Package 'moveEZ'

Title: Animated Biplots
Description: Create animated biplots that enables dynamic visualisation of temporal or sequential changes in multivariate data by animating a single biplot across the levels of a time variable. It builds on objects from the 'biplotEZ' package, Lubbe S, le Roux N, Nienkemper-Swanepoel J, Ganey R, Buys R, Adams Z, Manefeldt P (2024) <doi:10.32614/CRAN.package.biplotEZ>, allowing users to create animated biplots that reveal how both samples and variables evolve over time.
Authors: Raeesa Ganey [aut, cre, cph] (ORCID: <https://orcid.org/0009-0008-6973-0999>), Johané Nienkemper-Swanepoel [aut, cph] (ORCID: <https://orcid.org/0000-0001-6086-8272>)
Maintainer: Raeesa Ganey <[email protected]>
License: MIT + file LICENSE
Version: 1.2.0
Built: 2026-05-21 10:44:58 UTC
Source: https://github.com/muvisu/moveez

Help Index

Calibrate axis

Description

Calibrate axis

Usage

.calibrate.axis(
  j,
  Xhat,
  means,
  sd,
  axes.rows,
  ax.which,
  ax.tickvec,
  ax.orthogxvec,
  ax.orthogyvec
)

Arguments

j

j
Xhat

Xhat
means

means
sd

sd
axes.rows

axes.rows
ax.which

ax.which
ax.tickvec

ax.tickvec
ax.orthogxvec

ax.orthogxvec
ax.orthogyvec

ax.orothogyvec

Value

Calibrated axes

Climate studies example dataset

Description

Data extracted from ERA5 hourly data on single levels from 1940 to present

Format

A dataset with 960 observations and 9 variables.

Details

Year

8 years from 1950 to 2020

Month

12 calendar months

Region

10 IPCC climate reference regions

AccPrec

Accumulated precipitation

DailyEva

Daily evaporation

Temp

Mean temperature

SoilMois

Soil moisture

SPI6

6-month standardised precipitation index

wind

Windspeed

Source

DOI: 10.24381/cds.adbb2d47 (Accessed on 11-02-2025)

Climate studies target example dataset

Description

Data extracted from ERA5 hourly data on single levels for 1989

Format

A dataset with 120 observations and 9 variables.

Details

Year

8 years from 1950 to 2020

Month

12 calendar months

Region

10 IPCC climate reference regions

AccPrec

Accumulated precipitation

DailyEva

Daily evaporation

Temp

Mean temperature

SoilMois

Soil moisture

SPI6

6-month standardised precipitation index

wind

Windspeed

Source

DOI: 10.24381/cds.adbb2d47 (Accessed on 11-02-2025)

Provide axes coordinates

Description

Provide axes coordinates

Usage

axes_moveEZ(bp, which.var)

Arguments

bp

Object
which.var

which variable(s) to find coordinates

Value

Axes coordinates

Measures of comparison for move plot 3

Description

This function calculates measures of comparison after generalised orthogonal Procrustes Analysis is performed in moveplot3. Orthogonal Procrustes Analysis is used to compare a target to a testee configuration. The following measures are calculate: Procrustes Statistic (PS), Congruence Coefficient (CC), Absolute Mean Bias (AMB), Mean Bias (MB) and Root Mean Squared Bias (RMSB).

Usage

evaluation(bp, centring = TRUE)

Arguments

bp

biplot object from moveEZ
centring

logical argument to apply centring or not (default is TRUE)

Value

eval.tab

Returns a table of the measures of comparison for each level of the time variable compared to the target.
fit.plot

Returns a line plot with the fit measures that are bounded between zero and one: PS and CC. A small PS value and large CC value indicate good fit.
bias.plot

Returns a line plot with bias measures that are unbounded: AMB, MB and RMSB. Small values indicate low bias.

Examples

data(Africa_climate)
data(Africa_climate_target)
bp <- biplotEZ::biplot(Africa_climate, scaled = TRUE) |> biplotEZ::PCA()
results <- bp |> moveplot3(time.var = "Year", group.var = "Region", hulls = TRUE,
move = FALSE, target = NULL) |> evaluation()
results$eval.tab
results$fit.plot
results$bias.plot

data(Africa_climate)
data(Africa_climate_target)
bp <- biplotEZ::biplot(Africa_climate, scaled = TRUE) |> biplotEZ::PCA()
results <- bp |> moveplot3(time.var = "Year", group.var = "Region", hulls = TRUE,
move = FALSE, target = Africa_climate_target) |> evaluation()
results$eval.tab
results$fit.plot
results$bias.plot

Move plot

Description

Create animated biplot on samples in a biplot

Create animated biplot on samples in a biplot

Usage

moveplot(
  bp,
  time.var,
  group.var,
  move = TRUE,
  hulls = TRUE,
  scale.var = 5,
  shadow = FALSE
)

moveplot(
  bp,
  time.var,
  group.var,
  move = TRUE,
  hulls = TRUE,
  scale.var = 5,
  shadow = FALSE
)

Arguments

bp

biplot object from biplotEZ
time.var

time variable
group.var

group variable
move

whether to animate (TRUE) or facet (FALSE) samples, according to time.var
hulls

whether to display sample points or convex hulls
scale.var

scaling the vectors representing the variables
shadow

whether the animation will keep past states (only when hulls = FALSE)

Value

bp

Returns the elements of the biplot object bp from biplotEZ.
plot

An animated or a facet of biplots based on the dynamic frame.
bp

Returns the elements of the biplot object bp from biplotEZ.
plot

An animated or a facet of biplots based on the dynamic frame.

