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Momocs (version 1.2.9)

Morphometrics using R

Description

The goal of Momocs is to provide a complete, convenient, reproducible and open-source toolkit for 2D morphometrics. It includes most common 2D morphometrics approaches on outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout. It allows reproducible, complex morphometric analyses 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

653

Version

1.2.9

License

GPL-2 | GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/MomX/Momocs/

Maintainer

Vincent Bonhomme

Last Published

March 22nd, 2018

Functions in Momocs (1.2.9)

Hierarchical clustering

KMEANS on PCA objects

Coo "super" class

Multivariate analysis of (co)variance on Coe objects

Coe "super" class

Browse Momocs online doc

Builds an Ldk object

Linear Discriminant Analysis on Coe objects

Traditional morphometrics class

Shape variation along PC axes

Pairwise Multivariate analyses of variance

Adds new landmarks on Out and Opn objects

Install last version of Momocs

Converts Momocs objects to data.frames

Ptolemaic ellipses and illustration of efourier

Builds an Opn object

Retain groups with at least n shapes

Convert (x; y) coordinates to chaincoded coordinates

Boxplot on PCA objects

Builds an OutCoe object

Calculates Bezier coefficients from a shape

Jitters Coe (and others) objects

Principal component analysis on Coe objects

Builds an OpnCoe object

calibrate_harmonicpower

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

calibrate_reconstructions

Calibrate using reconstructed shapes

Builds an Out object

And now, what to do?

Quantitative r2 calibration for Opn objects

Split to several objects based on a factor

Calculates a shape from Bezier coefficients

Arrange rows by variables

Boxplot of morphometric coefficients

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

Convert between different classes

calibrate_deviations

Quantitative calibration, through deviations, for Out and Opn objects

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

coo_angle_edge1

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

classification_metrics

Calculate classification metrics on a confusion matrix

Aligns coordinates

coeff_rearrange

Rearrange a matrix of (typically Fourier) coefficients

Transparency helpers and palettes

coo_alignminradius

Aligns shapes using their shortest radius

coo_aligncalliper

Aligns shapes along their 'calliper length'

Some color palettes

Aligns shapes along the x-axis

coo_angle_edges

Calculates the angle of every edge of a shape

Combine several objects

Register new baselines

coo_angle_tangent

Calculates the tangent angle along the perimeter of a shape

Calculate centroid coordinates

Register Bookstein's coordinates

Plots (lollipop) differences between two configurations

Convert complex to/from cartesian coordinates

Calculates the area of a shape

Calculates the calliper length

coo_boundingbox

Calculates coordinates of the bounding box

Returns the distance between everypoints and the centroid

Closes/uncloses shapes

Calculates the (recursive) convex hull of a shape

Centers coordinates

Draw radii to the current plot

coo_circularity

Calculates the Haralick's circularity of a shape

Calculates centroid size

coo_down Retains coordinates with negative y-coordinates

Calculate abscissa and ordinate on a shape

Calculates the elongation of a shape

coo_eccentricity

Calculates the eccentricity of a shape

Adds a shape to the current plot

Calculates the convexity of a shape

coo_intersect_angle

Nearest intersection between a shape and a segment specified with an angle

coo_intersect_segment

Nearest intersection between a shape and a segment

Test if shapes are closed

coo_force2close

Forces shapes to close

Extract coordinates from a shape

coo_interpolate

Interpolates coordinates

Momocs' 'oscilloscope' for Fourier-based approaches

Calculates length and width of a shape

coo_likely_clockwise

Tests if shapes are (likely) developping clockwise or anticlockwise

Counts coordinates

coo_rotatecenter

Rotates shapes with a custom center

Calculates the length of a shape

Plots sets of shapes.

