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Morpho (version 2.0.2)

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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Install

install.packages('Morpho')

Monthly Downloads

1,790

Version

2.0.2

License

GPL-2

Issues

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Repository

https://github.com/zarquon42b/Morpho

Homepage

http://sourceforge.net/projects/morpho-rpackage/

Maintainer

Stefan Schlager

Last Published

February 24th, 2014

Functions in Morpho (2.0.2)

Assess differences in amount and direction of asymmetric variation

extract data from array names

predictShape.lm

Predict shapes based on linear models calculated from PCscores

convert a colored mesh to greyscale.

Create Matrices necessary for Thin-Plate Spline

rotate matrix of landmarks

deprecated functions of Morpho

merge multiple triangular meshes into a single one

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

read.csv.folder

batch import data from files

calculate the pooled within groups covariance matrix

Replace ID-strings of data and associated files.

calculates the barycenters for all faces of a triangular mesh

Project coordinates onto a target triangular surface mesh.

calculate mean of an array

Q-Q plot to assess normality of data

plot lines between landmarks

calculates distances and PC-coordinates of covariance matrices

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

fast calculation of a Matrix' per row/ per column mean - useful for very large matrices

landmarks and a triangular mesh representing a human nose

Canonical Variate Analysis

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

calculate Centroid Size for a landmark configuration

Import 3D surface mesh files

find nearest neighbours for point clouds

Create an atlas needed in placePatch

calulate regression scores for linear model

visualise differences between two superimposed sets of 3D landmarks

calculate angle between two vectors

Two-Block partial least square regression.

concatenate multiple arrays/matrices

visualize an atlas defined by createAtlas

plot histogram for multiple groups.

calculate variance of a distribution stemming from prediction models

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

convert PCs to landmark configuration

correlation between a reduced space and the original space

relax one specific 3D landmark configuration against a reference

estimate missing landmarks

Perform PCA based of the group means' covariance matrix

Project points onto the closest point on a mesh

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

Procrustes ANOVA for structures with object symmetry

estimate missing landmarks from their bilateral counterparts

readLandmarks.csv

import landmark data from csv files

Import landmarks and outlines from TPS files

exports a matrix containing landmarks into .pts format

Landmarks and a triangular mesh

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

performs permutation testing for group differences.

calculate typicality probabilities

Calculates the Riemannian distance between two superimposed landmark configs.

Procrustes registration

convert an 3D array into a matrix and back

reads pts files

warping a mesh onto another configuration

Workhorse function for procSym, responsible for Procrustes registration

Read saved pick-points from meshlab

Compute face or vertex normals of a triangular mesh

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

calculate the corners of a mesh's bouning box

projects the vertices of a mesh along its normals onto the surface of another one.

plots the normals of a triangular surface mesh.

scale a mesh of class "mesh3d"

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

some little helpers for vertex operations on triangular meshes

export mesh objects to disk

calculate weights inverse to the distances from the specified observation.

plot or save the results of meshDist

calculate relative Warp analysis

thin plate spline mapping

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

calculate common allometric component

visualization of shape variation

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

Rotate an object (matrix or mesh) around an arbitrary axis in 3D

calculate the orthogonal complement of a 3D-vector

predefined colors for bone and skin

correlation between shape space and tangent space

calculate average edge length of a triangular mesh

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

Export data to MorphoJ and Morphologika

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

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

invert faces' orientation of triangular mesh