updated examples

chencaf · Jul 23, 2015 · c9cb4fb · c9cb4fb
1 parent e842bd8
commit c9cb4fb
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Showing 21 changed files with 169 additions and 149 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,2 +1,3 @@
 ^.*\.Rproj$
+examples
 ^\.Rproj\.user$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -10,18 +10,19 @@ Maintainer: Tom Wenseleers <[email protected]>
 Depends:
     R (>= 3.0),
     ReporteRs (>= 0.7),
-    ReporteRsjars (>= 0.0.2),
+    ReporteRsjars (>= 0.0.2)
+Imports:   
     stats,
-    graphics,
-    grDevices,
     utils,
     datasets,
-    methods
-Imports:    
+    methods,
+    rJava,
     rtable (>= 0.1),
     xtable (>= 1.7),
     tikzDevice (>= 0.8),
-    stargazer (>= 5.1)
+    stargazer (>= 5.1),
+    graphics,
+    grDevices
 Suggests:
     lattice,
     latticeExtra,

diff --git a/NAMESPACE b/NAMESPACE
@@ -20,9 +20,13 @@ export(table2tex)
 export(table2tex2)
 import(ReporteRs)
 import(ReporteRsjars)
+import(datasets)
 import(grDevices)
+import(graphics)
 import(methods)
+import(rJava)
 import(rtable)
+import(stargazer)
 import(stats)
-import(utils)
+import(tikzDevice)
 import(xtable)
diff --git a/R/graph2bitmap.R b/R/graph2bitmap.R
@@ -58,7 +58,7 @@ graph2bitmap = function(x = NULL, file = "Rplot", fun = NULL, type = c("PNG","JP
     stop("base R plots cannot be passed as objects, use ggplot2 or lattice plots instead")
   myplot = if (is.null(fun)) function(pl = p) print(pl) else fun
 
-  plotsize = dev.size()  # also works if no graphics device is open
+  plotsize = grDevices::dev.size()  # also works if no graphics device is open
   w = plotsize[[1]]
   h = plotsize[[2]]
   plotaspectr = plotsize[[1]]/plotsize[[2]]
@@ -72,7 +72,7 @@ graph2bitmap = function(x = NULL, file = "Rplot", fun = NULL, type = c("PNG","JP
   w = w*scaling/100; h = h*scaling/100;
 
   if (type == "PNG") {
-      png( filename = file, 
+    grDevices::png( filename = file, 
         type = ifelse(cairo,"cairo-png","windows"),
         units = "in", 
         width = w, 
@@ -81,11 +81,11 @@ graph2bitmap = function(x = NULL, file = "Rplot", fun = NULL, type = c("PNG","JP
         res = dpi,
         bg = bg, ...)
     myplot()
-    invisible(dev.off())
+    invisible(grDevices::dev.off())
   }
 
   if (type == "TIF") {
-      tiff( filename = file, 
+    grDevices::tiff( filename = file, 
          type = ifelse(cairo,"cairo","windows"),
          compression = tiffcompression,
          units = "in", 
@@ -95,11 +95,11 @@ graph2bitmap = function(x = NULL, file = "Rplot", fun = NULL, type = c("PNG","JP
          res = dpi,
          bg = bg, ... )
     myplot()
-    invisible(dev.off())  
+    invisible(grDevices::dev.off())  
   }
 
   if (type == "JPEG") { 
-      jpeg( filename = file, 
+    grDevices::jpeg( filename = file, 
           #type = ifelse(cairo,"cairo","windows"),
           quality = jpegquality,
           units = "in", 
@@ -109,7 +109,7 @@ graph2bitmap = function(x = NULL, file = "Rplot", fun = NULL, type = c("PNG","JP
           res = dpi,
           bg = bg, ... )
     myplot()
-    invisible(dev.off())
+    invisible(grDevices::dev.off())
   }  
 
   message(paste0("Exported graph as ",file))

diff --git a/R/graph2office.R b/R/graph2office.R
@@ -3,10 +3,12 @@
 #' Save the currently active R graph or a graph passed as an object or function 
 #' to Microsoft Office / LibreOffice format with sensible defaults
 #' 
+#' @import datasets
+#' @import graphics
+#' @import rJava
 #' @import ReporteRs
 #' @import ReporteRsjars
 #' @import grDevices
-#' @import utils
 #' @aliases graph2office graph2doc graph2ppt
 #' @param x given \code{ggplot2} plot or \code{lattice} plot object to export; if
 #' set to \code{NULL} the currently active R graph will be exported; not
@@ -89,7 +91,7 @@ graph2office = function(x = NULL, file = "Rplot", fun = NULL, type = c("PPT","DO
       function(pl = p) print(pl) else fun
     #myplot()
 
