MSHAPES: Mean shape calculation for Coo, Coe, etc.

In Momocs: Morphometrics using R

Mean shape calculation for Coo, Coe, etc.

Description

Quite a versatile function that calculates mean (or median, or whatever function) on list or an array of shapes, an Ldk object. It can also be used on Coe objects. In that case, the reverse transformation (from coefficients to shapes) is calculated, (within groups defined with the fac argument if provided) and the Coe object is also returned (in ⁠$Coe⁠) along with a list of shapes (in ⁠$shp⁠) and can then be passed to plot_MSHAPES.

Usage

MSHAPES(x, fac = NULL, FUN = mean, nb.pts = 120, ...)

Arguments

x	a list, array, Ldk, LdkCoe, OutCoe or OpnCoe or PCA object
fac	factor specification for fac_dispatcher
FUN	a function to compute the mean shape (mean by default, by median can be considered)
nb.pts	numeric the number of points for calculated shapes (only Coe objects)
...	useless here.

Value

the averaged shape; on Coe objects, a list with two components: $Coe object of the same class, and $shp a list of matrices of (x, y) coordinates. On PCA and LDA objects, the FUN (typically mean or median) of scores on PCs or LDs. This method used on the latter objects may be moved to another function at some point.

See Also

Other multivariate: CLUST(), KMEANS(), KMEDOIDS(), LDA(), MANOVA_PW(), MANOVA(), MDS(), NMDS(), PCA(), classification_metrics()

Examples

#### on shapes
MSHAPES(wings)
MSHAPES(wings$coo)
MSHAPES(coo_sample(bot, 24)$coo)
stack(wings)
coo_draw(MSHAPES(wings))

bot.f <- efourier(bot, 12)
MSHAPES(bot.f) # the mean (global) shape
ms <- MSHAPES(bot.f, 'type')
ms$Coe
class(ms$Coe)
ms <- ms$shp
coo_plot(ms$beer)
coo_draw(ms$whisky, border='forestgreen')

Momocs documentation built on Nov. 13, 2023, 5:07 p.m.