Package 'ferrn' reference manual

Title:	Facilitate Exploration of touRR optimisatioN
Description:	Diagnostic plots for optimisation, with a focus on projection pursuit. These show paths the optimiser takes in the high-dimensional space in multiple ways: by reducing the dimension using principal component analysis, and also using the tour to show the path on the high-dimensional space. Several botanical colour palettes are included, reflecting the name of the package. A paper describing the methodology can be found at <https://journal.r-project.org/archive/2021/RJ-2021-105/index.html>.
Authors:	H. Sherry Zhang [aut, cre] , Dianne Cook [aut] , Ursula Laa [aut] , Nicolas Langrené [aut] , Patricia Menéndez [aut]
Maintainer:	H. Sherry Zhang <[email protected]>
License:	MIT + file LICENSE
Version:	0.2.0
Built:	2024-11-16 23:34:19 UTC
Source:	https://github.com/huizezhang-sherry/ferrn

A ggproto for drawing anchor points

Description

This is a wrapper function used by explore_space_pca() and should be be called directly by the user

Usage

add_anchor(dt, anchor_size = 3, anchor_alpha = 0.5, anchor_color = NULL, ...)
add_anchor(dt, anchor_size = 3, anchor_alpha = 0.5, anchor_color = NULL, ...)

Arguments

`dt`	A data object from the running the optimisation algorithm in guided tour
`anchor_size`	numeric; the size of the anchor points
`anchor_alpha`	numeric; the alpha of the anchor points
`anchor_color`	the variable to be coloured by
`...`	other aesthetics inherent from `explore_space_pca()`

Value

a wrapper for drawing anchor points in explore_space_pca()

A ggproto for annotating the symmetry of the starting points

Description

This is a wrapper function used by explore_space_pca() and should be be called directly by the user

Usage

add_anno(dt, anno_color = "black", anno_lty = "dashed", anno_alpha = 0.1, ...)
add_anno(dt, anno_color = "black", anno_lty = "dashed", anno_alpha = 0.1, ...)

Arguments

`dt`	A data object from the running the optimisation algorithm in guided tour
`anno_color`	character; the colour of the annotation line
`anno_lty`	character; the linetype of the annotation line
`anno_alpha`	numeric; the alpha of the annotation line
`...`	other aesthetics inherent from `explore_space_pca()`

Value

a wrapper for annotating the symmetry of start points in explore_space_pca()

A ggproto for drawing directional search points

Description

This is a wrapper function used by explore_space_pca() and should be be called directly by the user

Usage

add_dir_search(dt, dir_size = 0.5, dir_alpha = 0.5, dir_color = NULL, ...)
add_dir_search(dt, dir_size = 0.5, dir_alpha = 0.5, dir_color = NULL, ...)

Arguments

`dt`	A data object from the running the optimisation algorithm in guided tour
`dir_size`	numeric; the size of the directional search points in pseudo derivative search
`dir_alpha`	numeric; the alpha of the directional search points in pseudo derivative search
`dir_color`	the variable to be coloured by
`...`	other aesthetics inherent from `explore_space_pca()`

Value

a wrapper for drawing directional search points (used in pseudo derivative search) with buffer in explore_space_pca()

A ggproto for drawing start points

Description

This is a wrapper function used by explore_space_pca() and should be be called directly by the user

Usage

add_end(dt, end_size = 5, end_alpha = 1, end_color = NULL, ...)
add_end(dt, end_size = 5, end_alpha = 1, end_color = NULL, ...)

Arguments

`dt`	A data object from the running the optimisation algorithm in guided tour
`end_size`	numeric; the size of the end point
`end_alpha`	numeric; the alpha of the end point
`end_color`	the variable to be coloured by
`...`	other aesthetics inherent from `explore_space_pca()`

Value

a wrapper for drawing end points in explore_space_pca()

A ggproto for drawing interpolation path

Description

This is a wrapper function used by explore_space_pca() and should be be called directly by the user

Usage

add_interp(
  dt,
  interp_size = 1.5,
  interp_alpha = NULL,
  interp_color = NULL,
  interp_group = NULL,
  ...
)
add_interp(
  dt,
  interp_size = 1.5,
  interp_alpha = NULL,
  interp_color = NULL,
  interp_group = NULL,
  ...
)

Arguments

`dt`	A data object from the running the optimisation algorithm in guided tour
`interp_size`	numeric; the size of the interpolation path
`interp_alpha`	numeric; the alpha of the interpolation path
`interp_color`	the variable to be coloured by
`interp_group`	the variable to label different interpolation path
`...`	other aesthetics inherent from `explore_space_pca()`

Value

a wrapper for drawing the interpolation points in explore_space_pca()

A ggproto for drawing finish points

Description

This is a wrapper function used by explore_space_pca() and should be be called directly by the user

Usage

add_interp_last(
  dt,
  interp_last_size = 3,
  interp_last_alpha = 1,
  interp_last_color = NULL,
  ...
)
add_interp_last(
  dt,
  interp_last_size = 3,
  interp_last_alpha = 1,
  interp_last_color = NULL,
  ...
)

Arguments

`dt`	A data object from the running the optimisation algorithm in guided tour
`interp_last_size`	numeric; the size of the last interpolation points in each iteration
`interp_last_alpha`	numeric; the alpha of the last interpolation points in each iteration
`interp_last_color`	the variable to be coloured by
`...`	other aesthetics inherent from `explore_space_pca()`

Value

a wrapper for drawing the last interpolation points of each iteration in explore_space_pca()

A ggproto for annotating the interrupted path

Description

This is a wrapper function used by explore_space_pca() and should be be called directly by the user