-    plotsize = dev.size()  # also works if no graphics device is open
+    plotsize = grDevices::dev.size()  # also works if no graphics device is open
     w = plotsize[[1]]
     h = plotsize[[2]]
     plotaspectr = plotsize[[1]]/plotsize[[2]]
@@ -201,10 +203,10 @@ sizes=(5:1)[1:length(landscA)]
 portrA=lapply(landscA,rev) # size of A5 to A1 landscape PPT/DOC templates
 #w=8.9;h=6.7;
 if (orient=="auto") orient=ifelse(w>=h,"landscape","portrait")
-bestpagesize=suppressWarnings(ifelse( orient=="landscape", sizes[max( min(which(w<=unlist(lapply(landscA,head,n=1)))),
-                                                     min(which(h<=unlist(lapply(landscA,tail,n=1)))) )],
-                                      sizes[max( min(which(w<=unlist(lapply(portrA,head,n=1)))),
-                                                     min(which(h<=unlist(lapply(portrA,tail,n=1)))) )] ))
+bestpagesize=suppressWarnings(ifelse( orient=="landscape", sizes[max( min(which(w<=unlist(lapply(landscA,utils::head,n=1)))),
+                                                     min(which(h<=unlist(lapply(landscA,utils::tail,n=1)))) )],
+                                      sizes[max( min(which(w<=unlist(lapply(portrA,utils::head,n=1)))),
+                                                     min(which(h<=unlist(lapply(portrA,utils::tail,n=1)))) )] ))
 if (is.na(bestpagesize)) bestpagesize=min(sizes)
 return(paste0("A",bestpagesize,"_",orient)) }
 

diff --git a/R/graph2tex.R b/R/graph2tex.R
@@ -5,6 +5,7 @@
 #' 
 #' 
 #' @import grDevices
+#' @import tikzDevice
 #' @aliases graph2tex graph2tex2
 #' @param x given \code{ggplot2} plot or \code{lattice} plot object to export; if
 #' set to \code{NULL} the currently active R graph will be exported; not
@@ -50,7 +51,7 @@ graph2tex = function(x = NULL, file = "Rplot", fun = NULL,
   myplot = if (is.null(fun)) function(pl = p) print(pl) else fun
 
   if (!is.na(font)) {if (font=="sans-serif"|font=="Helvetica"|font=="Arial"|font=="Verdana"|font=="Tahoma") font="sans"}
-  plotsize = dev.size()  # also works if no graphics device is open
+  plotsize = grDevices::dev.size()  # also works if no graphics device is open
   w = plotsize[[1]]
   h = plotsize[[2]]
   plotaspectr = plotsize[[1]]/plotsize[[2]]
@@ -64,14 +65,14 @@ graph2tex = function(x = NULL, file = "Rplot", fun = NULL,
   if ((!is.null(width))&(!is.null(height))) { w = width; h = height }  
   w = w*scaling/100; h = h*scaling/100;
 
-  tikzDevice::tikz(file = file, 
+  tikz(file = file, 
         height = h, 
         width = w,
         bg = bg,
        standAlone = standAlone,
         ... )
     myplot()
-  dev.off()
+    grDevices::dev.off()
 
   if (!is.null(font)) {   if ("sans" %in% font) {
                           out = readLines(file) 

diff --git a/R/graph2vector.R b/R/graph2vector.R
@@ -60,7 +60,7 @@ graph2vector = function(x = NULL, file = "Rplot", fun = NULL, type = "SVG",
     stop("base R plots cannot be passed as objects, use ggplot2 or lattice plots instead")
   myplot = if (is.null(fun)) function(pl = p) print(pl) else fun
 
-  plotsize = dev.size()  # also works if no graphics device is open
+  plotsize = grDevices::dev.size()  # also works if no graphics device is open
   w = plotsize[[1]]
   h = plotsize[[2]]
   plotaspectr = plotsize[[1]]/plotsize[[2]]
@@ -75,20 +75,20 @@ graph2vector = function(x = NULL, file = "Rplot", fun = NULL, type = "SVG",
   w = w*scaling/100; h = h*scaling/100;
 
   if (type == "SVG") {
-    svg(filename = file, 
+    grDevices::svg(filename = file, 
              height = h, 
              width = w,
              family = font,
              onefile = FALSE,
              bg = bg,
              ... )
     myplot()
-    dev.off()
+    grDevices::dev.off()
   }
 
