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Momocs (version 1.1.6)

Morphometrics using R

Description

A complete toolkit for morphometrics, from data extraction to multivariate analyses. Most common 2D morphometrics approaches are included: outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout. Momocs allows reproducible, complex morphometric analyses, paves the way for a pure open-source workflow in R, and other morphometrics approaches should be easy to plug in, or develop from, on top of this canvas.

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Version

Install

install.packages('Momocs')

Monthly Downloads

616

Version

1.1.6

License

GPL-2 | GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/vbonhomme/Momocs/

Maintainer

Vincent Bonhomme

Last Published

April 17th, 2017

Functions in Momocs (1.1.6)

Coo "super" class

KMEANS on PCA objects

Boxplot on PCA objects

Jitters Coe (and others) objects

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

Some color palettes

Calculate abscissa and ordinate on a shape

coo_eccentricityboundingbox

Calculates the eccentricity (bounding box) of a shape

Plots differences as (colored) segments aka a ruban

Retains coordinates with positive y-coordinates

Calculates the width of a shape

Data: Landmarks coordinates of mosquito wings

coo_rotatecenter

Rotates shapes with a custom center

Defines new landmarks on Out and Opn objects

Calculates and draws 'dfourier' shapes

Dissolves Coe objects

Exports Coe objects and shapes

Full Procrustes alignment between two shapes

Histogram of morphometric coefficients

Plots a .jpg image

Tests if shapes are closed

is_equallyspacedradii

Tests if coordinates likely have equally spaced radii

Converts a matrix of coordinates to a data.frame

Converts a matrix of coordinates to a list of coordinates.

Plots Principal Component Analysis ala ggplot2

#' @describeIn plot.PCA

Objects exported from other packages

Renames (ala dplyr) on Momocs objects

Removes asymmetric and symmetric variation on OutCoe objects

Removes harmonics from Coe objects

Calcuates symmetry indices on OutCoe objects

Cross-tabulates objects

Transmutes (ala dplyr) on Momocs objects

Truss measurement

Momocs_lastversion

Install and load the last version of Momocs

Get Momocs version

Converts an array of coordinates to a matrix

Adds new landmarks on Out and Opn objects

Confidence ellipses

Aligns coordinates

Plots (lollipop) differences between two configurations

Register new baselines

Closes/uncloses shapes

Calculates the convexity of a shape

coo_eccentricityeigen

Calculates the eccentricity (using eigenvalues) of a shape

Calculates the elongation of a shape

Calculates length and width of a shape

Counts coordinates

Calculates the cumulative chordal distance along a shape.

Calculates the chordal distance along a shape.

Slides coordinates

coo_slidedirection

Slides coordinates in a particular direction

Calculates the tangent angle along the perimeter of a shape

'Templates' shapes

Data: Outline coordinates of various shapes

Data: Outline coordinates of cephalic outlines of trilobite

Calculates euclidean distance between two points.

Calculates euclidean intermediate between two points.

Filters (ala dplyr) on Momocs objects

Get paired individual on a Coe, PCA or LDA objects

Extracts sliding landmarks coordinates

Add landmarks labels

Draws links between landmarks

Hierarchical clustering

Coe "super" class

Plots confusion matrix of sample sizes within $fac

Builds an Opn object

Converts Momocs objects to data.frames

Retains group with at least a certain number of individuals

calibrate_deviations

Quantitative calibration, through deviations, for Out and Opn objects

calibrate_harmonicpower

Quantitative calibration, through harmonic power, for Out and Opn objects

coeff_rearrange

Rearrange a matrix of (typically Fourier) coefficients

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

Aligns shapes along the x-axis

Calculates the area of a shape

Partial Procrustes alignment between two shapes

Family picture of shapes

Plots a cross-validation table as an heatmap

coo_circularityharalick

Calculates the Haralick's circularity of a shape

coo_circularitynorm

Calculates the 'normalized' circularity of a shape

Defines landmarks interactively

Plots a cross-correlation table

Rescale coordinates from pixels to real length units

Radii variation Fourier transform (equally spaced radii)

Methods for PCA eigen values

Slides coordinates using the widest gap

Smoothes coordinates

Trims bottom coordinates from shape

Selects (ala dplyr) on Momocs objects

Family picture of shapes (ggplot2)

Subsets on Momocs objects

Deformation 'vector field' using Thin Plate Splines

Deformation grids using Thin Plate Splines

Trims top coordinates from shape

Data: Outline coordinates of hand-drawn hearts

Data: Outline coordinates of 360 molars

Data: Configuration of landmarks of oak leaves

Data: Outline coordinates of olive seeds open outlines.

Elliptical Fourier transform

Inverse elliptical Fourier transform

Normalizes harmonic coefficients.

Calculates and draw 'efourier' shapes.

Checks 'ldk' shapes

Draws convex hulls around landmark positions

Draws confidence ellipses for landmark positions

Draws kernel density contours around landmark

Linear Discriminant Analysis on Coe objects

Builds an Ldk object

Shape variation along PC axes

Ptolemaic ellipses and illustration of efourier

Arranges (ala dplyr) on Momocs objects

Convert an OutCoe object into an Out object

Imports .nts to Coo objects

Calculate orthogonal polynomial fits on open outlines

plot_devsegments

Draws colored segments from a matrix of coordinates.

