Update for CRAN resubmission

.Rbuildignore

@@ -1,5 +1,5 @@
-^.*\.Rproj$
 examples
 ^\.Rproj\.user$
 cran-comments.md
-revdep
+^revdep$
+^.git$

.gitignore

@@ -27,4 +27,5 @@ CMakeLists.txt.user
 .#*
 *.autosave
 *~
-.orig
+.orig
+/revdep/.cache.rds

DESCRIPTION

@@ -8,23 +8,20 @@ Authors@R: c(person("Tom", "Wenseleers", role = c("aut", "cre"),
   	       person("Christophe", "Vanderaa", role = c("aut"),
   	       email = "[email protected]"))
 Depends: R (>= 3.0)
-Imports:  officer (>= 0.2.2), 
-          rvg (>= 0.1.8), 
-          stats, 
+Imports:  stats, 
           utils, 
           datasets, 
-          xtable (>= 1.8-2), 
           grDevices,
+          officer (>= 0.2.2), 
+          rvg (>= 0.1.8), 
+          xtable (>= 1.8-2), 
           flextable (>= 0.4.3), 
           rgl (>= 0.99.16), 
           xml2 (>= 1.2.0), 
-          stargazer, 
+          stargazer (>= 5.2.1), 
           openxlsx (>= 4.0.17), 
           broom (>= 0.4.4)
-Suggests: lattice, 
-          ggplot2 (>= 1.0), 
-          latticeExtra (>= 0.6-28), 
-          tikzDevice
+Suggests: ggplot2 (>= 1.0)
 Description: Easily export 'R' graphs and statistical output to 'Microsoft
     Office' / 'LibreOffice', 'Latex' and 'HTML' Documents, using sensible defaults
     that result in publication-quality output with simple, straightforward commands.
@@ -34,11 +31,11 @@ Description: Easily export 'R' graphs and statistical output to 'Microsoft
     of the layout of 'R' graphs in 'Powerpoint' before final publication. Export
     of graphs is flexible, and functions enable the currently showing R graph
     or the currently showing 'R' stats object to be exported, but also allow the
-    graphs or stats output to be passed as objects. The package relies on package
-    'officer' for export to 'Office',and output files are also fully compatible
+    graphical or tabular output to be passed as objects. The package relies on package
+    'officer' for export to 'Office' documents,and output files are also fully compatible
     with 'LibreOffice'. Base 'R', 'ggplot2' and 'lattice' plots are supported, as
-    well as a wide variety of 'R' stats objects, via wrappers to 'xtable', 'broom::tidy' 
-    and 'stargazer', including 'aov', 'lm', 'glm', 'lme', 'lmer', 'glmer' and 'coxph' as
+    well as a wide variety of 'R' stats objects, via wrappers to xtable(), broom::tidy() 
+    and stargazer(), including aov(), lm(), glm(), lme(), glmnet() and coxph() as
     well as matrices and data frames and many more...
 License: GPL-2
 BugReports: https://github.com/tomwenseleers/export/issues

R/graph2bitmap.R

@@ -50,7 +50,7 @@ graph2bitmap = function(x = NULL, file = "Rplot", fun = NULL, type = c("PNG","JP
                         "Arial","Helvetica")[[1]], bg = "white", cairo = TRUE, 
                         tiffcompression = c("lzw","rle","jpeg","zip","lzw+p","zip+p"), jpegquality = 99, ...) {
   type = toupper(type)
-  type = match.arg(type)
+  type = match.arg(type, c("PNG","JPG","TIF"))
   if (type=="JPG") type="JPEG"
   if (type=="TIFF") type="TIF"
   tiffcompression = match.arg(tiffcompression)
@@ -104,15 +104,13 @@ graph2bitmap = function(x = NULL, file = "Rplot", fun = NULL, type = c("PNG","JP
   }
 
   if (type == "JPEG") { 
-    jpeg( filename = file, 
-          #type = ifelse(cairo,"cairo","windows"),
-          quality = jpegquality,
-          units = "in", 
-          width = w, 
-          height = h, 
-          #family = font,
-          res = dpi,
-          bg = bg, ... )
+    jpeg(filename = file, 
+         quality = jpegquality,
+         units = "in", 
+         width = w, 
+         height = h, 
+         res = dpi,
+         bg = bg)#, ... )
     myplot()
     invisible(dev.off())
   }  

