beginning the move to knitr 1.6 and knitcitations 0.6.0 in preparatio…

…n of rmarkdown

.Rbuildignore

@@ -24,4 +24,5 @@ vignettes/NOTES
 vignettes/TO_DO
 vignettes/knitcitations.bib
 vignettes/extra_functions.R
-inst/staticdocs
+inst/staticdocs
+inst/build.R

DESCRIPTION

@@ -2,7 +2,7 @@ Package: reports
 Type: Package
 Title: An R package to assist in the workflow of writing academic articles and
     other reports
-Version: 0.2.0
+Version: 0.3.0
 Date: 2013-07-01
 Author: Tyler Rinker
 Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
@@ -25,9 +25,10 @@ BugReports: http://github.com/trinker/reports/issues
 LazyData: TRUE
 VignetteBuilder: knitr
 Depends:
-    R (>= 3.0.0)
+    R (>= 3.0.0),
+    qdapTools (>= 1.0.1)
 Imports:
-    knitcitations (>= 0.5-0),
+    knitcitations (>= 0.6-0),
     markdown,
     slidify,
     tools,
@@ -38,10 +39,12 @@ Suggests:
     brew,
     googleVis,
     slidifyLibraries,
-    knitr,
+    knitr (>= 1.6),
     xtable,
     pander,
     ProjectTemplate,
     qdap,
     reporttools,
+    rmarkdown,
     sjPlot
+Roxygen: list(wrap = FALSE)

NAMESPACE

@@ -50,6 +50,7 @@ export(css_style_add)
 export(css_style_change)
 export(css_styles)
 export(custom_css)
+export(custom_pandoc_style)
 export(delete)
 export(doc_temp)
 export(folder)
@@ -66,7 +67,6 @@ export(md2tex)
 export(new_report)
 export(new_vignette)
 export(notes)
-export(pad)
 export(parenciteL)
 export(parenciteM)
 export(popup)
@@ -99,6 +99,7 @@ importFrom(XLConnect,appendWorksheet)
 importFrom(XLConnect,loadWorkbook)
 importFrom(XLConnect,saveWorkbook)
 importFrom(markdown,markdownToHTML)
+importFrom(qdapTools,pad)
 importFrom(slidify,author)
 importFrom(tools,file_ext)
 importFrom(tools,file_path_sans_ext)

NEWS

@@ -83,8 +83,8 @@ NEW FEATURES
 * The sync family of functions has been introduced.  These functions provide 
   quick syncing between directories.  See `?sync` for more details.
 
-* `custom_css` function for creating the components necessary for custom css 
-  file for use with RStudio + knitr.  See: 
+* `custom_css` and `custom_pandoc_style` functions for creating the components 
+  necessary for custom css file for use with RStudio + rmarkdown + knitr.  See: 
   http://www.rstudio.com/ide/docs/authoring/markdown_custom_rendering
 
 * `css_styles` and `css_style_change` compliment `custom_css`.  The former 
@@ -213,6 +213,13 @@ CHANGES
 * The NOTES.txt and TO_DO.txt files lose the file extensions to become NOTES and 
   TO_DO.
 
+* `knitr 1.6` and `knitcitations 0.6.0` that incorporate the `rmarkdown` package
+  and utilize yaml + pandoc have significant changes.  These changes are 
+  reflected in the `reports` package.
+
+* `pad` removed from reports package and added to `qdapTools` which is now 
+  imported.
+
 
 CHANGES IN reports VERSION 0.1.2
 ----------------------------------------------------------------