Pairwise comparison of a list of shapes

Samples a fraction of shapes in Momocs objects

Samples n shapes on Momocs objects

Deformation isolines using Thin Plate Splines.

Quantitative r2 calibration for Opn objects

calibrate_reconstructions

Calibrate using reconstructed shapes

Transparency helpers and palettes

Vanilla Thin Plate Splines

Combines Momocs objects

coo_aligncalliper

Aligns shapes along their 'calliper length'

coo_alignminradius

Aligns shapes using their shortest radius

Centers coordinates

Calculate centroid coordinates

coo_down -----------------

Adds a shape to the current plot

Retains coordinates with negative x-coordinates

Calculates the length of a shape

coo_rectilinearity

Calculates the rectilinearity of a shape

Reverses coordinates

Slices shapes between successive coordinates

coo_smoothcurve

Smoothes coordinates on curves

Calculates the solidity of a shape

Data: Outline coordinates of beer and whisky bottles.

Data: Landmark and semilandmark coordinates on cereal glumes

Data: Outline coordinates of mosquito wings.

Data: Outline coordinates of mouse molars

Discrete cosinus transform

Investe discrete cosinus transform

Calculates convex hull area/volume of PCA scores

Retrieves landmarks coordinates

Extracts outlines coordinates from an image silhouette

import_StereoMorph_curve1

Imports files creates by StereoMorph into Momocs

Imports a tps file

Imports coordinates from a .txt file

Extracts structure from filenames

Creates links (all pariwise combinations) between landmarks

Converts a matrix of coordinates into a list of matrices

Measures shape descriptors

Family picture of shapes (ggplot2)

Permutes and breed Coe (and others) objects

Calculates shape from a polynomial model

Calculates nice positions on a plane for drawing shapes

Calculates and draw 'sfourier' shapes.

Slices (ala dplyr) on Momocs objects

Calculates and draws 'tfourier' shapes.

Binds .jpg outlines from .txt landmarks taken on them

Identify outliers

Browse Momocs online doc

Builds an OpnCoe object

Builds an Out object

Traditional morphometrics class

Converts an array of coordinates to a list of matrices

Binds with a database

Boxplot of morphometric coefficients

Chops (rough slicing) Momocs objects

Classify using LDA

Register Bookstein's coordinates

coo_boundingbox

Calculates coordinates of the bounding box

Calculates the convex hull of a shape

coo_circularity

Calculates the circularity of a shape

Extract coordinates from a shape

Plots sets of shapes.

Plots (lollipop) differences between two configurations

Plots a single shape

coo_rectangularity

Calculates the rectangularity of a shape

Scales coordinates

Shrinks coordinates in one direction

Translates coordinates

Trims both ends coordinates from shape

A wrapper to calculates euclidean distances between two points

Data: Outline coordinates of Apodemus (wood mouse) mandibles

Defines links between landmarks

Defines sliding landmarks matrix

Extracts outline coordinates from multiple .jpg files

Extracts outline coordinates from a single .jpg file

Converts a list of coordinates to an array of coordinates

Converts a list of coordinates to a matrix of coordinates.

Creates links (Delaunay triangulation) between landmarks

Converts a matrix of coordinates to an array of coordinates

Imports .nef to Coe objects

Calculate natural polynomial fits on open outlines

Converts (x; y) coordinates to chaincoded coordinates

Graphical inspection of shapes

"Redo" a LDA on new data

"Redo" a PCA on a new Coe

Removes shapes with incomplete slices

Renames levels on Momocs objects

Radii variation Fourier transform (equally spaced curvilinear abscissa)

Inverse radii variation Fourier transform

Reads a single tps-like shape as lines

Thin Plate Splines for 2D data

Multivariate analysis of (co)variance on Coe objects

Pairwise Multivariate analyses of variance

Builds an OutCoe object

Principal component analysis on Coe objects

Calculates Bezier coefficients from a shape

Calculates a shape from Bezier coefficients

Converts chain-coded coordinates to Out object

Converts chain-coded coordinates to (x; y) coordinates

Calculates the calliper length

Returns the distance between everypoints and the centroid

Calculates centroid size

coo_force2close

Forces shapes to close

coo_interpolate

Interpolates coordinates

Momocs' 'oscilloscope' for Fourier-based approaches

Calculates the perimeter

Retains coordinates with positive x-coordinates

Rotates coordinates

Sample coordinates (among points)

Samples coordinates (regular radius)

Calculate the angle formed by three (x; y) coordinates

Calculates the angle of every edge of a shape

Data: Outline coordinates from an experimental charring on cereal grains

Data: Measurement of iris flowers

Calculates euclidean distance every pairs of points in two matrices.

Calculates the shortest euclidean distance found for every point of one

Full Generalized Procrustes alignment between shapes

Full Generalized Procrustes alignment between shapes with sliding landmarks

Harmonic contribution to shape

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

Various class/component testers

Tests if shapes are developping clockwise or anticlockwise

Mean shape calculation for Coo, Coe, etc.

Mutates (ala dplyr) on Momocs objects

Plots Linear Discriminant Analysis

Plots Principal Component Analysis

Inverse radii variation Fourier transform

Calculates and draw 'rfourier' shapes.

slidings_scheme

Extracts partitions of sliding coordinates

Family picture of shapes

Tangent angle Fourier transform

Inverse tangent angle Fourier transform

Validates Coo objects

Some vector utilities.