Usage

add_interrupt(
  dt,
  interrupt_size = 0.5,
  interrupt_alpha = NULL,
  interrupt_color = NULL,
  interrupt_group = NULL,
  interrupt_linetype = "dashed",
  ...
)
add_interrupt(
  dt,
  interrupt_size = 0.5,
  interrupt_alpha = NULL,
  interrupt_color = NULL,
  interrupt_group = NULL,
  interrupt_linetype = "dashed",
  ...
)

Arguments

`dt`	A data object from the running the optimisation algorithm in guided tour
`interrupt_size`	numeric; the size of the interruption path
`interrupt_alpha`	numeric; the alpha of the interruption path
`interrupt_color`	the variable to be coloured by
`interrupt_group`	the variable to label different interruption
`interrupt_linetype`	character; the linetype to annotate the interruption
`...`	other aesthetics inherent from `explore_space_pca()`

Value

a wrapper for annotating the interruption in explore_space_pca()

A ggproto for drawing search points

Description

This is a wrapper function used by explore_space_pca() and should be be called directly by the user

Usage

add_search(dt, search_size = 0.5, search_alpha = 0.5, search_color = NULL, ...)
add_search(dt, search_size = 0.5, search_alpha = 0.5, search_color = NULL, ...)

Arguments

`dt`	A data object from the running the optimisation algorithm in guided tour
`search_size`	numeric; the size of the search points
`search_alpha`	numeric; the alpha of the anchor points
`search_color`	the variable to be coloured by
`...`	other aesthetics inherent from `explore_space_pca()`

Value

a wrapper for drawing search points in explore_space_pca()

A ggproto for drawing circle

Description

This is a wrapper function used by explore_space_pca() and should be be called directly by the user

Usage

add_space(
  dt,
  space_alpha = 0.5,
  space_fill = "grey92",
  space_color = "white",
  cent_size = 1,
  cent_alpha = 1,
  cent_color = "black",
  ...
)
add_space(
  dt,
  space_alpha = 0.5,
  space_fill = "grey92",
  space_color = "white",
  cent_size = 1,
  cent_alpha = 1,
  cent_color = "black",
  ...
)

Arguments

`dt`	A data object from the running the optimisation algorithm in guided tour
`space_alpha`	numeric; the alpha of the basis space
`space_fill`	character; the colour of the space filling
`space_color`	character; the colour of the space brim
`cent_size`	numeric; the size of the centre point
`cent_alpha`	numeric; an alpha of the centre point
`cent_color`	character; the colour of the centre point
`...`	other aesthetics inherent from `explore_space_pca()`

Value

a wrapper for drawing the space in explore_space_pca()

Examples

library(ggplot2)
space <- tibble::tibble(x0 = 0, y0 = 0, r = 5)
ggplot() +
  add_space(space) +
  theme_void() +
  theme(aspect.ratio = 1)
library(ggplot2)
space <- tibble::tibble(x0 = 0, y0 = 0, r = 5)
ggplot() +
  add_space(space) +
  theme_void() +
  theme(aspect.ratio = 1)

A ggproto for drawing start points

Description

This is a wrapper function used by explore_space_pca() and should be be called directly by the user

Usage

add_start(dt, start_size = 5, start_alpha = 1, start_color = NULL, ...)
add_start(dt, start_size = 5, start_alpha = 1, start_color = NULL, ...)

Arguments

`dt`	A data object from the running the optimisation algorithm in guided tour
`start_size`	numeric; the size of start point
`start_alpha`	numeric; the alpha of start point
`start_color`	the variable to be coloured by
`...`	other aesthetics inherent from `explore_space_pca()`

Value

a wrapper for drawing start points in explore_space_pca()

Examples

library(ggplot2)
# construct the space and start df for plotting
space <- tibble::tibble(x0 = 0, y0 = 0, r = 5)
holes_1d_geo %>%
  compute_pca() %>%
  purrr::pluck("aug") %>%
  clean_method() %>%
  get_start()
library(ggplot2)
# construct the space and start df for plotting
space <- tibble::tibble(x0 = 0, y0 = 0, r = 5)
holes_1d_geo %>%
  compute_pca() %>%
  purrr::pluck("aug") %>%
  clean_method() %>%
  get_start()

A ggproto for drawing the theoretical basis, if applicable

Description

This is a wrapper function used by explore_space_pca() and should be be called directly by the user

Usage

add_theo(
  dt,
  theo_label = "*",
  theo_size = 25,
  theo_alpha = 0.8,
  theo_color = "#000000",
  ...
)
add_theo(
  dt,
  theo_label = "*",
  theo_size = 25,
  theo_alpha = 0.8,
  theo_color = "#000000",
  ...
)

Arguments

`dt`	A data object from the running the optimisation algorithm in guided tour
`theo_label`	character; a symbol to label the theoretical point
`theo_size`	numeric; the size of the theoretical point
`theo_alpha`	numeric; the alpha of the theoretical point
`theo_color`	character; the colour of the theoretical point in hex
`...`	other aesthetics inherent from `explore_space_pca()`

Value

a wrapper for drawing theoretical points in explore_space_pca()

Bind random bases in the projection bases space

Description

Given the orthonormality constraint, the projection bases live in a high dimensional hollow sphere. Generating random points on the sphere is useful to perceive the data object in the high dimensional space.

