Move plot 3 — moveplot3 • moveEZ

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
)

Arguments

bp: biplot object from biplotEZ
time.var: name of the time variable, given as a character string. Must be a factor column of the data supplied to biplot(); the order of its levels gives the order of the time slices and levels without observations are dropped. A numeric (e.g. integer year) or character column stops with an error, see Details.
group.var: name of the group variable, given as a character string. Must be a factor column of the data supplied to biplot().
move: whether to animate (TRUE) or facet (FALSE) samples and variables, according to time.var
hulls: whether to display sample points or convex hulls. A hull requires at least three non-collinear observations per group per level of time.var; groups with fewer are displayed as points instead.
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.

Details

time.var and group.var must both be factors. biplot() treats every numeric column as a variable of the biplot, so a time variable stored as a number (e.g. an integer year) has to be converted with factor() before biplot() is called, not afterwards.

Missing values are handled by biplot(), which removes every row containing an NA in any column (including time.var and group.var) with a warning. The plot is constructed from the remaining rows. Since moveplot3() requires the same number of observations at every level of time.var, removed rows will usually cause it to stop; impute the missing values, or remove the affected samples at every time level, beforehand. The same applies to target, which may not contain missing values.

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)

#> Object of class biplot, based on 960 samples and 9 variables.
#> 6 numeric variables.
#> 3 categorical variables.
# \donttest{
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)

#> Object of class biplot, based on 960 samples and 9 variables.
#> 6 numeric variables.
#> 3 categorical variables.