean{Sweave@gin}}{\setkeys{Gin}{width=\textwidth}}{}%
+\ifthenelse{\boolean{Sweave@ae}}{%
+\RequirePackage[T1]{fontenc}  
+\RequirePackage{ae}
+}{}%
+\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
+\DefineVerbatimEnvironment{Soutput}{Verbatim}{fontsize=\small,xleftmargin=0mm,xrightmargin=0mm}
+\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
+\newenvironment{Schunk}{}{}
+\newcommand{\Sconcordance}[1]{%
+\ifx\pdfoutput\undefined%
+\csname newcount\endcsname\pdfoutput\fi%
+\ifcase\pdfoutput\special{#1}%
+\else\immediate\pdfobj{#1}\fi}

R/lusweavedata.R

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+#' lusweavedata
+#' @description General lusweave-dataset
+#' @aliases lusweavedata
+#' @details Pleasde do not directly acces that data. It should be only used by library functions.
+#' @author Jan Philipp Dietrich
+#' @name lusweavedata
+#'
+
+NULL

R/swR.R

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+#' swR
+#' 
+#' Function to write R code to a \code{"\linkS4class{swStream}"} object.
+#' 
+#' Method designed to write the output of R commands to a swStream object,
+#' taking care that it is correctly embedded. As \code{func} argument, you can
+#' pass either the function itself or its name as a string. User defined
+#' functions will only work with option one, two is only for back
+#' compatibility.
+#' 
+#' @usage swR(stream,func,...,option = "echo=FALSE")
+#' @param stream The \code{swStream} object to be modified.
+#' @param func The R command, that shall be ecexuted. Can be specified as a
+#' string for back compatibility
+#' @param ... Additional parameters passed to the function.
+#' @param option Formatting options.
+#' @return No return value.
+#' @author Markus Bonsch
+#' @export
+#' @seealso
+#' \code{"\linkS4class{swStream}"},\code{\link{swopen}},\code{\link{swclose}},\code{\link{swlatex}},\code{\link{swtable}},\code{\link{swfigure}}
+#' @examples
+#' \dontrun{
+#' test<-swopen(outfile="test.pdf")
+#' swR(test,print,ls)
+#' swR(test,print,"bla_blubb")
+#' x<-c(1,2,3)
+#' swR(test,print,paste(x,"bla"))
+#' swclose(test)
+#' # Only for back compatibility
+#' swR(test,"print","bla_blubb")
+#' }
+#' 
+#' 
+# write R code to a sweaveStream object:
+# define the function and its arguments
+# <<"option">>= 
+# "func(...)" 
+# @
+swR<-function(stream,func,...,option = "echo=FALSE"){
+  envir<-stream
+  stream<-get("stream",envir=envir,inherits=FALSE)
+  orig_stream <- stream
+  stufftowrite <- NULL
+  if(class(stream)=="swStream"){
+    tryCatch({
+      pos<-length(stream@functions)
+      args<-list(...)
+
+      #save func (necessary in case, it is user defined)
+      if(is.function(func)){
+        stream@functions[[pos+1]]<-func
+      } else{ #needed for back compatibility
+        stream@functions[[pos+1]]<-get(func,pos=1,inherits=TRUE)
+      }
+      #paste the command
+      stufftowrite<-paste("stream@functions[[",pos+1,"]](",sep="")
+      if(length(args)>0){
+        #save all arguments as a list in the objects slot of the stream object.
+        stream@arguments[[pos+1]]<-args
+        #paste the arguments in the appropriate format
+        for(i in 1:length(args)){
+          if(any(names(args)!="")){
+            if(names(args)[i]!=""){
+              stufftowrite<-paste(stufftowrite,names(stream@arguments[[pos+1]])[i],"=","stream@arguments[[",pos+1,"]][[",i,"]],",sep="")
+            }else{
+              stufftowrite<-paste(stufftowrite,"stream@arguments[[",pos+1,"]][[",i,"]],",sep="")
+            }
+          }else{
+            stufftowrite<-paste(stufftowrite,"stream@arguments[[",pos+1,"]][[",i,"]],",sep="")
+          }
+        }
+      }
+      #remove last comma
+      if(substr(stufftowrite,nchar(stufftowrite),nchar(stufftowrite))==",") stufftowrite<-substr(stufftowrite,1,nchar(stufftowrite)-1)
+      #add options and closing bracket
+      stufftowrite<-paste(stufftowrite,")",sep="")
+      stufftowrite<-c(paste("<<",option,">>=",sep=""),stufftowrite,"@")
+    }, error=function(e){warning("Error occurred in swR, stream will be set back to previous value.\n   Error message: ",e$message,call. = FALSE);stream <- orig_stream})
+    # Save the updated stream object
+    assign("stream",stream,envir = envir)
+    swlatex(envir,stufftowrite)
+    }else{
+      stop("Input is not a sweaveStream!")
+    }
+}
+