   if (type == "PDF") {
     #cairo_surface_set_fallback_resolution() # check cairoSurfaceSetFallbackResolution in library(RGtk2)
-    if (!cairo) { pdf(file = file,  # also check cairo_pdf
+    if (!cairo) { grDevices::pdf(file = file,  # also check cairo_pdf
         height = h, 
         width = w,
         family = font,
@@ -97,7 +97,7 @@ graph2vector = function(x = NULL, file = "Rplot", fun = NULL, type = "SVG",
         colormodel = colormodel, 
         useDingbats = FALSE,
         ... ) } else { 
-          cairo_pdf(filename = file,  # also check cairo_pdf
+          grDevices::cairo_pdf(filename = file,  # also check cairo_pdf
               height = h, 
               width = w,
               family = font, 
@@ -106,19 +106,19 @@ graph2vector = function(x = NULL, file = "Rplot", fun = NULL, type = "SVG",
               ... ) 
         }
     myplot()
-    dev.off()
+    grDevices::dev.off()
   }
 
   if (type == "EPS") { 
-    if (!cairo) { postscript(file = file, 
+    if (!cairo) { grDevices::postscript(file = file, 
                height = h, 
                width = w,
                family = font,
                onefile = FALSE,
                bg = bg,
                colormodel = colormodel, 
                ... ) } else { 
-                 cairo_ps(filename = file, 
+                 grDevices::cairo_ps(filename = file, 
                            height = h, 
                            width = w,
                            family = font,
@@ -127,7 +127,7 @@ graph2vector = function(x = NULL, file = "Rplot", fun = NULL, type = "SVG",
                            ... )
                }
     myplot()
-    dev.off()
+    grDevices::dev.off()
   }
 
   message(paste0("Exported graph as ",file))

diff --git a/R/table2ppt.R b/R/table2ppt.R
@@ -3,13 +3,13 @@
 #' Export currently showing R stats object or stats object obj to a Microsoft
 #' Powerpoint / LibreOffice table
 #' 
+#' @import rJava
 #' @import ReporteRs
 #' @import xtable
 #' @import rtable
 #' @import methods 
 #' @import stats  
 #' @import grDevices
-#' @import utils
 #' @aliases table2ppt
 #' @param x given R stats object to export; if set to \code{NULL} the output of the 
 #' previous R command will be exported.
@@ -56,7 +56,7 @@ table2ppt = function(x = NULL, file = "Rtable", append = FALSE, digits = 2,
         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")
-    supobjects = c(as.character(gsub("xtable.", "", methods(xtable))), "xtabs", "ftable")  
+    supobjects = c(as.character(gsub("xtable.", "", utils::methods(xtable))), "xtabs", "ftable")  
     # objects supported by xtable
     # 'anova' 'aov' 'aovlist' 'coxph' 'data.frame' 'glm' 'lm' 
     # 'matrix' 'prcomp' 'summary.aov' 'summary.aovlist' 'summary.glm'
@@ -68,7 +68,7 @@ table2ppt = function(x = NULL, file = "Rtable", append = FALSE, digits = 2,
     # tempfile = tempfile(pattern='rhistory_', fileext='.txt') 
     # savehistory(tempfile)
     # myhistory = readLines(tempfile) 
-    # h = tail(h, 5) # last 5 commands eval(parse(text=h[length(h)-1])) 
+    # h = stats::tail(h, 5) # last 5 commands eval(parse(text=h[length(h)-1])) 
     # exec last command but 1 see
     # also http://stackoverflow.com/questions/20959561/accessing-r-history-from-r-code
 
@@ -94,12 +94,12 @@ table2ppt = function(x = NULL, file = "Rtable", append = FALSE, digits = 2,
 
