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Morpho (version 2.1)

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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Install

install.packages('Morpho')

Monthly Downloads

1,495

Version

2.1

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

September 25th, 2014

Functions in Morpho (2.1)

computeTransform

calculate an affine transformation matrix

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

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

Create Matrices necessary for Thin-Plate Spline

extract data from array names

concatenate multiple arrays/matrices

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

Calculates the Riemannian distance between two superimposed landmark configs.

correlation between shape space and tangent space

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

Q-Q plot to assess normality of data

calculate mean of an array

estimate missing landmarks

visualise differences between two superimposed sets of 3D landmarks

merge multiple triangular meshes into a single one

match two landmark configurations using iteratively closest point search

find indices of faces that contain specified vertices

calculate the pooled within groups covariance matrix

Perform PCA based of the group means' covariance matrix

invert faces' orientation of triangular mesh

read.csv.folder

batch import data from files

calculate variance of a distribution stemming from prediction models

export mesh objects to disk

getTrafoRotaxis

compute a 4x4 Transformation matrix for rotation around an arbitrary axis

Project coordinates onto a target triangular surface mesh.

meshPlaneIntersect

get intersections between mesh and a plane

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

estimate missing landmarks from their bilateral counterparts

Workhorse function for procSym, responsible for Procrustes registration

Landmarks and a triangular mesh

Procrustes registration

calculate Centroid Size for a landmark configuration

get 4x4 Transformation matrix

correlation between a reduced space and the original space

align two pointclouds/meshes by their principal axes

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

readLandmarks.csv

import landmark data from csv files

predefined colors for bone and skin

deprecated functions of Morpho

calculate the corners of a mesh's bouning box

retroDeformMesh

symmetrize a triangular mesh

classify specimen based on between-group PCA or CVA

meshDist.matrix

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

find nearest neighbours for point clouds

Assess differences in amount and direction of asymmetric variation

calculate the orthogonal complement of a 3D-vector

reads pts files

calculate average edge length of a triangular mesh

calculate typicality probabilities

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

Project points onto the closest point on a mesh

visualization of shape variation

plot histogram for multiple groups.

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

apply affine transformation to data

converts a mesh containing quadrangular faces into one only consisting of triangles

Two-Block partial least square regression.

calculates distances and PC-coordinates of covariance matrices

convert PCs to landmark configuration

Canonical Variate Analysis

calculate angle between two vectors

calculate weights inverse to the distances from the specified observation.

symmetrize a bilateral landmark configuration

Read saved pick-points from meshlab

convert a colored mesh to greyscale.

Procrustes ANOVA for structures with object symmetry

warping a mesh onto another configuration

Export data to MorphoJ and Morphologika

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

landmarks and a triangular mesh representing a human nose

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

calculate relative Warp analysis

render.matrixDist

plot or save the results of meshDist

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

exports a matrix containing landmarks into .pts format

rotate matrix of landmarks

Compute face or vertex normals of a triangular mesh

predictShape.lm

Predict shapes based on linear models calculated from PCscores

convert an 3D array into a matrix and back

scale a mesh of class "mesh3d"

returns the solution space (basis and translation vector) for an equation system

Replace ID-strings of data and associated files.

cut a mesh by a hyperplane and remove parts above/below that plane

Create an atlas needed in placePatch

Import 3D surface mesh files

calculates the barycenters for all faces of a triangular mesh

plots the normals of a triangular surface mesh.

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

relax one specific landmark configuration against a reference

plot lines between landmarks

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

some little helpers for vertex operations on triangular meshes

mirror landmarks or triangular mesh in place

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

calulate regression scores for linear model

performs permutation testing for group differences.

Import landmarks and outlines from TPS files

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

thin plate spline mapping

calculate common allometric component

separate a 3D-pointcloud by a hyperplane

visualize an atlas defined by createAtlas