Update style in documentation

DESCRIPTION

@@ -17,5 +17,6 @@ Imports:
     mime,
     rjson,
     Rook
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Encoding: UTF-8
+Roxygen: list(markdown = TRUE)

R/app.R

@@ -1,49 +1,50 @@
 # This file is part of digitizeR
-# 
+#
 # digitizeR is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
-# 
+#
 # digitizeR is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
-# 
+#
 # You should have received a copy of the GNU General Public License
 # along with digitizeR.  If not, see <http://www.gnu.org/licenses/>.
 
 #' @importFrom rjson fromJSON
-.wpd_createBackend <- function() {    
+.wpd_createBackend <- function() {
     backend <- list(
-        call = function(req) {                
-            # Handle HTTP requests       
-            
+        call = function(req) {
+            # Handle HTTP requests
+
             # Host files from checked out WebPlotDigitizer
             reqFile <- req$PATH_INFO
-            packagePath <- system.file('wpd', package="digitizeR")        
+            packagePath <- system.file('wpd', package="digitizeR")
             filepath <- paste(packagePath, reqFile, sep="/")
-            
+
             # If the file is not found, then return a 404 code.
             message <- list(status = 404L, headers = list('Content-Type' = 'text/html'), body = 'error!')
-
-            if (file.exists(filepath)) {            
-                # if this is a PHP script, then we probably got a POST request to generate a CSV or JSON file
-                # Maybe we can even run R scripts in the future?
-                # TODO: Use tryCatch here:            
+
+            if (file.exists(filepath)) {
+                # if this is a PHP script, then we probably got a POST request
+                # to generate a CSV or JSON file Maybe we can even run R scripts
+                # in the future?
+                # TODO: Use tryCatch here:
                 if (grepl("json.php$", reqFile)) {
                     # Generate JSON file
-                    
+
                     # Read POST data
                     postVariables <- list(data = "", filename = "")
-                    
+
                     postInput <- req[["rook.input"]]
                     postData <- postInput$read_lines()
                     postData <- Rook::Utils$unescape(postData)
-                    
-                    # There's probably a better way to do this:                
+
+                    # There's probably a better way to do this:
                     postRegexPattern <- "^data=(\\{.*)\\&filename=(.*)"
-                    if(grepl(postRegexPattern, postData)) { 
+                    if(grepl(postRegexPattern, postData)) {
                         postVariables$data <- gsub(postRegexPattern, "\\1", postData)
                         postVariables$filename <- gsub(postRegexPattern, "\\2", postData)
                         message <- list(status = 200L,
@@ -52,21 +53,21 @@
                                         body = postVariables$data
                         )
                     } else {
-                        cat("ERROR: Invalid POST data sent for", reqFile, "\n")                    
-                    }                                                                                
+                        cat("ERROR: Invalid POST data sent for", reqFile, "\n")
+                    }
                 } else if (grepl("csvexport.php$", reqFile)) {
                     # Generate CSV file
-                    
+
                     # Read POST data
                     postVariables <- list(data = "", filename = "")
-                    
+
                     postInput <- req[["rook.input"]]
-                    postData <- postInput$read_lines()                                
+                    postData <- postInput$read_lines()
                     postData <- Rook::Utils$unescape(postData)
-                    
-                    # There's probably a better way to do this:                
+
+                    # There's probably a better way to do this:
                     postRegexPattern <- "^data=(.*)\\&filename=(.*)"
-                    if(grepl(postRegexPattern, postData)) { 
+                    if(grepl(postRegexPattern, postData)) {
                         postVariables$data <- gsub(postRegexPattern, "\\1", postData)
                         postVariables$filename <- gsub(postRegexPattern, "\\2", postData)
                         csvData <- rjson::fromJSON(postVariables$data)
@@ -76,25 +77,25 @@
                                         body = csvData
                         )
                     } else {
-                        cat("ERROR: Invalid POST data sent for", reqFile, "\n")                    
-                    }          
-                    
+                        cat("ERROR: Invalid POST data sent for", reqFile, "\n")
+                    }
+
                 } else {
                     # if this is not a PHP file, then just determine the mime type and return
                     mimetype <- mime::guess_type(filepath)
                     message <- list(status = 200L,
                                     headers = list('Content-Type' = mimetype),
-                                    body = list(file = filepath))                    
-                }            
+                                    body = list(file = filepath))
+                }
             }
-            
+
             return(message)
         },
         onWSOpen = function(ws) {
-            # Handle WebSocket communication in the future        
+            # Handle WebSocket communication in the future
         }
     )
-    
+
     return(backend)
 }
-    
+

R/digitizeR.R

@@ -1,42 +1,43 @@
 # This file is part of digitizeR
-# 
+#
 # digitizeR is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
-# 
+#
 # digitizeR is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
-# 
+#
 # You should have received a copy of the GNU General Public License
 # along with digitizeR.  If not, see <http://www.gnu.org/licenses/>.
 
