Shape Analysis of Outlines

Documentation for package ‘Momocs’ version 0.2-6

DESCRIPTION file.

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A B C D E H I L M N P R S T V misc

Momocs-package

Outline Analysis using R.

-- A --

A.mshape	Calculates the mean shape of an array of landmarks.
A.plot	Plots an array of homologous coordinates, typically landmarks.
A.points	Plots the points that corresponds to landmarks provided as an array.
A.segments	Utilities to manipulate arrays of homologous coordinates, typically landmarks.
a2l	Converts an array of coordinates to a list.

-- B --

baseline	Re-register a 'Coo' on a new baseline.
baseline-method	Re-register a 'Coo' on a new baseline.
baseline-methods	Re-register a 'Coo' on a new baseline.
bot	bot dataset
boxplot-method	Class '"Coe"'

-- C --

chc2Coo	Imports '.chc' files from SHAPE to 'Coo' objects that can be used in Momocs.
chc2pix	Converts chain-coded coordinates to a matrix of coordinates.
clust	Hierarchical clustering on a matrix of coefficients
clust-method	Hierarchical clustering on a matrix of coefficients
clust-methods	Hierarchical clustering on a matrix of coefficients
Coe	Class '"Coe"'
Coe-class	Class '"Coe"'
Coe2nef	Exports 'Coe' objects to '.nef' files.
coeff.sel	Helps to select a given number of harmonics from a numerical vector.
coeff.split	Converts a numerical description of harmonic coefficients to a named list.
col.bcol	Some color palettes.
col.blackgallus	Some color palettes.
col.bw	Some color palettes.
col.gallus	Some color palettes.
col.india	Some color palettes.
col.sari	Some color palettes.
col.summer	Some color palettes.
col.wcol	Some color palettes.
Coo	Class '"Coo"'
Coo-class	Class '"Coo"'
Coo.align	Class '"Coo"'
coo.align	Aligns a list or matrix of coordinates.
Coo.align-method	Class '"Coo"'
Coo.align-methods	Class '"Coo"'
coo.baseline	Re-register a list or matrix of coordinates.
Coo.center	Class '"Coo"'
coo.center	Centers a list or matrix of coordinates.
Coo.center-method	Class '"Coo"'
Coo.center-methods	Class '"Coo"'
coo.centpos	Calculates the position of the centroid of a list or a matrix of coordinates.
coo.centsize	Calculates the centroid size of a list or matrix of coordinates.
Coo.close	Class '"Coo"'
coo.close	Closes a list or matrix of coordinates.
Coo.close-method	Class '"Coo"'
Coo.close-methods	Class '"Coo"'
coo.draw	Adds a single outline on the current plot.
coo.ef.amplify	Dilates shapes based on elliptical Fourier decomposition.
coo.force2close	Forces a list or matrix or coordinates to close.
coo.ldk	Utility to identify landmarks on a matrix or list of coordinates.
coo.list.panel	Plots sets of shapes.
coo.oscillo	Momocs' "oscilloscope" for periodic functions.
coo.oscillo1	Momocs' "oscilloscope" for periodic functions.
coo.perim	Calculates the perimeter of a list or matrix of coordinates.
coo.perim.pts	Calculates the euclidean distance between points of a list or matrix of coordinates.
coo.plot	Plots a single outline.
coo.rotate	Rotates a list or matrix of coordinates.
coo.rotate.center	Rotates a list or matrix of coordinates with any center of symmetry.
Coo.sample	Class '"Coo"'
coo.sample	Samples points along the curvilinear abscissa.
Coo.sample-method	Class '"Coo"'
Coo.sample-methods	Class '"Coo"'
coo.sample.int	Given an outline, interpolates points along the curvilinear abscissa.
coo.sample.rr	Samples points with "equally spaced" angles.
coo.scale	Scales a list or matrix of coordinates.
Coo.slide	Class '"Coo"'
coo.slide	"Slides" a list or a matrix of coordinates.
Coo.slide-method	Class '"Coo"'
Coo.slide-methods	Class '"Coo"'
Coo.smooth	Class '"Coo"'
coo.smooth	Smoothes list and matrices of coordinates.
Coo.smooth-method	Class '"Coo"'
Coo.smooth-methods	Class '"Coo"'
Coo.template	Class '"Coo"'
coo.template	"Templates" list and matrix of coordinates.
Coo.template-method	Class '"Coo"'
Coo.template-methods	Class '"Coo"'
coo.trans	Transles a list or a matrix of coordinates.
Coo.unclose	Class '"Coo"'
coo.unclose	Uncloses a list or matrix of coordinates.
Coo.unclose-method	Class '"Coo"'
Coo.unclose-methods	Class '"Coo"'
Coo2chc	Exports 'Coo' objects to '.chc' files that can be used in SHAPE.
cooLandmarks	Retrieves landmarks coordinates from a 'Coo' object.
cooLandmarks-method	Retrieves landmarks coordinates from a 'Coo' object.
cooLandmarks-methods	Retrieves landmarks coordinates from a 'Coo' object.

