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Momocs (version 0.1-01)

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 developped 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

538

Version

0.1-01

License

GPL (>= 2)

Maintainer

Vincent Bonhomme

Last Published

May 2nd, 2012

Functions in Momocs (0.1-01)

get.Nef

Calculates Elliptical Fourier Analysis.
show-methods

show methods for Momocs' objects
tps2d

Returns the position of interpolated coordinates.
Momocs-package

Outline Analysis using Elliptical Fourier Analysis.
Nef-class

Class "Nef".
bottles dataset

Two "bottles" datasets of outlines and harmonic coefficients.
draw.Fell

Draws "Fourier Ellipses".
panel.lm

Calculates and plots confidence ellipses.
Coo-class

Class "Coo".
harm.pow

Calculates and plots Fourier harmonic spectra.
tps

Produces deformation grids.
get.cont

Extract $(x; y)$ coordinates and create a Coo-object.
dev.quant

Calculates and plots sum of euclidean deviations between original and reconstructed outlines.
efourier

Computes the Fourier coefficients on a list of coordinates.
cont.sample

Samples points along a list of $(x; y)$ coordinates.
eFa

Elliptical Fourier Analysis on Coo objects.
col.sel

Helps to select the columns indices of an harmonic coefficient matrix.
closed.outline

Closes outlines.
manova.nef

Calculates MANOVA on a harmonic coefficient matrix.
pca

Calculates and plots Principal Component Analysis.
morph.sp

Plots the morphological space.
tps.grid

Thin Plate Splines deformation grids between two shapes.
iefourier

Calculates inverse Fourier Elliptical.
traj

Calculates shape intermediates.
plot

Plots coordinate outlines.
morph.PC

Plots the morphological space along PC axis.
pca2shp

Reconstructs a shape given using PCA.
cont.smooth

Smoothes a list or a matrix of $(x; y)$ coordinates.
dev.qual

Calculates and plots reconstructed outlines.
Outline: efourier

Elliptical Fourier Analysis core functions.
Outline: tps

Thin Plin Splines
Outline: tfourier

Fourier Tangent angle core functions.
Outline: Ptolemy

Methods for Function Ptolemy
Multivariate Analysis: manova.nef

Multivariate ANOVA on Nef objects
Outline: ellipse.par

Calculate ellipse parameters on a Nef-class object.
Multivariate Analysis: pca

A wrapper for dudi.pca on Nef-objects.
Outline: rfourier

Fourier Radius variation core functions.
Import: .txt

Everything to convert .txt files to a list of coordinates.
Utilities: coo.plot

Plots sets of shapes.
Class: Nef

Class "Nef"
Utilities: pca2shp

From a factorial map to a shape.
Dataset: bot

Bottles dataset
Class: Coo

Class "Coo"
Utilities: coo.oscillo

Momocs' "oscilloscope" for periodic functions.
Abstract: Momocs

Outline Analysis using R.
Utilities: ellpar

Calculate ellipse parameters.
Calibration: smooth.qual

Displays effect of smoothing on shape reconstruction.
Multivariate Analysis: dudi.plot

A wrapper for dudi.pca graphical functions.
Utilities: dev.plot

Calculates and plots series with associated error bars.
Import: .jpg

Everything to convert images to a list of coordinates.
Utilities: coeff.sel

Selection of harmonic coefficients.
Outline: ef.amplify

Dilation of shape based on elliptical Fourier decomposition.
Utilities: edm

Pairwaise euclidean distance between two matrices/lists of coordinates.
Calibration: harm.quant

Calculate harmonic effect.
Utilities: coo-family

Utilities to manipulate list and matrices of coordinates.
Dataset: hearts

Hearts dataset
Utilities: color palettes

Some color palettes.