R/graph2office.R

@@ -89,7 +89,11 @@ graph2office = function(x = NULL, file = "Rplot", fun = NULL, type = c("PPT","DO
     p = obj 
   }
   if (inherits(p,"list")) { 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
+  myplot = if (is.null(fun)){
+    function(pl = p) print(pl) 
+  } else {
+    fun
+  } 
 
   ### 2. Prepare the plotting region and the plot apsect
   plotsize = dev.size()  # also works if no graphics device is open
@@ -128,20 +132,21 @@ graph2office = function(x = NULL, file = "Rplot", fun = NULL, type = c("PPT","DO
   ### 4. Initialize the slide (ppt) or page (doc) that will contain the plot
   if (type == "PPT") {
     if (append & file.exists(file)){
-      doc <- officer::read_pptx(path = file)
+      doc <- read_pptx(path = file)
     } else {
-      doc <- officer::read_pptx(path = templ)
+      doc <- read_pptx(path = templ)
     }
-    doc = officer::add_slide(doc, layout = "Blank", master = "Office Theme")
+    doc = add_slide(doc, layout = "Blank", master = "Office Theme")
     pagesize = get.slide.size(doc) 
     pagesize["width"]=pagesize["width"]-(margins["left"]+margins["right"])
     pagesize["height"]=pagesize["height"]-(margins["top"]+margins["bottom"])
   }
   if (type == "DOC") {
     if (append & file.exists(file)){
-      doc <- officer::read_docx(path = file)
+      doc <- read_docx(path = file)
+      doc <- body_add_break(doc, pos = "after")
     } else {
-      doc <- officer::read_docx(path = templ)
+      doc <- read_docx(path = templ)
     }
     pagesize <- (doc$sect_dim$page - doc$sect_dim$margins[c(3,2)])/1440 # 1440 is a factor to convert to inches
   }

R/table2office.R

@@ -21,8 +21,10 @@
 #' for the column with p values.
 #' @param digitspvals number of significant digits to show for columns with p
 #' values.
-#' @param width desired width of table in inches.
-#' @param height desired height of table in inches.
+#' @param width desired width of table in inches. If the given width exceeds the page or slide 
+#' width, the table width becomes the page/slide width.
+#' @param height desired height of table in inches. If the given height exceeds the page or slide 
+#' height, the table height becomes the page/slide height.
 #' @param offx x offset in inches to specify horizontal location of table (only for \code{type=="PPT"}).
 #' @param offy y offset in inches to specify vertical location of table (only for \code{type=="PPT"}).
 #' @param font desired font to use for output table; defaults to \code{"Arial"} on Windows
@@ -206,6 +208,7 @@ table2office = function(x = NULL, file = "Rtable", type = c("PPT","DOC"), append
   } else if(type == "DOC"){
     if (append & file.exists(file)) { 
       doc = read_docx(path = file) 
+      doc = body_add_break(doc, pos = "after")
     } else { 
       doc = read_docx() 
     }

R/table2spreadsheet.R

@@ -17,8 +17,8 @@
 #' @param append logical value - if \code{TRUE} and \code{type="XLS"} it will add a new woorksheet to the given 
 #' file, where file can also be a given corporate.
 #' \code{append=FALSE} any existing file will be overwritten. 
-#' @param sheetName a string giving the name of the new sheet that is created (only when \code{type=="XLS"} and
-#' \code{append==TRUE}). It must unique (case insensitive) from any existing sheet in the file.
+#' @param sheetName a string giving the name of the new sheet that is created (only for \code{type=="XLS"}). 
+#' It must be unique (case insensitive) from any existing sheet name in the file. 
 #' @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