-- D --

defLandmarks	Define landmarks on a 'Coo' object
defLandmarks-method	Define landmarks on a 'Coo' object
defLandmarks-methods	Define landmarks on a 'Coo' object
dev.plot	Calculates and plots series with associated error bars.
dev.segments	Draws colored segments from a matrix of coordinates.
diapo	Plots a slideshow of each outline in a 'Coo' object.
diapo-method	Plots a slideshow of each outline in a 'Coo' object.
diapo-methods	Plots a slideshow of each outline in a 'Coo' object.
dudi.plot	A wrapper for 'dudi.pca' graphical functions.

-- E --

ed	Calculates euclidean distance between two points.
edi	Calculates euclidean intermediate between two points.
edm	Calculates euclidean distance every pairs of points in two matrices.
edm.nearest	Calculates the shortest euclidean distance found for every point of one matrix among those of a second.
ef.amplify	Dilates shapes based on elliptical Fourier decomposition.
eFourier	Calculates elliptical Fourier analysis on 'Coo' objects.
efourier	Calculates elliptical Fourier analysis.
eFourier-method	Calculates elliptical Fourier analysis on 'Coo' objects.
eFourier-methods	Calculates elliptical Fourier analysis on 'Coo' objects.
efourier.i	Calculates inverse elliptical Fourier analysis.
efourier.norm	Normalizes harmonic coefficients.
efourier.shape	Calculates and draw "efourier" shapes.
ellipse.par	Calculate ellipse parameters on a 'Coe'-class object.
ellipse.par-method	Calculate ellipse parameters on a 'Coe'-class object.
ellipse.par-methods	Calculate ellipse parameters on a 'Coe'-class object.
ellpar	Calculate ellipse parameters.

-- H --

harm.pow	Calculates harmonic power given a list from e/t/rfourier
hcontrib	Calculates and displays the contribution of every harmonic.
hcontrib-method	Calculates and displays the contribution of every harmonic.
hcontrib-methods	Calculates and displays the contribution of every harmonic.
hearts	hearts dataset
hist-method	Class '"Coe"'
hpow	Calculates harmonic power.
hpow-method	Calculates harmonic power.
hpow-methods	Calculates harmonic power.
hqual	Displays how shapes are described with a given number of harmonics.
hqual-method	Displays how shapes are described with a given number of harmonics.
hqual-methods	Displays how shapes are described with a given number of harmonics.
hquant	Calculates deviations between reconstructed and best possible shapes using different distance methods.
hquant-method	Calculates deviations between reconstructed and best possible shapes using different distance methods.
hquant-methods	Calculates deviations between reconstructed and best possible shapes using different distance methods.

-- I --

import.img.Conte	Everything to convert images to a list of coordinates.
import.img.prepare	Everything to convert images to a list of coordinates.
import.jpg	Everything to convert images to a list of coordinates.
import.multi1.jpg	Everything to convert images to a list of coordinates.
import.txt	Everything to convert '.txt' files to a list of coordinates.
is.closed	Tests if a list or matrix of coordinates is closed.