R/swStream-class.R

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+#' Class "swStream" ~~~
+#' 
+#' The swStream class provides an interface to the Sweave method and allows for
+#' easy creation of pdf's from R output.
+#' 
+#' The Sweave method is an interface between R and LaTeX. It processes .Rnw
+#' files, that can contain LaTeX code as well as R code into proper .tex files,
+#' replacing the R commands by their output. See
+#' \code{http://www.stat.uni-muenchen.de/~leisch/Sweave/} for details.\cr An
+#' additional style file is needed to compile the .tex file into a pdf.
+#' 
+#' @name swStream-class
+#' @docType class
+#' @section Objects from the Class: Objects can be created by calls of the form
+#' \code{new("swStream", name,folder, content, Sweave.sty, arguments,
+#' functions, auxfiles, envir)}.
+#' @author Markus Bonsch
+#' @seealso
+#' \code{\link{swopen}},\code{\link{swclose}},\code{\link{swlatex}},\code{\link{swR}},\code{\link{swtable}},\code{\link{swfigure}}
+#' @keywords classes
+#' @examples
+#' \dontrun{
+#' showClass("swStream")
+#' }
+setClass("swStream",representation(name = "character",content = "vector",Sweave.sty="vector",functions="list",arguments="list",auxfiles="vector",envir="environment"),prototype = list(name = "",content = c("",""),Sweave.sty=c("",""),functions=list(),arguments=list(),auxfiles=c("",""),envir=.GlobalEnv))