Examples

data(Africa_climate)
bp <- biplot(Africa_climate, scaled = TRUE) |> PCA()

# Convex hulls facet plot
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = TRUE, move = FALSE)

# Samples facet plot
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = FALSE, move = FALSE)

# Specifying colours with colour palette in biplotEZ
bp <- biplot(Africa_climate, scaled = TRUE, group.aes = Africa_climate$Region) |>
PCA() |> samples(col = RColorBrewer::brewer.pal(10, "Paired"))
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = TRUE, move = FALSE)

# Specifying plotting characters for grouping variable in biplotEZ
bp <- biplot(Africa_climate, scaled = TRUE, group.aes = Africa_climate$Region) |>
PCA() |> samples(pch = c(19, 21, 3))
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = FALSE, move = FALSE)

# Specifying opacity of plotting characters and size of variable lables
bp <- biplot(Africa_climate, scaled = TRUE, group.aes = Africa_climate$Region) |>
PCA() |> samples(opacity = 0.4) |> axes(label.cex = 1.2)
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = FALSE, move = FALSE)

# Specifying colours manually in biplotEZ
bp <- biplot(Africa_climate, scaled = TRUE, group.aes = Africa_climate$Region) |>
PCA() |> samples(col = c("firebrick4", "indianred3", "tomato", "sandybrown",
 "khaki1", "palegreen1", "darkseagreen2", "mediumaquamarine", "deepskyblue4", "mediumpurple4"))
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = TRUE, move = FALSE)

# Convex hulls move plot

if(interactive()) {
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = TRUE, move = TRUE)}

# Samples move plot with shadows

if(interactive()) {
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = FALSE, move = TRUE, shadow = TRUE)}
data(Africa_climate)
bp <- biplot(Africa_climate, scaled = TRUE) |> PCA()

# Convex hulls facet plot
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = TRUE, move = FALSE)

# Samples facet plot
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = FALSE, move = FALSE)

# Specifying colours with colour palette in biplotEZ
bp <- biplot(Africa_climate, scaled = TRUE, group.aes = Africa_climate$Region) |>
PCA() |> samples(col = RColorBrewer::brewer.pal(10, "Paired"))
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = TRUE, move = FALSE)

# Specifying plotting characters for grouping variable in biplotEZ
bp <- biplot(Africa_climate, scaled = TRUE, group.aes = Africa_climate$Region) |>
PCA() |> samples(pch = c(19, 21, 3))
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = FALSE, move = FALSE)

# Specifying opacity of plotting characters and size of variable lables
bp <- biplot(Africa_climate, scaled = TRUE, group.aes = Africa_climate$Region) |>
PCA() |> samples(opacity = 0.4) |> axes(label.cex = 1.2)
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = FALSE, move = FALSE)

# Specifying colours manually in biplotEZ
bp <- biplot(Africa_climate, scaled = TRUE, group.aes = Africa_climate$Region) |>
PCA() |> samples(col = c("firebrick4", "indianred3", "tomato", "sandybrown",
 "khaki1", "palegreen1", "darkseagreen2", "mediumaquamarine", "deepskyblue4", "mediumpurple4"))
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = TRUE, move = FALSE)

# Extracting measures of fit of PCA
bp <- biplot(Africa_climate, scaled = TRUE) |> PCA() |> fit.measures()
bp <- bp |> moveplot(time.var = "Year", group.var = "Region", hulls = TRUE, move = FALSE)
bp$quality
bp$axis.predictivity

# Convex hulls move plot

if(interactive()) {
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = TRUE, move = TRUE)}

# Samples move plot with shadows

if(interactive()) {
bp |> moveplot(time.var = "Year", group.var = "Region", hulls = FALSE, move = TRUE, shadow = TRUE)}

# CVA biplot
bp <- biplot(Africa_climate, scaled = TRUE) |> CVA(class = Africa_climate$Region)
bp |> moveplot2(group.var = "Region", time.var = "Year", move = FALSE)

# Extracting measures of fit of CVA
bp <- biplot(Africa_climate, scaled = TRUE) |> CVA(classes = Africa_climate$Region) |> fit.measures()
bp <- bp |> moveplot(time.var = "Year", group.var = "Region", hulls = TRUE, move = FALSE)
bp$quality
bp$axis.predictivity
bp$within.class.axis.predictivity
bp$within.class.sample.predictivity