Usage

bind_random(dt, n = 500, seed = 1)
bind_random(dt, n = 500, seed = 1)

Arguments

`dt`	a data object collected by the projection pursuit guided tour optimisation in the `tourr` package
`n`	numeric; the number of random bases to generate in each dimension by geozoo
`seed`	numeric; a seed for generating reproducible random bases from geozoo

Value

a tibble object containing both the searched and random bases

Examples

bind_random(holes_1d_better) %>% tail(5)
bind_random(holes_1d_better) %>% tail(5)

Bind random bases in the projection bases space as a matrix

Description

Bind random bases in the projection bases space as a matrix

Usage

bind_random_matrix(basis, n = 500, d = 1, front = FALSE, seed = 1)
bind_random_matrix(basis, n = 500, d = 1, front = FALSE, seed = 1)

Arguments

`basis`	a matrix returned by `get_basis_matrix()`
`n`	numeric; the number of random bases to generate in each dimension by geozoo
`d`	numeric; dimension of the basis, d = 1, 2, ...
`front`	logical; if the random bases should be bound before or after the original bases
`seed`	numeric; a seed for generating reproducible random bases from geozoo

Value

matrix

a matrix containing both the searched and random bases

Examples

data <- get_basis_matrix(holes_1d_geo)
bind_random_matrix(data) %>% tail(5)
data <- get_basis_matrix(holes_1d_geo)
bind_random_matrix(data) %>% tail(5)

Bind the theoretical best record

Description

The theoretical best basis is usually known for a simulated problem. Augment this information into the data object allows for evaluating the performance of optimisation against the theory.

Usage

bind_theoretical(dt, matrix, index, raw_data)
bind_theoretical(dt, matrix, index, raw_data)

Arguments

`dt`	a data object collected by the projection pursuit guided tour optimisation in the `tourr` package
`matrix`	a matrix of the theoretical basis
`index`	the index function used to calculate the index value
`raw_data`	a tibble of the original data used to calculate the index value

Value

a tibble object containing both the searched and theoretical best bases

Examples

best <- matrix(c(0, 1, 0, 0, 0), nrow = 5)
tail(holes_1d_better %>% bind_theoretical(best, tourr::holes(), raw_data = boa5), 1)
best <- matrix(c(0, 1, 0, 0, 0), nrow = 5)
tail(holes_1d_better %>% bind_theoretical(best, tourr::holes(), raw_data = boa5), 1)

A customised colour palette based on Australian botanies

Description

Available colours in the palettes

Usage

botanical_palettes

botanical_pal(palette = "fern", reverse = FALSE)
botanical_palettes

botanical_pal(palette = "fern", reverse = FALSE)

Arguments

`palette`	Colour palette from the botanical_palette
`reverse`	logical, if the colour should be reversed

Format

An object of class list of length 5.

Value

a function for interpolating colour in the botanical palette

Clean method names

Description

Clean method names

Usage

clean_method(dt)
clean_method(dt)

Arguments

`dt`	a data object

Value

a tibble with method cleaned

Examples

head(clean_method(holes_1d_better), 5)
head(clean_method(holes_1d_better), 5)

Plot the PCA projection of the projection bases space

Description

Plot the PCA projection of the projection bases space

Usage

explore_space_start(dt, group = NULL, pca = TRUE, ...)

explore_space_end(dt, group = NULL, pca = TRUE, ...)

explore_space_pca(
  dt,
  details = FALSE,
  pca = TRUE,
  group = NULL,
  color = NULL,
  facet = NULL,
  ...,
  animate = FALSE
)
explore_space_start(dt, group = NULL, pca = TRUE, ...)

explore_space_end(dt, group = NULL, pca = TRUE, ...)

explore_space_pca(
  dt,
  details = FALSE,
  pca = TRUE,
  group = NULL,
  color = NULL,
  facet = NULL,
  ...,
  animate = FALSE
)

Arguments

`dt`	a data object collected by the projection pursuit guided tour optimisation in `tourr`
`group`	the variable to label different runs of the optimiser(s)
`pca`	logical; if PCA coordinates need to be computed for the data
`...`	other arguments passed to `add_*()` functions
`details`	logical; if components other than start, end and interpolation need to be shown
`color`	the variable to be coloured by
`facet`	the variable to be faceted by
`animate`	logical; if the interpolation path needs to be animated

Value

a ggplot2 object

Examples

dplyr::bind_rows(holes_1d_geo, holes_1d_better) %>%
  bind_theoretical(matrix(c(0, 1, 0, 0, 0), nrow = 5),
    index = tourr::holes(), raw_data = boa5
  ) %>%
  explore_space_pca(group = method, details = TRUE) +
  scale_color_discrete_botanical()

## Not run: 
best <- matrix(c(0, 1, 0, 0, 0), nrow = 5)
dt <- bind_theoretical(holes_1d_jellyfish, best, tourr::holes(), raw_data = boa5)
explore_space_start(dt)
explore_space_end(dt, group = loop, theo_size = 10, theo_color = "#FF0000")
explore_space_pca(
  dt, facet = loop, interp_size = 0.5, theo_size = 10,
  start_size = 1, end_size = 3
  )

## End(Not run)
dplyr::bind_rows(holes_1d_geo, holes_1d_better) %>%
  bind_theoretical(matrix(c(0, 1, 0, 0, 0), nrow = 5),
    index = tourr::holes(), raw_data = boa5
  ) %>%
  explore_space_pca(group = method, details = TRUE) +
  scale_color_discrete_botanical()

## Not run: 
best <- matrix(c(0, 1, 0, 0, 0), nrow = 5)
dt <- bind_theoretical(holes_1d_jellyfish, best, tourr::holes(), raw_data = boa5)
explore_space_start(dt)
explore_space_end(dt, group = loop, theo_size = 10, theo_color = "#FF0000")
explore_space_pca(
  dt, facet = loop, interp_size = 0.5, theo_size = 10,
  start_size = 1, end_size = 3
  )

