documentation for the huber plot

DESCRIPTION

@@ -15,7 +15,7 @@ Description: Diagnostic plots for optimisation, with a focus on projection pursu
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-URL: https://github.com/huizezhang-sherry/ferrn/
+URL: https://github.com/huizezhang-sherry/ferrn/, https://huizezhang-sherry.github.io/ferrn
 BugReports: https://github.com/huizezhang-sherry/ferrn/issues
 Imports: 
  rlang (>= 0.1.2),
@@ -34,7 +34,7 @@ Imports:
  cli,
  progress,
  glue,
- GpGp,
+ GpGp
 RoxygenNote: 7.3.2
 Depends: 
  R (>= 2.10)
@@ -46,5 +46,5 @@ Suggests:
  forcats,
  patchwork,
  future.apply,
- ash
+ ash,
 Language: en-GB

R/explore-space-tour.R

@@ -35,9 +35,11 @@ explore_space_tour <- function(..., axes = "bottomleft") {
 #' @param axes see [tourr::animate_xy()]
 #' @param ... other argument passed to \code{tourr::animate_xy()} and \code{prep_space_tour()}
 #' @examples
+#' if (FALSE){
 #' explore_space_tour(dplyr::bind_rows(holes_1d_better, holes_1d_geo),
 #' group = method, palette = botanical_palettes$fern[c(1, 6)]
 #' )
+#' }
 #' @rdname explore_space_tour
 #' @export
 prep_space_tour <- function(dt, group = NULL, flip = FALSE, n_random = 2000,

R/huber-plot.R

@@ -1,33 +1,50 @@
 #' Create Huber plot with ggplot2
 #'
+#' The Huber plot presents the projection pursuit index values of 2D data in each 1D
+#' projection in polar coordinates, corresponding to each projection direction.
+#' It offers a simpler illustration of more complex projection from
+#' high-dimensional data to lower dimensions in projection pursuit. The
+#' function \code{prep_huber()} calculates each component required for the Huber plot
+#' (see details), which can then be supplied to various geom layers in ggplot2.
+#'
+#' @details the \code{prep_huber()} function calculates components required for
+#' making the Huber plots. It returns a list including three elements:
+#'\describe{
+#' \item{the \code{idx_df} data frame: }{the x/y coordinates of the index value, in polar
+#' coordinates. Used for plotting the index value at each projection direction,
+#' with the reference circle.}
+#' \item{the \code{proj_df} data frame: }{the best 1D projection. Used for plotting
+#' the 1D projection in histogram.}
+#' \item{the \code{slope} value: }{the slope to plot in the Huber plot to indicate the
+#' direction of the best 1D projection.}
+#' }
 #' @inheritParams ggplot2::layer
 #' @inheritParams ggplot2::geom_path
 #' @param index a function, the projection pursuit index function, see examples
 #' @rdname huber
 #' @export
 #' @examples
-#' if (require(ash, quietly = TRUE)) {
-#'  library(ggplot2)
-#'  library(tourr)
-#'  data(randu)
-#'  randu_std <- as.data.frame(apply(randu, 2, function(x) (x-mean(x))/sd(x)))
-#'  randu_std$yz <- sqrt(35)/6*randu_std$y-randu_std$z/6
-#'  randu_df <- randu_std[c(1,4)]
-#'  randu_huber <- prep_huber(randu_df, index = norm_bin(nr = nrow(randu_df)))
+#' library(ggplot2)
+#' library(tourr)
+#' library(ash)
+#' data(randu)
+#' randu_std <- as.data.frame(apply(randu, 2, function(x) (x-mean(x))/sd(x)))
+#' randu_std$yz <- sqrt(35)/6*randu_std$y-randu_std$z/6
+#' randu_df <- randu_std[c(1,4)]
+#' randu_huber <- prep_huber(randu_df, index = norm_bin(nr = nrow(randu_df)))
 #'
-#'  ggplot() +
-#'  geom_huber(data = randu_huber$idx_df, aes(x = x, y = y)) +
-#'  geom_point(data = randu_df, aes(x = x, y = yz)) +
-#'  geom_abline(slope = randu_huber$slope, intercept = 0) +
-#'  theme_huber() +
-#'  coord_fixed()
+#' ggplot() +
+#' geom_huber(data = randu_huber$idx_df, aes(x = x, y = y)) +
+#' geom_point(data = randu_df, aes(x = x, y = yz)) +
+#' geom_abline(slope = randu_huber$slope, intercept = 0) +
+#' theme_huber() +
+#' coord_fixed()
 #'
-#' ggplot(randu_huber$proj_df, aes(x = x)) +
-#' geom_histogram(breaks = seq(-2.2, 2.4, 0.12)) +
-#' xlab("") + ylab("") +
-#' theme_bw() +
-#' theme(axis.text.y = element_blank())
-#'}
+#' ggplot(randu_huber$proj_df, aes(x = x)) +
+#' geom_histogram(breaks = seq(-2.2, 2.4, 0.12)) +
+#' xlab("") + ylab("") +
+#' theme_bw() +
+#' theme(axis.text.y = element_blank())
 geom_huber <- function(mapping = NULL, data = NULL, stat = "identity",
  position = "identity", ...,
  show.legend = NA, inherit.aes = TRUE) {

_pkgdown.yml

@@ -2,9 +2,7 @@ url: https://huizezhang-sherry.github.io/ferrn/
 
 
 template:
- params:
- bootswatch: cosmo
- ganalytics: G-SPC6B94B10
+ bootstrap: 5
 
 reference:
 - title: Main plotting functions
@@ -18,6 +16,9 @@ reference:
  - plot_projection
  - flip_sign
  - geom_huber
+- title: Calculate projection pursuit index metrics
+ contents:
+ - starts_with("calc")
 - title: Get components
  desc: >
  Extracting components from existing data object
@@ -47,9 +48,6 @@ reference:
  contents:
  - starts_with("boa")
  - starts_with("holes")
-- title: Calculate projection pursuit optimisation properties
- contents:
- - starts_with("calc")
 - title: Miscellaneous
  desc: >
  Other misc functions