R/table2tex.R

@@ -10,18 +10,22 @@
 #' 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. A value of NA indicates that
-#' no rounding should be done.
+#' @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 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 \code{NULL}
-#' @details Objects that can be exported are all those supported by \code{\link[stargazer]{stargazer}}:
+#' @details Objects that can be exported are all those supported by \code{\link[xtable]{xtable}}, 
+#' \code{\link[broom]{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})
@@ -95,74 +99,50 @@
 #' }
 #' @author Tom Wenseleers, Christophe Vanderaa
 #' @example examples/table2tex.R
-#' @seealso \code{\link{table2office}} ,\code{\link{table2ppt}}, \code{\link{table2doc}}
+#' @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, summary=FALSE, standAlone=TRUE,
-                     add.rownames = FALSE,...) {
+table2tex = function(x = NULL, file = "Rtable", type="TEX", digits = 2, digitspvals = 2, 
+                     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=="DOC") { ext=".doc" }
   if (type=="HTML") { ext=".html" }
   if (type=="TEX") { ext=".tex" }
   file = sub("^(.*)[.].*", "\\1", file)  # remove extension if given
   file = paste0(file, ext)  # add extension
 
-  # define some additional methods for some objects
-  # not supported by default by stargazer
-  as.data.frame.summary.aov = function(x) {
-    if(length(x) == 1) {
-      as.data.frame(x[[1]])
-    } else {
-      lapply(unlist(x, FALSE), as.data.frame)
-    }
-  }
+  # 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)
+    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)
+    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}
-
-  # CHECK support for xtabs, ftable and CrossTable - contacted original author on this
-  # if ("xtabs" %in% class(outp)) outp = ftable(outp)
-  # if ("ftable" %in% class(outp)) XXX
-
   # 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."))
 
-  # objects supported by stargazer
-  # aftreg (eha), anova (stats), aov (stats), aovlist (stats), arima (stats), 
-  # betareg (betareg), binaryChoice (sampleSelection), bj (rms), brglm (brglm), 
-  # censReg (censReg), coeftest (lmtest), coxph (survival), coxreg (eha), 
-  # clm (ordinal), clogit (survival), cph (rms), dynlm (dynlm), ergm (ergm), 
-  # errorsarlm (spdev), felm (lfe), gam (mgcv), garchFit (fGarch), gee (gee), 
-  # glm (stats), Glm (rms), glmer (lme4), glmrob(robustbase), gls (nlme), 
-  # Gls (rms), gmm (gmm), heckit (sampleSelection), hetglm (glmx), hurdle (pscl), 
-  # ivreg (AER), lagarlm (spdep), lm(stats), lme (nlme), lmer (lme4), lmrob (robustbase), 
-  # lrm (rms), maBina (erer), mclogit (mclogit), mlogit (mlogit), mnlogit (mnlogit), 
-  # mlreg (eha), multinom (nnet), nlme (nlme), nlmer (lme4), ols (rms), pgmm (plm), 
-  # phreg (eha), plm (plm), pmg (plm), polr (MASS), psm (rms), rem.dyad (relevent), 
-  # rlm (MASS), rq (quantreg), Rq (rms), selection (sampleSelection), svyglm (survey), 
-  # survreg (survival), tobit (AER), weibreg (eha), zeroin (pscl), relogit (zelig), 
-  # cloglog.net (zelig), gamma.net (zelig), probit.net (zelig) and logit.net (zelig).
-  # not prcomp, ts or zoo?
-  # not ftable, xtab, CrossTable?
-
   # preview table in viewer or browser
-  htmlout = capture.output(stargazer(obj, type="html", summary=summary, rownames = add.rownames, ...)) 
-  texout = capture.output(stargazer(obj, type="latex", summary=summary, rownames = add.rownames, ...))
+  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}")