## End(Not run)

Plot the grand tour animation of the bases space in high dimension

Description

Plot the grand tour animation of the bases space in high dimension

Usage

explore_space_tour(..., axes = "bottomleft")

prep_space_tour(
  dt,
  group = NULL,
  flip = FALSE,
  n_random = 2000,
  color = NULL,
  rand_size = 1,
  rand_color = "#D3D3D3",
  point_size = 1.5,
  end_size = 5,
  theo_size = 3,
  theo_shape = 17,
  theo_color = "black",
  palette = botanical_palettes$fern,
  ...
)
explore_space_tour(..., axes = "bottomleft")

prep_space_tour(
  dt,
  group = NULL,
  flip = FALSE,
  n_random = 2000,
  color = NULL,
  rand_size = 1,
  rand_color = "#D3D3D3",
  point_size = 1.5,
  end_size = 5,
  theo_size = 3,
  theo_shape = 17,
  theo_color = "black",
  palette = botanical_palettes$fern,
  ...
)

Arguments

`...`	other argument passed to `tourr::animate_xy()` and `prep_space_tour()`
`axes`	see [tourr::animate_xy()]
`dt`	a data object collected by the projection pursuit guided tour optimisation in `tourr`
`group`	the variable to label different runs of the optimiser(s)
`flip`	logical; if the sign flipping need to be performed
`n_random`	numeric; the number of random basis to generate
`color`	the variable to be coloured by
`rand_size`	numeric; the size of random points
`rand_color`	character; the color hex code for random points
`point_size`	numeric; the size of points searched by the optimiser(s)
`end_size`	numeric; the size of end points
`theo_size`	numeric; the size of theoretical point(s)
`theo_shape`	numeric; the shape symbol in the basic plot
`theo_color`	character; the color of theoretical point(s)
`palette`	the colour palette to be used

Value

explore_space_tour(): an animation of the search path in the high-dimensional sphere
prep_space_tour(): a list containing various components needed for producing the animation

Examples

if (FALSE){
explore_space_tour(dplyr::bind_rows(holes_1d_better, holes_1d_geo),
  group = method, palette = botanical_palettes$fern[c(1, 6)]
)
}
if (FALSE){
explore_space_tour(dplyr::bind_rows(holes_1d_better, holes_1d_geo),
  group = method, palette = botanical_palettes$fern[c(1, 6)]
)
}

Plot the trace the search progression

Description

Trace the index value of search/ interpolation points in guided tour optimisation

Usage

explore_trace_interp(
  dt,
  iter = NULL,
  color = NULL,
  group = NULL,
  cutoff = 50,
  target_size = 3,
  interp_size = 1,
  accuracy_x = 5,
  accuracy_y = 0.01
)
explore_trace_interp(
  dt,
  iter = NULL,
  color = NULL,
  group = NULL,
  cutoff = 50,
  target_size = 3,
  interp_size = 1,
  accuracy_x = 5,
  accuracy_y = 0.01
)

Arguments

`dt`	a data object collected by the projection pursuit guided tour optimisation in `tourr`
`iter`	the variable to be plotted on the x-axis
`color`	the variable to be coloured by
`group`	the variable to label different runs of the optimiser(s)
`cutoff`	numeric; if the number of interpolating points is smaller than `cutoff`, all the interpolation points will be plotted as dots
`target_size`	numeric; the size of target points in the interpolation
`interp_size`	numeric; the size of interpolation points
`accuracy_x`	numeric; If the difference of two neighbour x-labels is smaller than `accuracy_x`, only one of them will be displayed. Used for better axis label
`accuracy_y`	numeric; the precision of y-axis label

Value

a ggplot object for diagnosing how the index value progresses during the interpolation

Examples

# Compare the trace of interpolated points in two algorithms
holes_1d_better %>%
  explore_trace_interp(interp_size = 2) +
  scale_color_continuous_botanical(palette = "fern")
# Compare the trace of interpolated points in two algorithms
holes_1d_better %>%
  explore_trace_interp(interp_size = 2) +
  scale_color_continuous_botanical(palette = "fern")

Plot the count in each iteration

Description

Plot the count in each iteration

Usage

explore_trace_search(
  dt,
  iter = NULL,
  color = NULL,
  cutoff = 15,
  extend_lower = 0.95,
  ...
)
explore_trace_search(
  dt,
  iter = NULL,
  color = NULL,
  cutoff = 15,
  extend_lower = 0.95,
  ...
)

Arguments

`dt`	a data object collected by the projection pursuit guided tour optimisation in `tourr`
`iter`	the variable to be plotted on the x-axis
`color`	the variable to be coloured by
`cutoff`	numeric; if the number of searches in one iteration is smaller than `cutoff`, a point geom, rather than boxplot geom, will be used.
`extend_lower`	a numeric for extending the y-axis to display text labels
`...`	arguments passed into geom_label_repel() for displaying text labels

Value

a ggplot object for diagnosing how many points the optimiser(s) have searched

Examples

# Summary plots for search points in two algorithms
library(patchwork)
library(dplyr)
library(ggplot2)
p1 <- holes_1d_better %>% explore_trace_search() +
  scale_color_continuous_botanical(palette = "fern")
p2 <- holes_2d_better_max_tries %>% explore_trace_search() +
  scale_color_continuous_botanical(palette = "daisy")
p1 / p2
# Summary plots for search points in two algorithms
library(patchwork)
library(dplyr)
library(ggplot2)
p1 <- holes_1d_better %>% explore_trace_search() +
  scale_color_continuous_botanical(palette = "fern")
p2 <- holes_2d_better_max_tries %>% explore_trace_search() +
  scale_color_continuous_botanical(palette = "daisy")
p1 / p2

Helper functions for 'explore_space_pca()'

Description

Helper functions for 'explore_space_pca()'

Usage

flip_sign(dt, group = NULL, ...)

compute_pca(dt, group = NULL, random = TRUE, flip = TRUE, ...)
flip_sign(dt, group = NULL, ...)

compute_pca(dt, group = NULL, random = TRUE, flip = TRUE, ...)