Move plot 2

Description

Create animated biplot on samples and variables in a biplot

Create animated biplot on samples and variables in a biplot

Usage

moveplot2(
  bp,
  time.var,
  group.var,
  move = TRUE,
  hulls = TRUE,
  scale.var = 5,
  align.time = NA,
  reflect = NA
)

moveplot2(
  bp,
  time.var,
  group.var,
  move = TRUE,
  hulls = TRUE,
  scale.var = 5,
  align.time = NA,
  reflect = NA
)

Arguments

bp

biplot object from biplotEZ
time.var

time variable
group.var

group variable
move

whether to animate (TRUE) or facet (FALSE) samples and variables, according to time.var
hulls

whether to display sample points or convex hulls
scale.var

scaling the vectors representing the variables
align.time

a vector specifying the levels of time.var for which the biplots should be aligned. Only biplots corresponding to these time points will be used to compute the alignment transformation.
reflect

a character vector specifying the axis of reflection to apply at each corresponding time point in align.time. One of FALSE (default), "x" for reflection about the x-axis, "y" for reflection about the y-axis and "xy" for reflection about both axes.

Value

bp

Returns the elements of the biplot object bp from biplotEZ.
plot

An animated or a facet of biplots based on the dynamic frame.
bp

Returns the elements of the biplot object bp from biplotEZ.
plot

An animated or a facet of biplots based on the dynamic frame.

Examples

data(Africa_climate)
bp <- biplot(Africa_climate, scaled = TRUE) |> PCA()

if(interactive()) {
bp |> moveplot2(time.var = "Year", group.var = "Region", hulls = TRUE, move = TRUE)}
data(Africa_climate)
bp <- biplot(Africa_climate, scaled = TRUE) |> PCA()

if(interactive()) {
bp <- bp |> moveplot2(time.var = "Year", group.var = "Region", hulls = TRUE, move = TRUE)}

# Extracting measures of fit for PCA
bp <- bp |> moveplot2(time.var = "Year", group.var = "Region", hulls = TRUE, move = FALSE)
bp$quality
bp$axis.predictivity

# Extracting measures of fit for CVA
bp <- biplot(Africa_climate) |> CVA(classes = Africa_climate$Region)
bp <- bp |> moveplot2(time.var = "Year", group.var = "Region", hulls = TRUE, move = FALSE)
bp$quality
bp$axis.predictivity
bp$within.class.axis.predictivity
bp$within.class.sample.predictivity

Move plot 3

Description

Create animated biplot on samples and variables in a biplot with a given target

Create animated biplot on samples and variables in a biplot with a given target

Usage

moveplot3(
  bp,
  time.var,
  group.var,
  move = TRUE,
  hulls = TRUE,
  scale.var = 5,
  target = NULL
)

moveplot3(
  bp,
  time.var,
  group.var,
  move = TRUE,
  hulls = TRUE,
  scale.var = 5,
  target = NULL
)

Arguments

bp

biplot object from biplotEZ
time.var

time variable
group.var

group variable
move

whether to animate (TRUE) or facet (FALSE) samples and variables, according to time.var
hulls

whether to display sample points or convex hulls
scale.var

scaling the vectors representing the variables
target

Target data set to which all biplots should be matched consisting of the the same dimensions. If not specified, the centroid of all available biplot sample coordinates from time.var will be used. Default NULL.

Value

bp

Returns the elements of the biplot object bp from biplotEZ.
iter_levels

The levels of the time variable.
coord_set

The coordinates of the configurations before applying Generalised Orthogonal Procrustes Analysis.
GPA_list

The coordinates of the configurations after applying Generalised Orthogonal Procrustes Analysis.
plot

An animated or a facet of biplots based on the dynamic frame.
bp

Returns the elements of the biplot object bp from biplotEZ.
iter_levels

The levels of the time variable.
coord_set

The coordinates of the configurations before applying Generalised Orthogonal Procrustes Analysis.
GPA_list

The coordinates of the configurations after applying Generalised Orthogonal Procrustes Analysis.
plot

An animated or a facet of biplots based on the dynamic frame.

Examples

data(Africa_climate)
data(Africa_climate_target)
bp <- biplot(Africa_climate, scaled = TRUE) |> PCA()
bp |> moveplot3(time.var = "Year", group.var = "Region", hulls = TRUE,
move = FALSE, target = NULL)

if(interactive()) {
bp |> moveplot3(time.var = "Year", group.var = "Region", hulls = TRUE,
move = TRUE, target = NULL)}
bp |> moveplot3(time.var = "Year", group.var = "Region", hulls = TRUE,
move = FALSE, target = Africa_climate_target)
data(Africa_climate)
data(Africa_climate_target)
bp <- biplot(Africa_climate, scaled = TRUE) |> PCA()
bp |> moveplot3(time.var = "Year", group.var = "Region", hulls = TRUE,
move = FALSE, target = NULL)

if(interactive()) {
bp |> moveplot3(time.var = "Year", group.var = "Region", hulls = TRUE,
move = TRUE, target = NULL)}
bp |> moveplot3(time.var = "Year", group.var = "Region", hulls = TRUE,
move = FALSE, target = Africa_climate_target)