small edits

NEWS.md

@@ -1,8 +1,11 @@
+# tukeyedar 0.2.1
+* Added the option to plot the density distribution alongside the Normal fit in `eda_normfit`.
+
 # tukeyedar 0.2.0
-* Added a Normal QQ plot option to `eda_qq`
-* Added symmetrical Normal fit plot function `eda_normfit`
-* Updated eda_boxls aesthetics
-* Updated median polish diagnostic plot aesthetics
+* Added a Normal QQ plot option to `eda_qq`.
+* Added symmetrical Normal fit plot function `eda_normfit`.
+* Updated eda_boxls aesthetics.
+* Updated median polish diagnostic plot aesthetics.
 
 # tukeyedar 0.1.1
 

R/eda_normfit.R

@@ -6,23 +6,23 @@
 #' @description \code{eda_normfit} generates a fitted Normal distribution to the
 #'   data with the option to compare it to a density distribution.
 #'
-#' @param dat Vector of values or a dataframe.
+#' @param dat Vector of values, or a dataframe.
 #' @param x  Column of values if \code{dat} is a dataframe, ignored otherwise.
 #' @param grp Column of grouping variables if \code{dat} is a dataframe, ignored
 #'   otherwise.
-#' @param p  Power transformation to apply to both sets of values.
+#' @param p  Power transformation to apply to all values.
 #' @param tukey Boolean determining if a Tukey transformation should be adopted
-#'   (FALSE adopts a Box-Cox transformation).
-#' @param show.par Boolean determining if power transformation should be
-#'   displayed in the plot's upper-right corner.
+#'   (\code{TRUE}) or if a Box-Cox transformation should be adopted (\code{FALSE}).
+#' @param show.par Boolean determining if the power transformation used with the
+#'   data should be displayed in the plot's upper-right corner.
 #' @param sq Boolean determining if the plot should be square.
 #' @param inner Fraction of values that should be captured by the inner color
-#'   band of the normal and density plots. Defaults to 0.6826 (inner 68% of
+#'   band of the normal and density plots. Defaults to 0.6826 (inner 68\% of
 #'   values).
-#' @param dens Boolean determining if the density plot should displayed
-#'   alongside the normal fit plot.
-#' @param bw Bandwidth parameter passed to the built-in \code{density} function.
-#' @param kernel Kernel parameter passed to the built-in \code{density}
+#' @param dens Boolean determining if the density plot should be displayed
+#'   alongside the Normal fit plot.
+#' @param bw Bandwidth parameter passed to the \code{density()} function.
+#' @param kernel Kernel parameter passed to the \code{density()}
 #'   function.
 #' @param pch Point symbol type.
 #' @param size Point side.
@@ -31,13 +31,14 @@
 #' @param p.col Color for point symbol.
 #' @param p.fill Point fill color passed to \code{bg} (Only used for \code{pch}
 #'   ranging from 21-25).
-#' @param grey Grey level to apply to plot elements (0 to 1 with 1 = black).
+#' @param grey Grey level to apply to plot elements such as axes, labels, etc...
+#'   (0 to 1 with 1 = black).
 #' @param col.ends Fill color for ends of the Normal distribution.
 #' @param col.mid Fill color for middle band of the Normal distribution.
 #' @param col.ends.dens Fill color for ends of the density distribution.
 #' @param col.mid.dens Fill color for middle band of the density distribution.
 #' @param offset A value (in x-axis units) that defines the gap between left and
-#'   right side plots. Ignored if \code{dens} is \code{TRUE}.
+#'   right side plots. Ignored if \code{dens} is \code{FALSE}.
 #' @param tsize Size of plot title.
 #' @param xlab X variable label.
 #' @param ylab Y variable label.
@@ -54,30 +55,29 @@
 #'   The plots have two fill colors: one for the inner band and the other for
 #'   the outer band. The inner band shows the area of the curve that encompasses
 #'   the desired fraction of values defined by \code{inner}. By default, this
-#'   value is 0.6826, or 68.26 percent (this is roughly the percentage of values
+#'   value is 0.6826, or 68.26\% (this is roughly the percentage of values
 #'   covered by +/- 1 standard deviations of a Normal distribution). For the
 #'   Normal fit plot, the range is computed from the theoretical Normal and not
 #'   from the actual values. For the density plot, the range is computed from
-#'   the actual values. By default, the colors are inverted between the Normal
-#'   curve and the density curve. If the density plot is not drawn, then the
-#'   Normal plot colors are identical about the vertical axis. \cr
+#'   the actual values. \cr
 #'   \cr
 #'   If a density plot is desired, \code{dens = TRUE}, a gap (defined by
 #'   \code{offset}) is created between the left side density plot and the right
-#'   side Normal fit plot. Points showing the location of values on the
-#'   y-axis are also added to help view their distribution relative to the
-#'   density and Normal fit curves. This function makes use of the built-in
-#'   \code{density} function. As such, you can pass the \code{bw} and
-#'   \code{kernel} parameters as you would for the \code{density} function.\cr
+#'   side Normal fit plot. This function makes use of the built-in
+#'   \code{stats::density} function. As such, you can pass the \code{bw} and
+#'   \code{kernel} parameters as you would for the \code{density()} function.
+#'   Points showing the location of values along the y-axis are also added to
+#'   help view their distributions relative to the density and Normal fit
+#'   curves. \cr
 #'   \cr
 #'   Measures of centrality are computed differently for the Normal fit and
 #'   density plots. The mean is computed for the Normal fit plot and the median
-#'   is computed for density plot. These measures of centrality are shown as
+#'   is computed for the density plot. These measures of centrality are shown as
 #'   black horizontal lines in the plot.\cr
 #'   \cr
 #'   The areas under the density and Normal fit plots are scaled to their
 #'   peak values, respectively. So, the areas should not be compared between
-#'   both plots.
+#'   both distributions.
 #'
 #'
 #' @seealso \code{\link[stats]{density}}
@@ -98,8 +98,8 @@
 #' # Limit the plot to just a Normal fit
 #' eda_normfit(x, dens = FALSE)
 #'
-#' # The inner band's range can be modified. Here, we view the inter-quartile
-#' # range, +/- 1 standard deviation range and the inner 95% range)
+#' # The inner band's range can be modified. Here, we view the interquartile
+#' # range, the +/- 1 standard deviation range and the inner 95% range)
 #' OP <- par(mfrow = c(1,3))
 #' invisible(sapply(c(0.5, 0.6826, 0.95),
 #'       function(prop) eda_normfit(x, inner = prop, tsize = 1,
@@ -153,7 +153,7 @@ eda_normfit <- function(dat, x=NULL, grp=NULL, p = 1,  tukey = FALSE,
                         pch = 16, size = 0.8, alpha = 0.3, p.col = "grey50",
                         p.fill = "grey80",grey = 0.7,
                         col.ends = "grey90", col.mid = "#EBC89B",
-                        col.ends.dens = "#EBC89B" , col.mid.dens = "grey90",
+                        col.ends.dens = "grey90" , col.mid.dens = "#EBC89B",
                         offset = 0.02, tsize=1.5,
                         xlab = NULL, ylab = NULL, ...){
 
@@ -254,7 +254,7 @@ eda_normfit <- function(dat, x=NULL, grp=NULL, p = 1,  tukey = FALSE,
 
   # Create list of density distributions by group
   out2 <- lapply(split(x, grp), function(x)
-  {dnsty <- density(x, n=120, bw = bw, kernel = kernel)
+  {dnsty <- stats::density(x, n=120, bw = bw, kernel = kernel)
   densx <- dnsty$x
   densy <- dnsty$y
   data.frame(densx,densy)})