Arguments

`dt`	a data object collected by the projection pursuit guided tour optimisation in `tourr`
`group`	the variable to label different runs of the optimiser(s)
`...`	other arguments received from `explore_space_pca()`
`random`	logical; if random bases from the basis space need to be added to the data
`flip`	logical; if the sign flipping need to be performed

Value

flip_sign(): a list containing a matrix of all the bases, a logical value indicating whether a flip of sign is performed, and a data frame of the original dataset.

compute_pca(): a list containing the PCA summary and a data frame with PC coordinates augmented.

Examples

dt <- dplyr::bind_rows(holes_1d_geo, holes_1d_better)
 flip_sign(dt, group = method) %>% str(max = 1)
compute_pca(dt, group = method)
dt <- dplyr::bind_rows(holes_1d_geo, holes_1d_better)
 flip_sign(dt, group = method) %>% str(max = 1)
compute_pca(dt, group = method)

Better label formatting to avoid overlapping

Description

Better label formatting to avoid overlapping

Usage

format_label(labels, accuracy)
format_label(labels, accuracy)

Arguments

`labels`	a numerical vector of labels
`accuracy`	the accuracy of the label

Value

a vector of adjusted labels

Examples

format_label(c(0.87, 0.87, 0.9, 0.93, 0.95), 0.01)
format_label(c(0.87, 0.87, 0.9, 0.93, 0.95, 0.96, 0.96), 0.01)
format_label(c(0.87, 0.87, 0.9, 0.93, 0.95), 0.01)
format_label(c(0.87, 0.87, 0.9, 0.93, 0.95, 0.96, 0.96), 0.01)

Create Huber plot with ggplot2

Description

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 prep_huber() calculates each component required for the Huber plot (see details), which can then be supplied to various geom layers in ggplot2.

Usage

geom_huber(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  show.legend = NA,
  inherit.aes = TRUE
)

prep_huber(data, index)

theme_huber(...)
geom_huber(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  show.legend = NA,
  inherit.aes = TRUE
)

prep_huber(data, index)

theme_huber(...)

Arguments

`mapping`	Set of aesthetic mappings created by `aes()`. If specified and `inherit.aes = TRUE` (the default), it is combined with the default mapping at the top level of the plot. You must supply `mapping` if there is no plot mapping.
`data`	The data to be displayed in this layer. There are three options: If `NULL`, the default, the data is inherited from the plot data as specified in the call to `ggplot()`. A `data.frame`, or other object, will override the plot data. All objects will be fortified to produce a data frame. See `fortify()` for which variables will be created. A `function` will be called with a single argument, the plot data. The return value must be a `data.frame`, and will be used as the layer data. A `function` can be created from a `formula` (e.g. `~ head(.x, 10)`).
`stat`	The statistical transformation to use on the data for this layer. When using a `⁠geom_*()⁠` function to construct a layer, the `stat` argument can be used the override the default coupling between geoms and stats. The `stat` argument accepts the following: A `Stat` ggproto subclass, for example `StatCount`. A string naming the stat. To give the stat as a string, strip the function name of the `stat_` prefix. For example, to use `stat_count()`, give the stat as `"count"`. For more information and other ways to specify the stat, see the layer stat documentation.
`position`	A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The `position` argument accepts the following: The result of calling a position function, such as `position_jitter()`. This method allows for passing extra arguments to the position. A string naming the position adjustment. To give the position as a string, strip the function name of the `position_` prefix. For example, to use `position_jitter()`, give the position as `"jitter"`. For more information and other ways to specify the position, see the layer position documentation.
`...`	Other arguments passed on to `layer()`'s `params` argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the `position` argument, or aesthetics that are required can not be passed through `...`. Unknown arguments that are not part of the 4 categories below are ignored. Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, `colour = "red"` or `linewidth = 3`. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the `params`. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data. When constructing a layer using a `⁠stat_()⁠` function, the `...` argument can be used to pass on parameters to the `geom` part of the layer. An example of this is `stat_density(geom = "area", outline.type = "both")`. The geom's documentation lists which parameters it can accept. Inversely, when constructing a layer using a `⁠geom_()⁠` function, the `...` argument can be used to pass on parameters to the `stat` part of the layer. An example of this is `geom_area(stat = "density", adjust = 0.5)`. The stat's documentation lists which parameters it can accept. The `key_glyph` argument of `layer()` may also be passed on through `...`. This can be one of the functions described as key glyphs, to change the display of the layer in the legend.
`show.legend`	logical. Should this layer be included in the legends? `NA`, the default, includes if any aesthetics are mapped. `FALSE` never includes, and `TRUE` always includes. It can also be a named logical vector to finely select the aesthetics to display.
`inherit.aes`	If `FALSE`, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. `borders()`.
`index`	a function, the projection pursuit index function, see examples

Details

the prep_huber() function calculates components required for making the Huber plots. It returns a list including three elements:

the 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.
the proj_df data frame:: the best 1D projection. Used for plotting the 1D projection in histogram.
the slope value:: the slope to plot in the Huber plot to indicate the direction of the best 1D projection.