     # deal with specific classes of objects not supported by xtable
     if ("summary.merMod" %in% class(outp)) 
-        outp = data.frame(coef(summary(outp)), check.names = F)
+        outp = data.frame(stats::coef(summary(outp)), check.names = F)
     if ("xtabs" %in% class(outp)) 
-        outp = ftable(outp)
-    supobjects = as.character(gsub("xtable.", "", methods(xtable)))
+        outp = stats::ftable(outp)
+    supobjects = as.character(gsub("xtable.", "", utils::methods(xtable)))
     if ("ftable" %in% class(outp)) 
-        tab = ftable(outp) else {
+        tab = stats::ftable(outp) else {
         if (length(intersect(class(outp), supobjects)) >= 1) 
             tab = xtable2(outp, ...) else outp = data.frame(outp, check.names = F)
     }
@@ -108,10 +108,10 @@ table2ppt = function(x = NULL, file = "Rtable", append = FALSE, digits = 2,
     # see https://davidgohel.github.io/ReporteRs/formatting_properties.html
     flextab = as.FlexTable(x = tab, add.rownames = add.rownames)
     #if (zebra) flextab=setZebraStyle( flextab, odd = odd, even = even)
-    flextab[] = ReporteRs::textProperties(font.size=pointsize, font.family=font) 
+    flextab[] = textProperties(font.size=pointsize, font.family=font) 
     # flextab[1,, to="header"] = textProperties(color=headertext, 
     # font.size=pointsize, font.weight = "bold", font.family=font)
-    flextab[1,, to="header"] = ReporteRs::textProperties(font.size=pointsize, 
+    flextab[1,, to="header"] = textProperties(font.size=pointsize, 
                                               font.weight = "bold", font.family=font)
     # flextab[1,, to="header"] = parProperties(shading.color=header) 
     # change to setFlexTableBackgroundColors
@@ -120,8 +120,8 @@ table2ppt = function(x = NULL, file = "Rtable", append = FALSE, digits = 2,
     file = sub("^(.*)[.].*", "\\1", file)  # remove extension if given
     file = paste0(file, ext)  # add extension
 
-    if (append & file.exists(file)) { doc = ReporteRs::pptx(template = file) } else { doc = ReporteRs::pptx() }
-    doc = ReporteRs::addSlide(doc, slide.layout = "Blank")
+    if (append & file.exists(file)) { doc = pptx(template = file) } else { doc = pptx() }
+    doc = addSlide(doc, slide.layout = "Blank")
     pagesize = dim(doc)$slide.dim
 
     tblaspectr = flextab$numcol * 0.7/flextab$numrow  # guess table aspect ratio
@@ -141,9 +141,9 @@ table2ppt = function(x = NULL, file = "Rtable", append = FALSE, digits = 2,
     if (!is.null(height)) 
         h = height
 
-    doc = ReporteRs::addFlexTable(doc, flextab, offx = offx, offy = offy, width = w, height = h)
+    doc = addFlexTable(doc, flextab, offx = offx, offy = offy, width = w, height = h)
 
-  ReporteRs::writeDoc(doc, file)
+  writeDoc(doc, file)
 
   message(paste0("Exported table as ",file))
 

diff --git a/R/table2tex.R b/R/table2tex.R
@@ -3,8 +3,8 @@
 #' Export currently showing R stats object or stats object obj to a
 #' Microsoft Word / LibreOffice, HTML or Latex table
 #' @import stats
-#' @import utils
 #' @import grDevices
+#' @import stargazer
 #' @aliases table2tex table2tex2 table2html table2doc
 #' @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.
@@ -65,15 +65,15 @@ table2tex = function(x = NULL, file = "Rtable", type="TEX", digits = 2, summary=
     }
   }
 
-  if ("aov" %in% class(obj)) {obj=as.data.frame(anova(obj));summary=FALSE}
+  if ("aov" %in% class(obj)) {obj=as.data.frame(stats::anova(obj));summary=FALSE}
   if ("summary.aov" %in% class(obj)) {obj=as.data.frame(obj);summary=FALSE}
 
   # CHECK support for xtabs, ftable and CrossTable - contacted original author on this
-  # if ("xtabs" %in% class(outp)) outp = ftable(outp)
+  # if ("xtabs" %in% class(outp)) outp = stats::ftable(outp)
   # if ("ftable" %in% class(outp)) XXX
 
   # object supported by stargazer?
-  supported=!grepl("Unrecognized object type",paste(capture.output(stargazer::stargazer(obj)),collapse=""))
+  supported=!grepl("Unrecognized object type",paste(utils::capture.output(stargazer(obj)),collapse=""))
   if (!supported) stop(paste0("Object of class ",class(obj)," is not supported by stargazer."))
 
   # objects supported by stargazer
@@ -95,8 +95,8 @@ table2tex = function(x = NULL, file = "Rtable", type="TEX", digits = 2, summary=
   # not ftable, xtab, CrossTable?
 
   # preview table in viewer or browser
-  htmlout = capture.output(stargazer::stargazer(obj, type="html", summary=summary, ...)) 
-  texout = capture.output(stargazer::stargazer(obj, type="latex", summary=summary, ...))
+  htmlout = utils::capture.output(stargazer(obj, type="html", summary=summary, ...)) 
+  texout = utils::capture.output(stargazer(obj, type="latex", summary=summary, ...))
   outp = preview(htmlout)
 
   # export to HTML/Word/Latex