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Morpho (version 1.0-1)

Calculations and visualisations related to Geometric Morphometrics

Description

A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.

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Version

Install

install.packages('Morpho')

Monthly Downloads

1,495

Version

1.0-1

License

GPL-2

Maintainer

Stefan Schlager

Last Published

November 4th, 2013

Functions in Morpho (1.0-1)

invert faces' orientation of triangular mesh

Workhorse function for procSym, responsible for Procrustes registration

visualise differences between two superimposed sets of 3D landmarks

Visually browse through a sample rendering its landmarks and corresponding surfaces.

plots the normals of a triangular surface mesh.

calculates the barycenters for all faces of a triangular mesh

estimate missing landmarks

correlation between a reduced space and the original space

concatenate multiple arrays/matrices

calculate angle between two vectors

deprecated functions of Morpho

readLandmarks.csv

import landmark data from csv files

landmarks and a triangular mesh representing a human nose

Perform PCA based of the group means' covariance matrix

Procrustes registration

visualize an atlas defined by createAtlas

Create Matrices necessary for Thin-Plate Spline

Q-Q plot to assess normality of data

calculate variance of a distribution stemming from a prediction model

calculate relative Warp analysis

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

thin plate spline mapping

plot lines between landmarks

calculate the corners of a mesh's bouning box

visualization of shape change

warping a mesh onto another configuration

calculate weights inverse to the distances from the specified observation.

Read saved pick-points from meshlab

Import landmarks and outlines from TPS files

Calculates the Riemannian distance between two superimposed landmark configs.

calculate the orthogonal complement of a 3D-vector

convert PCs to landmark configuration

Landmarks and a triangular mesh

Compute face or vertex normals of a triangular mesh

Import 3D surface mesh files

Project coordinates onto a target triangular surface mesh.

convert an 3D array into a matrix

Project points onto the closest point on a mesh

rotates, translates and scales one matrix onto an other using Procrustes fitting

calculate the pooled within groups covariance matrix

calculates and visualises distances between surface meshes or 3D coordinates and a surface mesh.

Creates a sequence of images showing predefined steps of warping two meshes or landmark configurations (2D and 3D) into each other

Replace ID-strings of data and associated files.

plot histogram for multiple groups.

predefined colors for bone and skin

exports a matrix containing landmarks into .pts format

extract data from array names

extract information about fixed landmarks, curves and patches from and atlas generated by "landmark"

perfom permutation testing on angles and distances between subgroups of two major groups.

some little helpers for vertex operations on triangular meshes

Create an atlas needed in placePatch

calculate Centroid Size for a landmark configuration

predictShape.lm

Predict shapes based on linear models calculated from PCscores

find nearest neighbours for point clouds

projects the vertices of a mesh onto the surface of another one.

calculate average edge length of a triangular mesh

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

calculate distances and PC-coordinates of covariance matrices

convert a colored mesh to greyscale.

Canonical Variate Analysis

rotate ,scale and translate a mesh based on landmark information.

Procrustes ANOVA for structures with object symmetry

A toolbox providing methods for data-acquisitiopn, visualisation and statistical methods related to Geometric Morphometrics and shape analysis

Project semi-landmarks from a predefined atlas onto all specimen in a sample

reads pts files

calculate typicality probabilities

slides Semilandmarks along curves and surfaces in 3D by minimising bending energy of a thin-plate spline deformation.

correlation between shape space and tangent space

export mesh objects to disk.

Rotate an object around an arbitrary axis in 3D

render.meshDist

plot or save the results of meshDist

Two-Block partial least square regression.

performs permutation testing for group differences.

merge multiple triangular meshes into a single one

read.csv.folder

batch import data from files

calculate a rotation matrix around an arbitrary axis through the origin in 3D

Export data to MorphoJ and Morphologika

rotate matrix of landmarks

scale a mesh of class "mesh3d"

relax one specific 3D landmark configuration against a reference