Examples

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(randu_huber$proj_df, aes(x = x)) +
  geom_histogram(breaks = seq(-2.2, 2.4, 0.12)) +
  xlab("") + ylab("") +
  theme_bw() +
  theme(axis.text.y = element_blank())
library(ggplot2)
library(tourr)
library(ash)
data(randu)
randu_std <- as.data.frame(apply(randu, 2, function(x) (x-mean(x))/sd(x)))
randu_std$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(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())

Functions to get components from the data collecting object

Description

Functions to get components from the data collecting object

Usage

get_best(dt, group = NULL)

get_start(dt, group = NULL)

get_interp(dt, group = NULL)

get_interp_last(dt, group = NULL)

get_anchor(dt, group = NULL)

get_search(dt)

get_dir_search(dt, ratio = 5, ...)

get_space_param(dt, ...)

get_theo(dt)

get_interrupt(dt, group = NULL, precision = 0.001)

get_search_count(dt, iter = NULL, group = NULL)

get_basis_matrix(dt)
get_best(dt, group = NULL)

get_start(dt, group = NULL)

get_interp(dt, group = NULL)

get_interp_last(dt, group = NULL)

get_anchor(dt, group = NULL)

get_search(dt)

get_dir_search(dt, ratio = 5, ...)

get_space_param(dt, ...)

get_theo(dt)

get_interrupt(dt, group = NULL, precision = 0.001)

get_search_count(dt, iter = NULL, group = NULL)

get_basis_matrix(dt)

Arguments

`dt`	a data object collected by the projection pursuit guided tour optimisation in the `tourr` package
`group`	the variable to label different runs of the optimiser(s)
`ratio`	numeric; a buffer value to deviate directional search points from the anchor points
`...`	other arguments passed to `compute_pca()`
`precision`	numeric; if the index value of the last interpolating point and the anchor point differ by `precision`, an interruption is registered
`iter`	the variable to be counted by

Details

get_best: extract the best basis found by the optimiser(s)

get_start: extract the start point of the optimisation

get_interp: extract the interpolation points

get_interp_last: extract the last point in each interpolation

get_anchor: extract the anchor points on the geodesic path

get_search: extract search points in the optimisation (for search_geodesic)

get_dir_search: extract directional search points (for search_geodesic)

get_space_param: estimate the radius of the background circle based on the randomly generated points. The space of projected bases is a circle when reduced to 2D. A radius is estimated using the largest distance from the bases in the data object to the centre point.

get_theo: extract the theoretical basis, if exist

get_interrupt: extract the end point of the interpolation and the target point in the iteration when an interruption happens. The optimiser can find better basis on the interpolation path, an interruption is implemented to stop further interpolation from the highest point to the target point. This discrepancy is highlighted in the PCA plot.

get_search_count: summarise the number of search points in each iteration

get_basis_matrix: extract all the bases as a matrix

Value

a tibble object containing the best basis found by the optimiser(s)

Examples

get_search(holes_1d_geo)

get_anchor(holes_1d_geo)

get_start(holes_1d_better)

get_interrupt(holes_1d_better)

get_interp(holes_1d_better) %>% head()

get_basis_matrix(holes_1d_better) %>% head()

get_best(dplyr::bind_rows(holes_1d_better, holes_1d_geo), group = method)

get_search_count(holes_1d_better)
get_search_count(dplyr::bind_rows(holes_1d_better, holes_1d_geo), group = method)

get_interp_last(holes_1d_better)
get_interp_last(dplyr::bind_rows(holes_1d_better, holes_1d_geo), group = method)

res <- holes_1d_geo %>% compute_pca() %>% purrr::pluck("aug")
get_dir_search(res)

best <- matrix(c(0, 1, 0, 0, 0), nrow = 5)
holes_1d_better %>%
  bind_theoretical(best, tourr::holes(), raw_data = boa5) %>%
  get_theo()
get_search(holes_1d_geo)

get_anchor(holes_1d_geo)

get_start(holes_1d_better)

get_interrupt(holes_1d_better)

get_interp(holes_1d_better) %>% head()

get_basis_matrix(holes_1d_better) %>% head()

get_best(dplyr::bind_rows(holes_1d_better, holes_1d_geo), group = method)

get_search_count(holes_1d_better)
get_search_count(dplyr::bind_rows(holes_1d_better, holes_1d_geo), group = method)

get_interp_last(holes_1d_better)
get_interp_last(dplyr::bind_rows(holes_1d_better, holes_1d_geo), group = method)

res <- holes_1d_geo %>% compute_pca() %>% purrr::pluck("aug")
get_dir_search(res)

best <- matrix(c(0, 1, 0, 0, 0), nrow = 5)
holes_1d_better %>%
  bind_theoretical(best, tourr::holes(), raw_data = boa5) %>%
  get_theo()

Data objects collected during the projection pursuit optimisation

Description

Simulated data to demonstrate the usage of four diagnostic plots in the package, users can create their own guided tour data objects and diagnose with the visualisation designed in this package.

Usage

holes_1d_geo

holes_1d_better

holes_1d_jellyfish

holes_2d_jellyfish

holes_2d_better

holes_2d_better_max_tries
holes_1d_geo

holes_1d_better

holes_1d_jellyfish

holes_2d_jellyfish

holes_2d_better

holes_2d_better_max_tries

Format

An object of class tbl_df (inherits from tbl, data.frame) with 416 rows and 8 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 79 rows and 8 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 2500 rows and 8 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 98 rows and 8 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 1499 rows and 8 columns.

Details

The prefix holes_* indicates the use of holes index in the guided tour. The suffix *_better/geo/jellyfish indicates the optimiser used: search_better, search_geodesic, search_jellyfish.