R/swclose.R

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+#' Close a swStream
+#' 
+#' Function to create a pdf from a \code{"\linkS4class{swStream}"} object
+#' 
+#' Creates a pdf with of the name specified in \code{stream@name}, with the
+#' content specified in \code{stream@content}, using \code{stream@Sweave.sty}
+#' as the style file.
+#' 
+#' @usage swclose(stream,outfile="",latexpath="",clean_output=TRUE,
+#' engine="knitr", save_stream=TRUE, knitquiet = FALSE)
+#' @param stream The \code{swStream} object to be processed.
+#' @param outfile Name of the pdf to be produced. Overwrites the name given in
+#' swopen
+#' @param latexpath Path of the LaTeX distribution (only necessary if not part
+#' of the PATH variable).
+#' @param clean_output If true, all auxiliary files will be deleted. If False,
+#' they remain, including each plot in its own pdf.
+#' @param engine Engine to use for conversion. Currently available: Sweave and
+#' knitr.
+#' @param save_stream If true (default) stream is saved to .rda file.
+#' @param knitquiet If false (default) progressbar and messages are printed
+#' otherwise suppressed.
+#' @return No return value.
+#' @author Markus Bonsch, David Klein
+#' @export
+#' @seealso
+#' \code{"\linkS4class{swStream}"},\code{\link{swopen}},\code{\link{swlatex}},\code{\link{swR}},\code{\link{swtable}},\code{\link{swfigure}}
+#' @examples
+#' \dontrun{
+#' test<-swopen(outfile="test.pdf")
+#' swlatex(test,"tttteeeesssstttt")
+#' swclose(test)
+#' #Change the name
+#' swclose(test,outfile="test_2.pdf")
+#' }
+#' 
+#method to create a pdf from the swStream object
+swclose<-function(stream,outfile="",latexpath="",clean_output=TRUE, engine="knitr", save_stream=TRUE, knitquiet = FALSE){
+
+  #Write "content" (extended by "\end{document}")to an Rnw file, 
+  #sweave this file and produce the pdf from the .tex file. Then delete the sweaveStream
+  if(is.environment(stream)) {
+    envir<-stream
+    stream<-get("stream",envir=envir,inherits=FALSE)
+  } else {
+    envir <- new.env()
+    assign("stream",stream,envir=envir)
+  }
+  if(class(stream)=="swStream"){
+     #update the name if necessary
+     if(outfile!=""){
+       if(length(strsplit(outfile,split="/")[[1]])>1){
+         tmp<-strsplit(outfile,split="/")[[1]]
+         outfile<-tmp[length(tmp)]
+         folder<-paste(tmp[1:(length(tmp)-1)],collapse="/") 
+       } else{
+         folder<-""
+       }
+       outfile<-strsplit(outfile,".pdf", fixed=TRUE)[[1]]
+       outfile<-gsub("\\.","-_-_-",outfile)
+       stream@auxfiles<-gsub(strsplit(stream@name,".pdf", fixed=TRUE)[[1]],strsplit(outfile,".pdf", fixed=TRUE)[[1]],stream@auxfiles)
+       stream@name<-outfile
+       stream@folder<-folder
+       assign("stream",stream,envir = envir)
+     }
+
+  	 stream@content<-c(stream@content,"\\end{document}")
+
+     this_dir<-getwd()
+     if(stream@folder!="") setwd(stream@folder)
+
+     if(save_stream) save(stream,file=paste0(stream@name,".rda"),compress = "xz")
+
+		 writeLines(stream@content,paste(strsplit(stream@name,".pdf", fixed=TRUE)[[1]],".Rnw",sep=""))
+		 #create the style file if no external one is specified
+		 writeLines(stream@Sweave.sty,"Sweave.sty")
+		 #execute the Sweave routine which executes the R code in the Rnw file and produces a tex file
+
+
+     #Attach the stream to the global environment because this is where Sweave does the evaluation
+		 globalenv = .GlobalEnv
+     tmp<-try(get("stream",envir=globalenv),silent=TRUE)
+     assign("stream",stream,envir=globalenv)
+     #now run Sweave or knitr
+		 rnwfile <- paste(strsplit(stream@name,".pdf", fixed=TRUE)[[1]],".Rnw",sep="")
+     if(engine=="Sweave") {
+       Sweave(rnwfile,encoding="bytes")
+     } else if(engine=="knitr"){
+       if (!requireNamespace("knitr", quietly = TRUE)) stop("The package knitr is not available!")
+       knitr::Sweave2knitr(rnwfile,output = rnwfile)
+       suppressWarnings(knitr::knit(rnwfile,quiet = knitquiet))
+     } else {
+       stop("Unknown engine ",engine)
+     }
+
+     #restore stream object in the global environment
+     if(!is(tmp,"try-error")) assign("stream",tmp,envir=globalenv)
+
+     #check for command pdflatex and change latexpath in the case that it cannot be found
+     latexpaths <- c(latexpath,"/iplex/01/sys/applications/texlive/bin/x86_64-linux/","","not found")
+     for(latexpath in latexpaths) {
+       if(Sys.which(paste0(latexpath,"pdflatex"))!="") break
+     }     
+     if(latexpath=="not found") stop("Executable pdflatex could not be found. Please check your latexpath setting")
+    #compile to pdf, needed two times for generation of table of contents
+    for(i in 1:2) {
+      error_code<-suppressWarnings(system(paste0(latexpath,"pdflatex --interaction=nonstopmode ",paste0(strsplit(stream@name,".pdf", fixed=TRUE)[[1]],".tex")),intern=TRUE))
+    }
+    if(!is.null(attr(error_code,"status"))) warning("Execution of pdflatex reported an error (code ",attr(error_code,"status"),") please check the corresponding log file for further information.")
+    file.rename(paste(strsplit(stream@name,".pdf", fixed=TRUE)[[1]],".pdf",sep=""),paste(gsub("-_-_-","\\.",strsplit(stream@name,".pdf", fixed=TRUE)[[1]]),".pdf",sep=""))
+    file.rename(paste(strsplit(stream@name,".pdf", fixed=TRUE)[[1]],".log",sep=""),paste(gsub("-_-_-","\\.",strsplit(stream@name,".pdf", fixed=TRUE)[[1]]),".log",sep=""))
+    #remove unnecessary compilation files
+    if(clean_output==TRUE) log<-suppressWarnings(file.remove(stream@auxfiles))
+    setwd(this_dir)
+  }else{
+	  stop("Input is not a sweaveStream!")
+	 }
+}