R/utils.R

@@ -24,15 +24,15 @@ xtable2 = function(x, ndigits = 2, ndigitspvals = 2, ...) {
   whch = grep("\\QPr(\\E|\\Qp-value\\E|\\Qp value\\E|\\Qpadj\\E|^p$|^padj$", colnames(sm))
   if (length(whch) != 0) {
     digs[whch + 1] = ndigitspvals
-    disp[whch + 1] = "g"
+    disp[whch + 1] = "f"
   }
   whch = grep("^Df$|^df$", colnames(sm))
   if (length(whch) != 0){
     digs[whch + 1] = 0
     disp[whch + 1] = "d"
   }
-  digs[c(1,which(!sapply(x,is.numeric))+1)] <- 0
-  disp[c(1,which(!sapply(x,is.numeric))+1)] <- "s"
+  digs[c(1,which(!apply(sm,2,is.numeric))+1)] <- 0
+  disp[c(1,which(!apply(sm,2,is.numeric))+1)] <- "s"
   for(i in 2:length(digs)){
     if(!is.na(digs[i])) sm[,i-1] <- round(sm[,i-1], digits = digs[i])
   }

cran-comments.md

@@ -16,6 +16,23 @@ Platform: x86_64-pc-linux-gnu (64-bit)
 
 Running under: Ubuntu 17.10
 
+## Resubmission
+
+This is a resubmission. In this version I have:
+
+* Changed function names in the DESCRIPTION by adding  '()'.
+
+* Reorganized the examples and replaced every '\dontrun' 
+  satement by the '\donttest' statement. This is needed 
+  because some examples require screen devices to be 
+  opened which is not allowed for examples (R CMD CHECK 
+  gives following error when the example is executed 
+  without '\donttest': "screen devices should not be used 
+  in examples etc"").
+
+* Files in the examples are now written in a temporary folder
+  (using tempdir()) instead of the package directory in order
+  to comply to CRAN policy.
 
 ## R CMD check results
 

examples/graph2bitmap.R

@@ -1,12 +1,32 @@
+# Create a file name
+dir <- tempdir()
+filen <- paste0(dir,"\\ggplot")
+
+# Generate graphical output
 library(ggplot2)
+library(datasets)
 x=qplot(Sepal.Length, Petal.Length, data = iris, 
         color = Species, size = Petal.Width, alpha = I(0.7))
-x
-graph2png(x=x,dpi=400)
-graph2tif(x=x)
-graph2jpg(x=x)
+plot.fun <- function(){
+  print(qplot(Sepal.Length, Petal.Length, data = iris, 
+              color = Species, size = Petal.Width, alpha = 0.7))
+}
 
-\dontrun{
-# use active graph instead of passing plot as object
-graph2png(aspectr=1.7)
+# There are 3 ways to use graph2bitmap():
+### 1. Pass the plot as an object
+graph2png(x=x, file=filen, dpi=400, height = 5, aspectr=4)
+graph2tif(x=x, file=filen, dpi=400, height = 5, aspectr=4)
+graph2jpg(x=x, file=filen, dpi=400, height = 5, aspectr=4) 
+### 2. Get the plot from current screen device
+\donttest{ # Because the example uses screen devices 
+  x
+  graph2png(file=filen, dpi=400, height = 5, aspectr=4)
+  graph2tif(file=filen, dpi=400, height = 5, aspectr=4)
+  graph2jpg(file=filen, dpi=400, height = 5, aspectr=4) 
 }
+### 3. Pass the plot as a function
+\donttest{ # Because the example uses screen devices 
+  graph2png(file=filen, fun=plot.fun, dpi=400, height = 5, aspectr=4)
+  graph2tif(file=filen, fun=plot.fun, dpi=400, height = 5, aspectr=4)
+  graph2jpg(file=filen, fun=plot.fun, dpi=400, height = 5, aspectr=4)
+}