Examples

holes_1d_better %>%
explore_trace_interp(interp_size = 2) +
  scale_color_continuous_botanical(palette = "fern")
holes_1d_better %>%
explore_trace_interp(interp_size = 2) +
  scale_color_continuous_botanical(palette = "fern")

Plot the projection from the optimisation data collected from projection pursuit

Description

Plot the projection from the optimisation data collected from projection pursuit

Usage

plot_projection(
  dt,
  data,
  id = NULL,
  cols = NULL,
  label = TRUE,
  animate_along = NULL,
  keep = 0.2
)

compute_projection(dt, data, id = NULL, cols = NULL)
plot_projection(
  dt,
  data,
  id = NULL,
  cols = NULL,
  label = TRUE,
  animate_along = NULL,
  keep = 0.2
)

compute_projection(dt, data, id = NULL, cols = NULL)

Arguments

`dt`	a data object collected by the projection pursuit guided tour optimisation in `tourr`
`data`	the original data
`id`	the grouping variable
`cols`	additional columns to include in the plot
`label`	logical, whether to label each panel by its index value
`animate_along`	the variable to animate along
`keep`	numeric, the proportion of the data to keep for animation (default is 0.2). Only used when 'animate_along' is not NULL

Value

a ggplot object

Examples

library(dplyr)
holes_2d_jellyfish |>
  filter(loop == 1, tries %in% seq(1, 50, 5)) |>
  plot_projection(data = boa6)
## Not run: 
library(dplyr)
# track the first jellyfish (loop == 1)
holes_2d_jellyfish |>
  filter(loop == 1) |>
  plot_projection(data = boa6, animate_along = tries, id = loop)

## End(Not run)

library(dplyr)
holes_2d_jellyfish |>
  filter(loop == 1, tries %in% seq(1, 50, 5)) |>
  plot_projection(data = boa6)
## Not run: 
library(dplyr)
# track the first jellyfish (loop == 1)
holes_2d_jellyfish |>
  filter(loop == 1) |>
  plot_projection(data = boa6, animate_along = tries, id = loop)

## End(Not run)

Function to calculate smoothness and squintability

Description

Function to calculate smoothness and squintability

Usage

sample_bases(
  idx,
  data = sine1000,
  n_basis = 300,
  parallel = FALSE,
  best = matrix(c(0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1), nrow = 6),
  min_proj_dist = NA,
  step_size = NA,
  seed = 123
)

## S3 method for class 'basis_df'
print(x, width = NULL, ...)

## S3 method for class 'basis_df'
tbl_sum(x)

calc_smoothness(
  basis_df,
  start_params = c(0.001, 0.5, 2, 2),
  other_gp_params = NULL,
  verbose = FALSE
)

## S3 method for class 'smoothness_res'
print(x, width = NULL, ...)

## S3 method for class 'smoothness_res'
tbl_sum(x)

calc_squintability(
  basis_df,
  method = c("ks", "nls"),
  scale = TRUE,
  bin_width = 0.005,
  other_params = NULL
)

## S3 method for class 'squintability_res'
print(x, width = NULL, ...)

## S3 method for class 'squintability_res'
tbl_sum(x)

fit_ks(basis_df, idx, other_params = NULL)

fit_nls(basis_df, other_params = NULL)
sample_bases(
  idx,
  data = sine1000,
  n_basis = 300,
  parallel = FALSE,
  best = matrix(c(0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1), nrow = 6),
  min_proj_dist = NA,
  step_size = NA,
  seed = 123
)

## S3 method for class 'basis_df'
print(x, width = NULL, ...)

## S3 method for class 'basis_df'
tbl_sum(x)

calc_smoothness(
  basis_df,
  start_params = c(0.001, 0.5, 2, 2),
  other_gp_params = NULL,
  verbose = FALSE
)

## S3 method for class 'smoothness_res'
print(x, width = NULL, ...)

## S3 method for class 'smoothness_res'
tbl_sum(x)

calc_squintability(
  basis_df,
  method = c("ks", "nls"),
  scale = TRUE,
  bin_width = 0.005,
  other_params = NULL
)

## S3 method for class 'squintability_res'
print(x, width = NULL, ...)

## S3 method for class 'squintability_res'
tbl_sum(x)

fit_ks(basis_df, idx, other_params = NULL)

fit_nls(basis_df, other_params = NULL)

Arguments

`idx`	character, the name of projection pursuit index function, e.g. "holes"
`data`	a matrix or data frame, the high dimensional data to be projected
`n_basis`	numeric, the number of random bases to generate
`parallel`	logic, whether to use parallel computing for calculating the index. Recommend for the stringy index.
`best`	a matrix, the theoretical/ empirical best projection matrix to calculate the projection distance from the simulated random bases.
`min_proj_dist`	only for squintability, the threshold for projection distance for the random basis to be considered in sampling
`step_size`	numeric, step size for interpolating from each random basis to the best basis, recommend 0.005
`seed`	numeric, seed for sampling random bases
`x`	objects with specialised printing methods
`width`	only used when `max.levels` is NULL, see above.
`...`	further arguments passed to or from other methods.
`basis_df`	the basis data frame returned from `sample_bases`
`start_params`	list, the starting parameters for the Gaussian process for smoothness
`other_gp_params`	list, additional parameters to be passed to [GpGp::fit_model()] for calculating smoothness
`verbose`	logical, whether to print optimisation progression when fitting the Gaussian process
`method`	either "ks" (kernel smoothing) or "nls" (non-linear least square) for calculating squintability.
`scale`	logic, whether to scale the index value to 0-1 in squintability
`bin_width`	numeric, the bin width to average the index value before fitting the kernel, recommend to set as the same as 'step' parameter
`other_params`	list additional parameters for fitting kernel smoothing or non-linear least square, see [stats::ksmooth()] and [stats::nls()] for details

