Prepare for CRAN tests

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ggpmisc
 Type: Package
 Title: Miscellaneous Extensions to 'ggplot2'
-Version: 0.5.4-1.9001
+Version: 0.5.5
 Date: 2023-11-12
 Authors@R:
     c(

R/stat-peaks.R

@@ -3,9 +3,11 @@
 #' This method finds peaks (local maxima) in a vector, using a user selectable
 #' span and size threshold relative to the tallest peak (global maximum).
 #'
-#' @param x numeric vector
+#' @param x numeric vector.
 #' @param ignore_threshold numeric value between 0.0 and 1.0 indicating the size
-#'   threshold below which peaks will be ignored.
+#'   threshold below which peaks will be ignored, or a negative value >= -1,
+#'   to ignore peaks above a threshold. These values are relative to the range
+#'   of \code{x}.
 #' @param span a peak is defined as an element in a sequence which is greater
 #'   than all other elements within a window of width span centered at that
 #'   element. The default value is 3, meaning that a peak is bigger than both of
@@ -20,12 +22,12 @@
 #'   peaks in vector \code{x} and can be used to extract the rows corresponding
 #'   to peaks from a data frame.
 #'
-#' @details This function is a wrapper built on function
+#' @details This function is a wrapper built onto function
 #'   \code{\link[splus2R]{peaks}} from \pkg{splus2R} and handles non-finite
 #'   (including NA) values differently than \code{peaks}, instead of giving an
-#'   error when \code{na.rm = FALSE} they are replaced with the smallest finite
-#'   value in \code{x}. \code{span = NULL} is treated as a special case and
-#'   returns \code{max(x)}.
+#'   error when \code{na.rm = FALSE} and \code{x} contains \code{NA} values,
+#'   \code{NA} values are replaced with the smallest finite value in \code{x}.
+#'   \code{span = NULL} is treated as a special case and returns \code{max(x)}.
 #'
 #' @note The default for parameter \code{strict} is \code{FALSE} in functions
 #'   \code{peaks()} and \code{find_peaks()}, as in \code{stat_peaks()} and in
@@ -44,14 +46,21 @@
 #'              as.numeric = TRUE) # years -> as numeric
 #'
 #' which(find_peaks(lynx_num.df$lynx, span = 31))
-#' lynx_num.df[find_peaks(lynx_num.df$lynx, span = 31), ]
+#' lynx_num.df[find_peaks(lynx_num.df$lynx, span = 15), ]
+#' lynx_num.df[find_peaks(lynx_num.df$lynx, span = NULL), ]
+#' lynx_num.df[find_peaks(lynx_num.df$lynx,
+#'                        span = 31,
+#'                        ignore_threshold = 0.75), ]
 #'
 #' lynx_datetime.df <-
 #'    try_tibble(lynx,
 #'               col.names = c("year", "lynx")) # years -> POSIXct
 #'
 #' which(find_peaks(lynx_datetime.df$lynx, span = 31))
-#' lynx_datetime.df[find_peaks(lynx_num.df$lynx, span = 31), ]
+#' lynx_datetime.df[find_peaks(lynx_datetime.df$lynx, span = 31), ]
+#' lynx_datetime.df[find_peaks(lynx_datetime.df$lynx,
+#'                             span = 31,
+#'                             ignore_threshold = 0.75), ]
 #'
 find_peaks <-
   function(x,

_pkgdown.yml

@@ -42,15 +42,16 @@ reference:
     - stat_multcomp
     - use_label
   - title: Utilities
-    desc: Low level functions that can be useful to developers of other ggplot2 extensions.
+    desc: Low level functions used to build some of the functions above, but possibly useful also in other contexts.
     contents:
-    - swap_xy
-    - keep_tidy
+    - find_peaks
     - coef.lmodel2
     - confint.lmodel2
     - predict.lmodel2
+    - keep_tidy
+    - swap_xy
   - title: Changes
-    desc: Geometries, statistics and functions moved to package 'gginnards'.
+    desc: List of geometries, statistics and functions moved to package 'gginnards'.
     contents:
     - Moved