 #' digitizeR: Tool to extract numerical data from images of plots, maps etc.
-#' 
-#' The digitizeR package provides a web based interface (WebPlotDigitizer) to interactively extract 
-#' numerical data from images of plots, maps, microscope images etc. Some tools to make simple distance
-#' and angle measurements are also available. In the future, this package will also allow 
-#' real-time interaction between R and the hosted web application via WebSockets.
-#' 
+#'
+#' The digitizeR package provides a web based interface (WebPlotDigitizer) to
+#' interactively extract numerical data from images of plots, maps, microscope
+#' images etc. Some tools to make simple distance and angle measurements are
+#' also available. In the future, this package will also allow real-time
+#' interaction between R and the hosted web application via WebSockets.
+#'
 #' @section Available Functions:
-#' 
-#' \itemize{
-#'      \item \code{\link{wpd_launch}}: Start HTTP server that hosts WebPlotDigitizer and 
+#'
+#'
+#' - [wpd_launch()]: Start HTTP server that hosts WebPlotDigitizer and
 #'      open the local URL in the browser.
-#'      \item \code{\link{wpd_close}}: Shutdown the HTTP server.
-#'      \item \code{\link{wpd_isOpen}}: Check is the HTTP server is currently running.
-#' }
-#'   
-#' 
+#' - [wpd_close()]: Shutdown the HTTP server.
+#' - [wpd_isOpen()]: Check is the HTTP server is currently running.
+#'
+#'
+#'
 #' @docType package
 #' @name digitizeR
 NULL
 
-#' Start a local HTTP server that hosts WebPlotDigitizer. 
+#' Start a local HTTP server that hosts WebPlotDigitizer.
 #' This will also open a browser window pointing to the local URL.
-#' 
+#'
 #' @param location IP address or machine name of the server. Defaults to "0.0.0.0".
 #' @param port Port number of the HTTP server. Defaults to 8000.
 #' @return Server handle that is later used to shutdown the server using wpd_close()
@@ -48,14 +49,14 @@ NULL
 #' app <- wpd_launch(location="192.168.1.100", port=8080)
 #' }
 wpd_launch <- function(location = '0.0.0.0', port = 8000) {
-        
+
     app <- new.env()
-    
+
     # Start httpuv based server in the background
     app$backend = .wpd_createBackend()
-    
+
     app$serverInstance <- httpuv::startDaemonizedServer(location, port, app$backend)
-    
+
     # Construct the hosted URL link
     url <- 'http://'
     if (location == '0.0.0.0') {
@@ -64,16 +65,16 @@ wpd_launch <- function(location = '0.0.0.0', port = 8000) {
         url <- paste(url, location, sep='')
     }
     url <- paste(url, ':', port, '/index.html', sep='')
-    
+
     utils::browseURL(url) # Launch browser with the WPD url
-    
+
     cat('Starting WPD. If a browser window does not open, then browse to:', url, '\n')
     app$isOpen <- TRUE
     return(app)
 }
 
 #' Shutdown the HTTP server that is currently hosting WebPlotDigitizer.
-#' 
+#'
 #' @param app Server handle that was obtained by executing wpd_launch()
 #' @export
 #' @examples
@@ -89,7 +90,7 @@ wpd_close <- function(app) {
 }
 
 #' Check if the HTTP server is currently running.
-#' 
+#'
 #' @param app Server handle that was obtained by executng wpd_launch()
 #' @export
 wpd_isOpen <- function(app) {

R/read_wpd.R

@@ -1,10 +1,9 @@
 #' Read WebPlotDigitizer JSON data
 #'
 #' @inheritParams rjson::fromJSON
-#' @param include_pixel Include the pixel data in the returned data frame
-#' @return A data.frame with colums for \code{x}, \code{y}, and \code{DataSet}
-#'   and optionally (if \code{include_pixel=TRUE}) \code{x_pixel} and
-#'   \code{y_pixel}.
+#' @param include_pixel Include the pixel data in the returned data frame.
+#' @return A data.frame with colums for `x`, `y`, and `DataSet` and optionally
+#'        (if `include_pixel=TRUE`) `x_pixel` and `y_pixel`.
 #' @export
 #' @importFrom rjson fromJSON
 read_wpd <- function(json_str, file, include_pixel=FALSE) {

digitizeR.Rproj

@@ -12,7 +12,9 @@ Encoding: UTF-8
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
 
+StripTrailingWhitespace: Yes
+
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd
+PackageRoxygenize: rd,collate,namespace,vignette