R/BV.R

@@ -6,29 +6,34 @@
 #' the .bib file (working directory first and then "main_dir/REPORTS/_.bib", 
 #' last "main_dir/PRESENTATION/_.bib" in that order).
 #' @param col.width An integer value of the maximum width of columns.
-#' @return Returns a truncated view of user notes.
+#' @return Returns a truncated view of user references (.bib file).
 #' @export
 #' @import knitcitations
 #' @importFrom tools file_ext
 #' @examples 
 #' ## BV()
 BV <- 
 function(bib = NULL, col.width = 40) {
-    loc1 <- getwd()
-    loc2 <- file.path(loc1, "REPORT")
-    loc3 <- file.path(loc1, "PRESENTATION")
-    locs <- list(loc1, loc2, loc3)    	    	    	
-    FUN <- function(x) {
-    	fls <- dir(file.path(x)) 
-        if (identical(fls, character(0))) return(NULL) 
-    	fls[file_ext(fls) == "bib"][1]
-    }
-    check <-lapply(locs, FUN)
-    test <- function(x) suppressWarnings((!is.null(x) & !is.na(x)))
-    x <- sapply(check, test)
-    x[sapply(x, identical, logical(0))] <- FALSE
-    mark <- which(unlist(x))[1]
-    bibloc <- file.path(locs[mark], FUN(locs[mark]))
+	if (is.null(bib)){
+        loc1 <- getwd()
+        loc2 <- file.path(loc1, "REPORT")
+        loc3 <- file.path(loc1, "PRESENTATION")
+        locs <- list(loc1, loc2, loc3) 
+        FUN <- function(x) {
+         	fls <- dir(file.path(x)) 
+            if (identical(fls, character(0))) return(NULL) 
+            fls[file_ext(fls) == "bib"][1]
+        }
+        check <-lapply(locs, FUN)
+        test <- function(x) suppressWarnings((!is.null(x) & !is.na(x)))
+        x <- sapply(check, test)
+        x[sapply(x, identical, logical(0))] <- FALSE
+        mark <- which(unlist(x))[1]
+        bibloc <- file.path(locs[mark], FUN(locs[mark]))
+	} else {
+		bibloc <- bib
+	}
+
     bibin <- suppressMessages(suppressWarnings(invisible(read.bibtex(bibloc))))
     title <- sapply(bibin, function(x) {
         tryCatch(clean(unlist(x)[grepl("\\.title", names(unlist(x)))]), 

R/custom_css.R

@@ -177,3 +177,67 @@ css_style_add <- function(loc = QP("PRESENTATION/assets/css")) {
 	}
 }
 
+
+#' Generate Custom css for RStudio + knitr
+#'
+#' \code{custom_pandoc_style} - Generate the components necessary for a custom 
+#' pandoc styling for use with RStudio and knitr.
+#'  
+#' @rdname custom_css
+#' @export
+custom_pandoc_style <-
+function(rprofile = FALSE, loc = QP("REPORT"), source = TRUE) {	
+
+    if (!is.null(loc)) {	
+    	if (!file.exists(loc)) {
+            stop(sprintf("%s does not exist", loc))	
+    	}
+    }
+
+    ## Create the pandoc style
+    x <- c("options(rstudio.markdownToHTML =", 
+        "  function(inputFile, outputFile) { ",     
+        "    system(paste(\"pandoc\", shQuote(inputFile), \"-o\", shQuote(outputFile)))",
+        "  }",
+        ")\n"  
+    )
+
+    if (!is.null(loc)) {
+        cat(paste(x, collapse = "\n"), file = file.path(loc, "style.R"))
+
+        ## Direct where to change css options
+            message("Custom pandoc styling has been generated for your report.\n\n")        
+    }
+
+    ## Add style.R to .Rprofile for sourcing on load
+    if (rprofile) {
+    	if (sum(dir(all.files = TRUE) == ".Rprofile") > 0) {
+
+        ## Test if .Rprofile already contains the style.R function
+        RP <- gsub("\\s", "", paste(suppressWarnings(readLines(".Rprofile")), 
+            collapse = ""))
+        XP <- gsub("\\s", "", paste(x, collapse=""))
+            if (!grepl(XP, RP, fixed = TRUE)) {
+                cat(paste(c("\n\n", x), collapse = "\n"), file = ".Rprofile", 
+                append=TRUE)
+            } else {
+                warning(paste0(".Rprofile already contains style.R function:\n",
+                    "`rprofile = TRUE` argument ignored")) 
+            }
+    	} else {
+    		cat(paste(x, collapse = "\n"), file = ".Rprofile")
+    	}
+    }    
+
+    ## Source it for the first time
+    if (source) {
+        options(rstudio.markdownToHTML = 
+          function(inputFile, outputFile) {      
+            system(paste("pandoc", shQuote(inputFile), "-o", shQuote(outputFile)))
+          }
+        )  
+    }
+}
+
+
+

