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Momocs (version 0.2-6)

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

0.2-6

License

GPL (>= 2)

Maintainer

Vincent Bonhomme

Last Published

March 7th, 2014

Functions in Momocs (0.2-6)

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

Outline Analysis using R.

Plots a slideshow of each outline in a Coo object.

Some color palettes.

Multivariate ANOVA on Coe objects

Utilities to manipulate arrays of homologous coordinates, typically landmarks.

cooLandmarks(Coo)

Retrieves landmarks coordinates from a Coo object.

Calculates inverse elliptical Fourier analysis.

Rotates a list or matrix of coordinates.

Calculates euclidean distance every pairs of points in two matrices.

"Templates" list and matrix of coordinates.

From a factorial map to a shape.

Calculates euclidean distance between two points.

Plots sets of shapes.

Converts chain-coded coordinates to a matrix of coordinates.

Transles a list or a matrix of coordinates.

Calculates radii variation Fourier analysis.

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

"Slides" a list or a matrix of coordinates.

Calculates the mean shape of an array of landmarks.

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

coo.rotate.center

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

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

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

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

Imports .nef files and creates Coe objects.

Exports Coe objects to .nef files.

Define landmarks on a Coo object

Draws colored segments from a matrix of coordinates.

Adds a single outline on the current plot.

Re-register a Coo on a new baseline.

dataset: hearts

Displays effect of smoothing on shape reconstruction.

dataset: mosquito

mosquito dataset

Thin Plate Splines for 2D data.

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

Aligns a list or matrix of coordinates.

Re-register a list or matrix of coordinates.

Converts a list of coordinates to an array.

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

Deformation grids using Thin Plate Splines.

Smoothes list and matrices of coordinates.

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

Given an outline, interpolates points along the curvilinear abscissa.

Converts an array of coordinates to a list.

Converts a list of coordinates to a matrix.

Closes a list or matrix of coordinates.

Centers a list or matrix of coordinates.

Tests if a list or matrix of coordinates is closed.

Deformation "vector field" using Thin Plate Splines.

Convert a matrix of coordinates to a list of coordinates.

Samples points along the curvilinear abscissa.

Calculates the perimeter of a list or matrix of coordinates.

coo.force2close

Forces a list or matrix or coordinates to close.

Calculates and displays the contribution of every harmonic.

Momocs' "oscilloscope" for periodic functions.

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

A wrapper for dudi.pca graphical functions.

Shape variation along PC axis

Calculate and plots morphological spaces.

Normalizes harmonic coefficients.

Calculates elliptical Fourier analysis on Coo objects.

Plots an array of homologous coordinates, typically landmarks.

Ptolemaic ellipses and illustration of eFourier

Calculates inverse radii variation analysis.

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

Calculate ellipse parameters on a Coe-class object.

Calculate groups mean shapes from Coe

Calculates euclidean intermediate between two points.

A wrapper for dudi.pca on Coe-objects.

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

Deformation isolines using Thin Plate Splines.

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

Calculates tangent angle Fourier analysis.

Calculates and draw "rfourier" shapes.

Calculate ellipse parameters.

procGPAlign(Coo)

Performs a Generalized Procrustes Alignement on a Coo object.

Plots a single outline.

Uncloses a list or matrix of coordinates.

Calculates harmonic power.

Scales a list or matrix of coordinates.

Calculates and draw "tfourier" shapes.

Calculates inverse tangent angle Fourier analysis.

Hierarchical clustering on a matrix of coefficients

Dilates shapes based on elliptical Fourier decomposition.

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

Everything to convert images to a list of coordinates.

Calculates and draw "efourier" shapes.

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

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

Some vector utilities.

Samples points with "equally spaced" angles.

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

Calculates and plots series with associated error bars.