Clean up documentation and comments.

Fixes #2

.Rbuildignore

@@ -7,3 +7,7 @@
 
 # Travis configuration file
 .travis.yml
+
+# License and readme
+LICENSE.md
+README.md

.travis.yml

@@ -3,7 +3,6 @@
 notifications:
   email:
     - robert.link@pnnl.gov
-#    - catherine.ledna@pnnl.gov
 
 language: r
 warnings_are_errors: false

R/Map_Functions.R

@@ -420,7 +420,7 @@ theme_GCAM <- function(base_size = 11, base_family = "", legend = F) {
 #'
 #' For specifying the projection you can use any Proj4 string.
 #' Projections specified this way are computed using
-#' \code{ggalt::coord_proj}.  For convenience, this package
+#' \code{\link[ggalt]{coord_proj}}.  For convenience, this package
 #' defines the following proj4 strings:
 #' \itemize{
 #'   \item \code{\link{eck3}} - Eckert III
@@ -431,7 +431,7 @@ theme_GCAM <- function(base_size = 11, base_family = "", legend = F) {
 #' }
 #'
 #' For orthographic projections, we compute the projection using the
-#' \code{mapproj::coord_map} function.  To get this projection
+#' \code{\link[ggplot2]{coord_map}} function.  To get this projection
 #' pass the \code{\link{ortho}} symbol as the \code{proj} argument.
 #' You will then need to pass a vector in the \code{orientation}
 #' argument.  We have defined the following fequently used orientation
@@ -487,8 +487,9 @@ theme_GCAM <- function(base_size = 11, base_family = "", legend = F) {
 #' @param ... Other parameters passed on to \code{colorfcn}.
 #' @examples \dontrun{
 #'
-#' ##Plot a map of GCAM regions; color it with a palette based on RColorBrewer's 'Set3' palette.
-#'   map_32_wo_Taiwan<-rgdal::readOGR(system.file('extdata/rgn32', 'GCAM_32_wo_Taiwan_clean.geojson',
+#' ## Plot a map of GCAM regions; color it with a palette based on RColorBrewer's 'Set3' palette.
+#'   map_32_wo_Taiwan<-rgdal::readOGR(system.file('extdata/rgn32',
+#'                                                'GCAM_32_wo_Taiwan_clean.geojson',
 #'                                                package='gcammaptools'))
 #'   map_32_wo_Taiwan.fort<-ggplot2::fortify(map_32_wo_Taiwan, region='GCAM_ID')
 #'   mp1<-plot_GCAM(map_32_wo_Taiwan.fort, col = 'id', proj = eck3, colorfcn=qualPalette)
@@ -497,9 +498,12 @@ theme_GCAM <- function(base_size = 11, base_family = "", legend = F) {
 #'   tables<-parse_mi_output(fn = system.file('extdata','sample-batch.csv',package='gcammaptools'))
 #'   prim_en<-process_batch_q(tables, 'primary_energy', 'Reference', c(fuel='a oil'))
 #'   prim_en<-addRegionID(prim_en, file.path(basedir.viz,
-#'                                 system.file('extdata/rgn32', 'lookup.txt', package='gcammaptools'),
-#'                                 system.file('extdata/rgn32', 'drop-regions.txt', package='gcammaptools')))
-#'   mp2<-plot_GCAM(map_primen, col = 'X2050', colors = c('white', 'red'), title='Robinson World', qtitle='Oil Consumption, 2050', legend=T)
+#'                                 system.file('extdata/rgn32', 'lookup.txt',
+#'                                             package='gcammaptools'),
+#'                                 system.file('extdata/rgn32',
+#'                                             'drop-regions.txt', package='gcammaptools')))
+#'   mp2<-plot_GCAM(map_primen, col = 'X2050', colors = c('white', 'red'),
+#'                  title='Robinson World', qtitle='Oil Consumption, 2050', legend=T)
 #' }
 #' @export
 plot_GCAM <- function(mapdata, col = NULL, proj = robin, extent = EXTENT_WORLD,

R/diag_header.R

@@ -38,22 +38,6 @@
 # Ben Bond-Lamberty, November 2012
 
 
-# -----------------------------------------------------------------------------
-# Load required libraries
-# NB this diag has been tested with the following libraries:
-#   rgdal 1.1-3
-#   ggplot2 2.1.0
-#   ggalt # must install the github version:  install_github('hrbrmstr/ggalt')
-#   graticule 0.1.0
-#   rgeos 0.3-15
-#   maptools 0.8-37 , "gpclib"
-#   gpclib [[???]]
-#   sp 1.2-1
-#   mapproj 1.2-4
-#   RColorBrewer 1.1-2
-#   dplyr 0.5.0
-
-
 # -----------------------------------------------------------------------------
 # Global settings (in CAPITALS)
 # This first group of settings is protected--we don't want it re-set every time
@@ -218,7 +202,7 @@ ch_aea <- "+proj=aea +lat_1=27 +lat_2=45 +x_0=0 +y_0=0 +lat_0=35 +lon_0=105 +ell
 #' Projection string for orthographic projections
 #'
 #' Unlike most projections, the orthographic does not use proj4; it
-#' uses the \code{mapproj::coord_map} function.  You can pass
+#' uses the \code{\link[ggplot2]{coord_map}} function.  You can pass
 #' this value to the \code{proj} argument of \code{\link{plot_GCAM}}
 #' to get an orthographic projection.
 #' @export