R/rdirs.R

@@ -20,6 +20,7 @@
 #' \code{\link[base]{dir.create}}
 #' @keywords file, directory, folder
 #' @export
+#' @importFrom qdapTools pad
 #' @examples
 #' ## fx <- folder(delete_me)
 #' ## owd <- getwd(); setwd(fx)

inst/CITATION

@@ -6,11 +6,11 @@ citEntry(entry = "manual",
     author = "Tyler W. Rinker",
     organization = "University at Buffalo/SUNY",
     address = "Buffalo, New York",
-    note = "version 0.2.0",
+    note = "version 0.3.0",
     year = "2013",
     url = "http://github.com/trinker/reports",
     textVersion  = paste("Rinker, T. W. (2013).",
         "reports: Package to assist in report writing.",
-        "version 0.2.0. University at Buffalo. Buffalo, New York.",
+        "version 0.3.0. University at Buffalo. Buffalo, New York.",
         "http://github.com/trinker/reports")
 )

inst/build.R

@@ -0,0 +1,30 @@
+curd <- getwd()
+loc <- "C:/Users/trinker/Desktop"
+setwd(loc)
+
+qman <- function(x = "reports", db = "C:/Users/trinker/Dropbox/Public", dir=loc) {
+    path <- file.path(dir, paste0(x, ".pdf"))
+    if (!file.exists(path)) stop(paste(x, "does not exist..."))
+    opath <- file.path(db, paste0(x, ".pdf"))
+    file.copy(path, opath, overwrite = TRUE)
+    message("manual copied!\n")
+}
+
+
+repo <- pack <- "reports"
+base.git = "C:/Users/trinker/GitHub"
+quick = TRUE
+library(devtools)
+
+unlink(paste0(pack, ".pdf"), recursive = TRUE, force = TRUE)
+x <- file.path(base.git, pack)
+document(x)
+install(x, quick = quick, build_vignettes = FALSE, dependencies = TRUE)
+
+path <- find.package(pack)
+system(paste(shQuote(file.path(R.home("bin"), "R")), 
+    "CMD", "Rd2pdf", shQuote(path)))
+
+qman(repo, dir=loc)
+setwd(curd)
+message("Done!")

inst/extdata/vign_library/vignette_rmd/doc.Rmd

@@ -1,3 +1,17 @@
+---
+title:  "vignette_name"
+author: "name"
+date:   '`r Sys.Date()`'
+output: 
+  html_document:
+    css: assets/fix-bootstrap.css
+    toc: yes  
+    pandoc_args: [
+      "--biblio", "references.bib",
+      "--csl", "ecology.csl"
+      ]
+---
+
 <!--
 %\VignetteEngine{knitr}
 %\VignetteIndexEntry{A Markdown Vignette with knitr}
@@ -7,27 +21,27 @@
 # set global chunk options
 library(knitr)
 opts_chunk$set(cache=FALSE)
+
 library(knitcitations); library(reports)
-#bib <- read.bibtex(dir()[tools::file_ext(dir()) == "bib"][1])
-#cite in text using `r citet(bib[1])`
+cleanbib()
+options("citation_format" = "pandoc")
 ```
-# vignette_name 
-## name
-### `r as.character(format(Sys.Date(), "%m-%d-%Y"))`
 
 To enable Markdown vignettes in an R package, you need to
 
 - add `*.Rmd` files under the `inst/doc` or `vignettes` directory
 - add `VignetteBuilder: knitr` to the `DESCRIPTION` file
 - specify the vignette engine `\VignetteEngine{knitr}` in the `Rmd` files (inside HTML comments)
 
-You can use your own CSS file instead of the built-in style in the **markdown** package -- just set the option `markdown.HTML.stylesheet`, e.g.
+You can use your own CSS file instead of the built-in style in the **markdown** package -- just set the css in the yaml.
 
-```{r css, echo = FALSE}
-options(markdown.HTML.stylesheet = "css/style.css")
-```
 
 ## References
-```{r, echo=FALSE, results='asis'}
-#bibliography("html") 
+```{r, echo=FALSE, message=FALSE}
+#write.bibtex(file="references.bib")
+```
+
+```{r clean-up, include=FALSE}
+# R compiles all vignettes in the same session, which can be bad
+rm(list = ls(all = TRUE))
 ```

inst/maintenance.R

@@ -1,3 +1,13 @@
+#========
+# BUILD
+#========
+source("inst/build.R")
+
+#==========================
+# Run unit tests
+#==========================
+devtools::test()
+
 #========================
 # Delete manuals Rd files
 #========================

man/BV.Rd

@@ -13,7 +13,7 @@ last "main_dir/PRESENTATION/_.bib" in that order).}
 \item{col.width}{An integer value of the maximum width of columns.}
 }
 \value{
-Returns a truncated view of user notes.
+Returns a truncated view of user references (.bib file).
 }
 \description{
 Allows a truncated view of your .bib.