Morpho (version 2.1)

NNshapeReg: Estimate the shape by averaging the shape of the nearest neighbours.

Description

Estimate the shape of one set of landmarks by averaging the shape of the nearest neighbours obtained by a second set of landmarks. Weights are calculated either form Mahalanobis or Procrustes distances. This can be useful for data with missing landmarks.

Usage

NNshapeReg(x, y = NULL, n = 3, mahalanobis = FALSE,
  mc.cores = parallel::detectCores())

Arguments

x

an array or matrix (one row per specim) with data used for estimating weights.

y

an array or matrix (one row per specim) with landmark data on which the weighted averaging is applied for prediction. If NULL, x will be used for both tasks.

n

amount of nearest neighbours to consider

mahalanobis

logical: use mahalanobis distance

mc.cores

integer: amount of cores used for parallel processing.

Value

• matrix or array of estimates.

Details

This function calculates weights from one set of shape data and then estimates the shape of another (or same) set of landmarks. CAUTION: landmark data has to be registered beforehand.

See Also

proc.weight, fixLMtps

Examples

library(shapes)
proc <- procSym(gorf.dat)
#use the closest 3 specimen based on the first 4 landmarks
#to estimate the shape
estim <- NNshapeReg(proc$rotated[1:4,,],proc$rotated,n=3,mc.cores=1)
#compare estimation and true config
plot(proc$rotated[,,1],asp=1)
points(estim[,,1],col=2)