Examples

## Not run: 
library(GpGp)
library(fields)
library(tourr)
basis_smoothness <- sample_bases(idx = "holes")
calc_smoothness(basis_smoothness)
basis_squint <- sample_bases(idx = "holes", n_basis = 100, step_size = 0.01, min_proj_dist = 1.5)
calc_squintability(basis_squint, method = "ks", bin_width = 0.01)

## End(Not run)
## Not run: 
library(GpGp)
library(fields)
library(tourr)
basis_smoothness <- sample_bases(idx = "holes")
calc_smoothness(basis_smoothness)
basis_squint <- sample_bases(idx = "holes", n_basis = 100, step_size = 0.01, min_proj_dist = 1.5)
calc_squintability(basis_squint, method = "ks", bin_width = 0.01)

## End(Not run)

continuous scale colour function

Description

continuous scale colour function

Discrete scale colour function

continuous scale fill function

discrete scale fill function

Usage

scale_color_continuous_botanical(palette = "fern", reverse = FALSE, ...)

scale_color_discrete_botanical(palette = "fern", reverse = FALSE, ...)

scale_fill_continuous_botanical(palette = "fern", reverse = FALSE, ...)

scale_fill_discrete_botanical(palette = "fern", reverse = FALSE, ...)
scale_color_continuous_botanical(palette = "fern", reverse = FALSE, ...)

scale_color_discrete_botanical(palette = "fern", reverse = FALSE, ...)

scale_fill_continuous_botanical(palette = "fern", reverse = FALSE, ...)

scale_fill_discrete_botanical(palette = "fern", reverse = FALSE, ...)

Arguments

`palette`	colour palette from the botanical_palette
`reverse`	logical; if the colour should be reversed
`...`	other arguments passed into scale_color_gradientn

Value

a wrapper for continuous scales in the botanical palette

a wrapper for discrete scales in the botanical palette

a wrapper for continuous fill in the botanical palette

a wrapper for discrete fill in the botanical palette

Simulated sine, pipe, and gaussian mixture

Description

Simulated sine and pipe data for calculating optimisation features. Each dataset has 1000 observations and the last two columns contain the intended structure with the rest being noise.

Usage

sine1000

sine1000_8d

pipe1000

pipe1000_8d

pipe1000_10d

pipe1000_12d

boa

boa5

boa6
sine1000

sine1000_8d

pipe1000

pipe1000_8d

pipe1000_10d

pipe1000_12d

boa

boa5

boa6

Format

An object of class matrix (inherits from array) with 1000 rows and 6 columns.

An object of class matrix (inherits from array) with 1000 rows and 8 columns.

An object of class matrix (inherits from array) with 1000 rows and 6 columns.

An object of class matrix (inherits from array) with 1000 rows and 8 columns.

An object of class matrix (inherits from array) with 1000 rows and 10 columns.

An object of class matrix (inherits from array) with 1000 rows and 12 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 1000 rows and 10 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 1000 rows and 5 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 1000 rows and 6 columns.

Examples

library(ggplot2)
library(tidyr)
library(dplyr)
boa %>%
  pivot_longer(cols = x1:x10, names_to = "var", values_to = "value") %>%
  mutate(var = forcats::fct_relevel(as.factor(var), paste0("x", 1:10))) %>%
  ggplot(aes(x = value)) +
  geom_density() +
  facet_wrap(vars(var))

sine1000 |> ggplot(aes(x = V5, y = V6)) + geom_point() + theme(aspect.ratio = 1)
pipe1000_8d |> ggplot(aes(x = V5, y = V6)) + geom_point() + theme(aspect.ratio = 1)
pipe1000_8d |> ggplot(aes(x = V7, y = V8)) + geom_point() + theme(aspect.ratio = 1)
library(ggplot2)
library(tidyr)
library(dplyr)
boa %>%
  pivot_longer(cols = x1:x10, names_to = "var", values_to = "value") %>%
  mutate(var = forcats::fct_relevel(as.factor(var), paste0("x", 1:10))) %>%
  ggplot(aes(x = value)) +
  geom_density() +
  facet_wrap(vars(var))

sine1000 |> ggplot(aes(x = V5, y = V6)) + geom_point() + theme(aspect.ratio = 1)
pipe1000_8d |> ggplot(aes(x = V5, y = V6)) + geom_point() + theme(aspect.ratio = 1)
pipe1000_8d |> ggplot(aes(x = V7, y = V8)) + geom_point() + theme(aspect.ratio = 1)

A specific theme for trace plots

Description

A specific theme for trace plots

Usage

theme_fern()
theme_fern()

Value

a ggplot2 theme for explore_trace_interp()

Package 'ferrn'

Help Index

A ggproto for drawing anchor points

Description

Usage

Arguments

Value

See Also

A ggproto for annotating the symmetry of the starting points

Description

Usage

Arguments

Value

See Also

A ggproto for drawing directional search points

Description

Usage

Arguments

Value

See Also

A ggproto for drawing start points

Description

Usage

Arguments

Value

See Also

A ggproto for drawing interpolation path

Description

Usage

Arguments

Value

See Also

A ggproto for drawing finish points

Description

Usage

Arguments

Value

See Also

A ggproto for annotating the interrupted path

Description

Usage

Arguments

Value

See Also

A ggproto for drawing search points

Description

Usage

Arguments

Value

See Also

A ggproto for drawing circle

Description

Usage

Arguments

Value

See Also

Examples

A ggproto for drawing start points

Description

Usage

Arguments

Value

See Also

Examples

A ggproto for drawing the theoretical basis, if applicable

Description

Usage

Arguments

Value

See Also

Bind random bases in the projection bases space

Description

Usage

Arguments

Value

See Also

Examples

Bind random bases in the projection bases space as a matrix

Description

Usage