-- L --

l2a	Converts a list of coordinates to an array.
l2m	Converts a list of coordinates to a matrix.

-- M --

m2l	Convert a matrix of coordinates to a list of coordinates.
manova.Coe	Multivariate ANOVA on 'Coe' objects
manova.Coe-method	Multivariate ANOVA on 'Coe' objects
manova.Coe-methods	Multivariate ANOVA on 'Coe' objects
meanShapes	Calculate groups mean shapes from 'Coe'
meanShapes-method	Calculate groups mean shapes from 'Coe'
meanShapes-methods	Calculate groups mean shapes from 'Coe'
Momocs	Outline Analysis using R.
morpho.space	Calculate and plots morphological spaces.
mosquito	mosquito dataset

-- N --

nef2Coe

Imports '.nef' files and creates 'Coe' objects.

-- P --

panel	Displays a one-page plot of a 'Coo'-object.
panel-method	Displays a one-page plot of a 'Coo'-object.
panel-methods	Displays a one-page plot of a 'Coo'-object.
PC.contrib	Shape variation along PC axis
pca	A wrapper for 'dudi.pca' on 'Coe'-objects.
pca-method	A wrapper for 'dudi.pca' on 'Coe'-objects.
pca-methods	A wrapper for 'dudi.pca' on 'Coe'-objects.
pca2shp	From a factorial map to a shape.
pix2chc	Converts lists and matrices of coordinates into '.chc' (chain-coded) files.
plot-method	Plots all the outlines from a 'Coo' on the same graph.
procGPAlign	Performs a Generalized Procrustes Alignement on a 'Coo' object.
procGPAlign-method	Performs a Generalized Procrustes Alignement on a 'Coo' object.
procGPAlign-methods	Performs a Generalized Procrustes Alignement on a 'Coo' object.
Ptolemy	Ptolemaic ellipses and illustration of eFourier
Ptolemy-method	Ptolemaic ellipses and illustration of eFourier
Ptolemy-methods	Ptolemaic ellipses and illustration of eFourier

-- R --

rFourier	Calculates radii variation analysis on 'Coo' objects.
rfourier	Calculates radii variation Fourier analysis.
rFourier-method	Calculates radii variation analysis on 'Coo' objects.
rFourier-methods	Calculates radii variation analysis on 'Coo' objects.
rfourier.i	Calculates inverse radii variation analysis.
rfourier.shape	Calculates and draw "rfourier" shapes.

-- S --

sample	Class '"Coo"'
sample-methods	Class '"Coo"'
show-method	Class '"Coe"'
show-method	Class '"Coo"'
smooth.qual	Displays effect of smoothing on shape reconstruction.
smooth.qual-method	Displays effect of smoothing on shape reconstruction.
smooth.qual-methods	Displays effect of smoothing on shape reconstruction.
stack	Plots all the outlines from a 'Coo' on the same graph.
stack-method	Plots all the outlines from a 'Coo' on the same graph.
stack-methods	Plots all the outlines from a 'Coo' on the same graph.

-- T --

tFourier	Calculates tangent angle analysis on 'Coo' objects.
tfourier	Calculates tangent angle Fourier analysis.
tFourier-method	Calculates tangent angle analysis on 'Coo' objects.
tFourier-methods	Calculates tangent angle analysis on 'Coo' objects.
tfourier.i	Calculates inverse tangent angle Fourier analysis.
tfourier.shape	Calculates and draw "tfourier" shapes.
tps.arr	Deformation "vector field" using Thin Plate Splines.
tps.grid	Deformation grids using Thin Plate Splines.
tps.iso	Deformation isolines using Thin Plate Splines.
tps2d	Thin Plate Splines for 2D data.
trilo	trilo dataset

-- V --

vecs.param

Some vector utilities.

-- misc --

[-method	Class '"Coo"'
[<--method	Class '"Coo"'