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Momocs (version 0.2-03)

Shape Analysis of Outlines

Description

Momocs is intended to ease and popularize shape analysis of outlines (especially using elliptical Fourier analysis). It mostly hinges on the functions developed in Morphometrics with R (Claude, 2008). From outline extraction of images and elliptical Fourier calculation to multivariate analysis and the visualization of transformations within the morphological space, Momocs provides a complete and convenient toolkit to specialists within every field that are, or may be, interested in morphological comparisons of outlines.

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Version

Install

install.packages('Momocs')

Monthly Downloads

653

Version

0.2-03

License

GPL (>= 2)

Maintainer

Vincent Bonhomme

Last Published

February 26th, 2013

Functions in Momocs (0.2-03)

Plots an array of homologous coordinates, typically landmarks.

Calculates the perimeter of a list or matrix of coordinates.

Dilates shapes based on elliptical Fourier decomposition.

Ptolemaic ellipses and illustration of eFourier

Adds a single outline on the current plot.

Samples points with "equally spaced" angles.

Calculates the euclidean distance between points of a list or matrix of coordinates.

Exports Coe objects to .nef files.

dataset: hearts

"Slides" a list or a matrix of coordinates.

Transles a list or a matrix of coordinates.

cooLandmarks(Coo)

Retrieves landmarks coordinates from a Coo object.

Converts chain-coded coordinates to a matrix of coordinates.

Centers a list or matrix of coordinates.

Re-register a list or matrix of coordinates.

Calculates euclidean distance every pairs of points in two matrices.

Convert a matrix of coordinates to a list of coordinates.

Calculates deviations between reconstructed and best possible shapes using different distance methods.

Momocs' "oscilloscope" for periodic functions.

Everything to convert .txt files to a list of coordinates.

Calculates the position of the centroid of a list or a matrix of coordinates.

Rotates a list or matrix of coordinates.

Imports .nef files and creates Coe objects.

Converts a numerical description of harmonic coefficients to a named list.

Calculate groups mean shapes from Coe

Converts an array of coordinates to a list.

Shape variation along PC axis

Normalizes harmonic coefficients.

coo.rotate.center

Rotates a list or matrix of coordinates with any center of symmetry.

Plots a slideshow of each outline in a Coo object.

Samples points along the curvilinear abscissa.

Calculates the centroid size of a list or matrix of coordinates.

Calculates harmonic power.

Aligns a list or matrix of coordinates.

A wrapper for dudi.pca on Coe-objects.

Tests if a list or matrix of coordinates is closed.

Converts a list of coordinates to an array.

Calculates the shortest euclidean distance found for every point of one matrix among those of a second.

Helps to select a given number of harmonics from a numerical vector.

Calculate ellipse parameters on a Coe-class object.

Utility to identify landmarks on a matrix or list of coordinates.

Plots the points that corresponds to landmarks provided as an array.

Calculates the mean shape of an array of landmarks.

Calculates elliptical Fourier analysis.

coo.force2close

Forces a list or matrix or coordinates to close.

Closes a list or matrix of coordinates.

Smoothes list and matrices of coordinates.

Calculates inverse elliptical Fourier analysis.

Calculate ellipse parameters.

Everything to convert images to a list of coordinates.

Uncloses a list or matrix of coordinates.

Calculates and plots series with associated error bars.

Exports Coo objects to .chc files that can be used in SHAPE.

Calculate and plots morphological spaces.

Calculates euclidean intermediate between two points.

Displays a one-page plot of a Coo-object.

Utilities to manipulate arrays of homologous coordinates, typically landmarks.

Calculates tangent angle analysis on Coo objects.

Calculates and draw "efourier" shapes.

Define landmarks on a Coo object

Re-register a Coo on a new baseline.

Calculates and draw "tfourier" shapes.

Displays effect of smoothing on shape reconstruction.

A wrapper for dudi.pca graphical functions.

Calculates radii variation Fourier analysis.

procGPAlign(Coo)

Performs a Generalized Procrustes Alignement on a Coo object.

Calculates and draw "rfourier" shapes.

Calculates inverse tangent angle Fourier analysis.

Plots all the outlines from a Coo on the same graph.

Thin Plate Splines for 2D data.

"Templates" list and matrix of coordinates.

Calculates harmonic power given a list from e/t/rfourier

Draws colored segments from a matrix of coordinates.

Plots sets of shapes.

Displays how shapes are described with a given number of harmonics.

Multivariate ANOVA on Coe objects

Deformation "vector field" using Thin Plate Splines.

Some vector utilities.

Converts lists and matrices of coordinates into .chc (chain-coded) files.

Some color palettes.

Given an outline, interpolates points along the curvilinear abscissa.

Outline Analysis using R.

Scales a list or matrix of coordinates.

Imports .chc files from SHAPE to Coo objects that can be used in Momocs.

dataset: mosquito

mosquito dataset

Converts a list of coordinates to a matrix.

Calculates and displays the contribution of every harmonic.

Deformation isolines using Thin Plate Splines.

From a factorial map to a shape.

Calculates euclidean distance between two points.

Calculates inverse radii variation analysis.

Deformation grids using Thin Plate Splines.

Plots a single outline.