From 7b382e60763c03779fc2a4be9dd5d1e56f80cf1a Mon Sep 17 00:00:00 2001
From: levisc8 <levisc8@gmail.com>
Date: Thu, 29 Mar 2018 11:52:17 +0200
Subject: [PATCH] Remove unnecessary function argument, add example

---
 R/base_figure.R            | 40 +++++++++++++++++++++++++++++++-------
 man/whittaker_base_plot.Rd | 29 +++++++++++++++++++++++----
 2 files changed, 58 insertions(+), 11 deletions(-)

diff --git a/R/base_figure.R b/R/base_figure.R
index f1c258f..af0b28c 100644
--- a/R/base_figure.R
+++ b/R/base_figure.R
@@ -2,14 +2,13 @@
 #'
 #' @description Creates the Whittaker biome figure from the vignette example.
 #' This can be modified by passing additional \code{\link{ggplot2}} style
-#' arguments to it
+#' arguments to it.
 #' @param color_palette A named or unnamed vector of length 9 that contains either
 #' color names or values. If named, the names should correspond to biome names in the
 #' \code{Whittaker_biomes} data object. See details for additional information.
 #' The default is to use the colors from Figure 5.5 in Ricklefs, R. E. (2008),
 #' \emph{The economy of nature} (Chapter 5, Biological Communities, The biome concept).
 #' If the vector is not named, the function will insert the names automatically
-#' @param extra_features Additional arguments to customize the Whittaker biome plot
 #'
 #' @return An object of class \code{gg} and \code{ggplot}.
 #'
@@ -30,14 +29,35 @@
 #'   \item{\code{Woodland/shrubland}}
 #' }
 #'
+#' If the vector is unnamed, the names from \emph{Ricklefs (2008)} will be
+#' inserted automatically.
+#'
+#' Add additional features (e.g. \code{theme()} elements) using normal
+#' \code{ggplot2} syntax. See examples.
+#'
+#' @examples
+#'
+#' library(ggplot2)
+#' # Create the base plot
+#'
+#' whittaker_base_plot()
+#'
+#' # move the legend to top left corner, add border box,
+#' # and adjust the background fill and grid.
+#'
+#' whittaker_base_plot() +
+#'   theme(legend.position = c(0.15, 0.75),
+#'         panel.background = element_blank(),
+#'         panel.grid.major = element_line(gray(0.7)),
+#'         panel.border = element_rect(fill = NA))
+#'
 #' @author Sam Levin, Valentin Stefan
 #'
 #' @import ggplot2
 #' @importFrom utils data
 #' @export
 
-whittaker_base_plot <- function(color_palette = NULL,
-                                extra_features = NULL) {
+whittaker_base_plot <- function(color_palette = NULL) {
   utils::data('Whittaker_biomes', envir = environment())
   utils::data("Ricklefs_colors", envir = environment())
 
@@ -46,8 +66,15 @@ whittaker_base_plot <- function(color_palette = NULL,
   xlabel <- expression("Temperature " ( degree*C))
   if(is.null(color_palette)) {
     color_palette <- Ricklefs_colors
-  } else if(is.null(names(color_palette))) {
+  } else if(is.null(names(color_palette)) |
+            any(is.na(names(color_palette)))) {
+    # ^^second condition throws warning when names aren't specified.
+    # consider changing
+
     names(color_palette) <- names(Ricklefs_colors)
+
+    message("Names for 'color_palette' either not specified or too few",
+            " were specified. Using names from 'Ricklefs_colors'.")
   }
 
   plt <- ggplot2::ggplot() +
@@ -65,8 +92,7 @@ whittaker_base_plot <- function(color_palette = NULL,
                                labels = names(color_palette),
                                values = color_palette) +
     ggplot2::scale_x_continuous(xlabel) +
-    ggplot2::scale_y_continuous('Precipitation (cm)') +
-    extra_features
+    ggplot2::scale_y_continuous('Precipitation (cm)')
 
 
   return(plt)
diff --git a/man/whittaker_base_plot.Rd b/man/whittaker_base_plot.Rd
index d95308a..523490c 100644
--- a/man/whittaker_base_plot.Rd
+++ b/man/whittaker_base_plot.Rd
@@ -4,7 +4,7 @@
 \alias{whittaker_base_plot}
 \title{Create the Whittaker biome base figure}
 \usage{
-whittaker_base_plot(color_palette = NULL, extra_features = NULL)
+whittaker_base_plot(color_palette = NULL)
 }
 \arguments{
 \item{color_palette}{A named or unnamed vector of length 9 that contains either
@@ -13,8 +13,6 @@ color names or values. If named, the names should correspond to biome names in t
 The default is to use the colors from Figure 5.5 in Ricklefs, R. E. (2008),
 \emph{The economy of nature} (Chapter 5, Biological Communities, The biome concept).
 If the vector is not named, the function will insert the names automatically}
-
-\item{extra_features}{Additional arguments to customize the Whittaker biome plot}
 }
 \value{
 An object of class \code{gg} and \code{ggplot}.
@@ -22,7 +20,7 @@ An object of class \code{gg} and \code{ggplot}.
 \description{
 Creates the Whittaker biome figure from the vignette example.
 This can be modified by passing additional \code{\link{ggplot2}} style
-arguments to it
+arguments to it.
 }
 \details{
 To specify your own color palette, create a named vector
@@ -41,6 +39,29 @@ character (e.g. 'red' or '#C1E1DD'). The names for each biome are as follows:
 \item{\code{Temperate grassland/desert}}
 \item{\code{Woodland/shrubland}}
 }
+
+If the vector is unnamed, the names from \emph{Ricklefs (2008)} will be
+inserted automatically.
+
+Add additional features (e.g. \code{theme()} elements) using normal
+\code{ggplot2} syntax. See examples.
+}
+\examples{
+
+library(ggplot2)
+# Create the base plot
+
+whittaker_base_plot()
+
+# move the legend to top left corner, add border box,
+# and adjust the background fill and grid.
+
+whittaker_base_plot() +
+  theme(legend.position = c(0.15, 0.75),
+        panel.background = element_blank(),
+        panel.grid.major = element_line(gray(0.7)),
+        panel.border = element_rect(fill = NA))
+
 }
 \author{
 Sam Levin, Valentin Stefan