find.outliers: Graphical interface to find outliers and/or to switch...

In Morpho: Calculations and Visualisations Related to Geometric Morphometrics

Graphical interface to find outliers and/or to switch mislabeld landmarks

Description

Graphical interface to find outliers and/or to switch mislabeld landmarks

Usage

find.outliers(
  A,
  color = 4,
  lwd = 1,
  lcol = 2,
  mahalanobis = FALSE,
  PCuse = NULL,
  text = TRUE,
  reflection = FALSE
)

Arguments

A	Input k x m x n real array, where k is the number of points, m is the number of dimensions, and n is the sample size.
color	color of Landmarks points to be plotted
lwd	linewidth visualizing distances of the individual landmarks from mean.
lcol	color of lines visualizing distances of the individual landmarks from mean.
mahalanobis	logical: use mahalanobis distance to find outliers.
PCuse	integer: Restrict mahalanobis distance to the first n Principal components.
text	logical: if TRUE, landmark labels (rownumbers) are displayed
reflection	logical: specify whether reflections are allowed for superimpositioning.

Details

This function performs a procrustes fit and sorts all specimen according to their distances (either Procrustes or Mahalanobis-distance) to the sample's consensus. It provides visual help for rearranging landmarks and/or excluding outliers.

Value

data.cleaned	array (in original coordinate system) containing the changes applied and outliers eliminated
outlier	vector with integers indicating the positions in the original array that have been marked as outliers
dist.sort	table showing the distance to mean for each observation - decreasing by distance
type	what kind of distance was used

Author(s)

Stefan Schlager

See Also

typprob,typprobClass

Examples

data(boneData)
## look for outliers using the mahalanobis distance based on the first
# 10 PCscores
# to perform the example below, you need,of course, uncomment the answers
if (interactive()){
outliers <- find.outliers(boneLM, mahalanobis= TRUE, PCuse=10)
# n # everything is fine 
# n # proceed to next
# s # let's switch some landmarks (3 and 4)
# 3
# 4
# n # we are done
# y # yes, because now it is an outlier
# s #enough for now
}

Morpho documentation built on Feb. 16, 2023, 10:51 p.m.