final touches

DESCRIPTION

@@ -1,10 +1,15 @@
 Package: melviewr
 Type: Package
 Title: View and Classify MELODIC Output for ICA+FIX
-Version: 0.0.0.9000
-Authors@R: person("Andrew", "Poppe", email = "Poppe076 at gmail.com", role = c("aut", "cre"))
-Description: More about what it does (maybe more than one line)
-    Use four spaces when indenting paragraphs within the Description.
+Version: 0.0.1
+Authors@R: person("Andrew", "Poppe", email = "Poppe076@gmail.com", role = c("aut", "cre"))
+Description: The melviewr package provides a graphical interface that allows the
+    user to easily view and classify MELODIC output for the purposes of later 
+    running ICA+FIX. The user categorizes a component as signal or noise based on 
+    its spatial characteristics as well as its temporal profile. melviewr can then 
+    save a text file of these classifications in the format required by ICA+FIX.
+URL: https://github.com/AndrewPoppe/melviewr
+BugReports: https://github.com/AndrewPoppe/melviewr/issues
 License: GPL-3
 Encoding: UTF-8
 LazyData: true

R/melviewr.R

@@ -677,9 +677,13 @@ createViewrObject <- function() {
 
 #==============================================================================#
 # Main function the user will see.
-#' melviewr
+#' melviewr: View and Classify Components from a Melodic Analysis
 #'
-#' View and Classify Components from a Melodic Analysis
+#' The melviewr GUI allows for convenient viewing and classification of the
+#' results of a single-subject MELODIC analysis. Classification can then be
+#' saved to a text file for use by ICA+FIX to train its classifier. Various
+#' graphics options are available in the GUI, and these settings can be saved
+#' via a button in the GUI.
 #' @param melodic_dir string Path to MELODIC output directory. This directory
 #' must include a melodic_IC.nii or melodic_IC.nii.gz file.
 #' @param standard_file string Optional path to a 3-dimensional Nifti standard file
@@ -692,14 +696,21 @@ createViewrObject <- function() {
 #' @import gWidgetsRGtk2
 #' @importFrom methods new
 #' @return Invisibly returns a reference class object of class "Viewr"
+#' @details The directory specified in \code{melodic_dir} must contain a nifti
+#' file called either "melodic_IC.nii.gz" or "melodic_IC.nii" for the GUI to run.
+#' It must have a directory called "report" with text files inside in order to
+#' display timecourse and powerspectrum plots. Normally, this directory is
+#' created automatically with the \code{-report} flag in MELODIC.
+#'
+#' When saving graphical settings, a JSON file is saved in the user's HOME
+#' directory with the name: \code{.melviewR.config}
 #' @examples \dontrun{
 #' melodic_dir <- system.file("extdata", "example.ica", package = "melviewr")
 #' standard_file <- system.file("extdata", "MNI152_T1_2mm_brain.nii.gz", package = "melviewr")
 #' motion_file <- system.file("extdata", "Movement_RelativeRMS.txt", package = "melviewr")
 #' melviewr(melodic_dir)
 #' melviewr(melodic_dir, standard_file)
-#' melviewr(melodic_dir, standard_file, motion_file)
-#' }
+#' melviewr(melodic_dir, standard_file, motion_file)}
 melviewr <- function(melodic_dir, standard_file = NULL, motion_file = NULL) {
     # Keep environment tidy
     old <- options(stringsAsFactors = FALSE)
@@ -757,20 +768,3 @@ melviewr <- function(melodic_dir, standard_file = NULL, motion_file = NULL) {
 #==============================================================================#
 
 
-
-#==============================================================================#
-# Documentation for the package
-#' melviewr: A viewer for MELODIC output and ICA+FIX classification.
-#'
-#' The melviewr package allows the user to easily view and classify
-#' MELODIC output for the purposes of later running ICA+FIX. The user
-#' categorizes a component as signal or noise based on its spatial
-#' characteristics as well as its temporal profile. melviewr can then save
-#' a text file of these classifications in the format required by ICA+FIX.
-#'
-#' @section melviewr functions:
-#' melviewr
-#'
-#' @docType package
-#' @name melviewr-package
-NULL

R/package_documentation.R

@@ -0,0 +1,17 @@
+
+#==============================================================================#
+# Documentation for the package
+#' melviewr: A viewer for MELODIC output and ICA+FIX classification.
+#'
+#' The melviewr package allows the user to easily view and classify
+#' MELODIC output for the purposes of later running ICA+FIX. The user
+#' categorizes a component as signal or noise based on its spatial
+#' characteristics as well as its temporal profile. melviewr can then save
+#' a text file of these classifications in the format required by ICA+FIX.
+#'
+#' @section melviewr functions:
+#' melviewr
+#'
+#' @docType package
+#' @name melviewr-package
+NULL

melviewr.Rcheck/00_pkg_src/melviewr/DESCRIPTION

@@ -0,0 +1,23 @@
+Package: melviewr
+Type: Package
+Title: View and Classify MELODIC Output for ICA+FIX
+Version: 0.0.0.9000
+Authors@R: person("Andrew", "Poppe", email = "Poppe076@gmail.com", role = c("aut", "cre"))
+Description: The melviewr package provides a graphical interface that allows the
+    user to easily view and classify MELODIC output for the purposes of later 
+    running ICA+FIX. The user categorizes a component as signal or noise based on 
+    its spatial characteristics as well as its temporal profile. melviewr can then 
+    save a text file of these classifications in the format required by ICA+FIX.
+URL: https://github.com/AndrewPoppe/melviewr
+BugReports: https://github.com/AndrewPoppe/melviewr/issues
+License: GPL-3
+Encoding: UTF-8
+LazyData: true
+Imports: gtools, RColorBrewer, RNifti, grDevices, RGtk2, cairoDevice,
+        methods, jsonlite
+Depends: gWidgetsRGtk2, gWidgets
+RoxygenNote: 5.0.1
+NeedsCompilation: no
+Packaged: 2016-12-04 17:42:32 UTC; poppe076
+Author: Andrew Poppe [aut, cre]
+Maintainer: Andrew Poppe <Poppe076@gmail.com>

melviewr.Rcheck/00_pkg_src/melviewr/NAMESPACE

@@ -0,0 +1,6 @@
+# Generated by roxygen2: do not edit by hand
+
+export(melviewr)
+import(gWidgets)
+import(gWidgetsRGtk2)
+importFrom(methods,new)