Calculates perimeter and variations

Plots differences as (colored) segments aka a ruban

Defines landmarks interactively

Calculate coordinates range

Plots (lollipop) differences between two configurations

Retains coordinates with negative x-coordinates

coo_rectangularity

Calculates the rectangularity of a shape

Sample coordinates (among points)

Retains coordinates with positive x-coordinates

Rotates coordinates

coo_rectilinearity

Calculates the rectilinearity of a shape

Reverses coordinates

Plots a single shape

coo_slidedirection

Slides coordinates in a particular direction

Slides coordinates

Slices shapes between successive coordinates

Smoothes coordinates

Slides coordinates using the widest gap

Samples coordinates (regular radius)

coo_smoothcurve

Smoothes coordinates on curves

Scales coordinates

Calculates the width of a shape

coo_sample_prop

Sample a proportion of coordinates (among points)

A wrapper to calculates euclidean distances between two points

Truss measurement

Retains coordinates with positive y-coordinates

Translates coordinates

Data: Landmark and semilandmark coordinates on cereal glumes

Trims both ends coordinates from shape

Data: Outline coordinates from an experimental charring on cereal grains

Trims bottom coordinates from shape

Data: Outline coordinates of 360 molars

Trims top coordinates from shape

'Templates' shapes

Data: Outline coordinates of various shapes

Data: Outline coordinates of mosquito wings.

Data: Outline coordinates of cephalic outlines of trilobite

Calculates the solidity of a shape

Data: Configuration of landmarks of oak leaves

Data: Outline coordinates of olive seeds open outlines.

Data: Outline coordinates of hand-drawn hearts

grindr drawers for shape plots

Defines links between landmarks

Calculates euclidean distance between two points.

Data: Outline coordinates of mouse molars

Data: Landmarks coordinates of mosquito wings

Defines sliding landmarks matrix

Data: Outline coordinates of North Sea fishes

Defines new landmarks on Out and Opn objects

Brew and serve fac from Momocs object

Data: Measurement of iris flowers

Add new landmarks based on angular positions

Full Generalized Procrustes alignment between shapes

Data: Outline coordinates of Apodemus (wood mouse) mandibles

Discrete cosinus transform

Define tips as new landmarks

Data: Outline coordinates of beer and whisky bottles.

Investe discrete cosinus transform

Calculates euclidean intermediate between two points.

Calculates and draws 'dfourier' shapes

Inverse elliptical Fourier transform

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

Calculates euclidean distance every pairs of points in two matrices.

Calculates and draw 'efourier' shapes.

Dissolve Coe objects

Extracts sliding landmarks coordinates

Exports Coe objects and shapes

Elliptical Fourier transform (and its normalization)

Harmonic contribution to shape

Full Procrustes alignment between two shapes

Full Generalized Procrustes alignment between shapes with sliding landmarks

Calculates convex hull area/volume of PCA scores

Retrieves landmarks coordinates

grindr layers for multivariate plots

Subset based on conditions

Extract outline coordinates from a single .jpg file

Get paired individual on a Coe, PCA or LDA objects

Draws kernel density contours around landmark

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

import_StereoMorph_curve1

Import files creates by StereoMorph into Momocs

Import a tps file

Extract outline coordinates from multiple .jpg files

Add landmarks labels

Histogram of morphometric coefficients

Plots a .jpg image

Import coordinates from a .txt file

Checks 'ldk' shapes

Draws convex hulls around landmark positions

Extract outlines coordinates from an image silhouette

Graphical inspection of shapes

Measures shape descriptors

Draws confidence ellipses for landmark positions

Draws links between landmarks

morphospace_positions

Calculates nice positions on a plane for drawing shapes

Class and component testers

Graphical pile of shapes

bind_db.Coe <- bind_db.Coo Extracts structure from filenames

Plots mosaics of shapes.

is_equallyspacedradii

Tests if coordinates likely have equally spaced radii

Plots Linear Discriminant Analysis

Add new variables

Mean shape calculation for Coo, Coe, etc.

Creates links (all pairwise combinations) between landmarks

plot_devsegments

Draws colored segments from a matrix of coordinates.

Calculate natural polynomial fits on open outlines

Pairwise comparison of a list of shapes

Remove shapes with incomplete slices

Creates links (Delaunay triangulation) between landmarks

Plots Principal Component Analysis

grindr papers for shape plots

Renames levels on Momocs objects

Plots a cross-validation table as an heatmap

Family picture of shapes

Rescale coordinates from pixels to real length units

Permutes and breed Coe (and others) objects

Inverse radii variation Fourier transform

Radii variation Fourier transform (equally spaced radii)

Calculates and draw 'rfourier' shapes.

"Redo" a LDA on new data

slidings_scheme

Extracts partitions of sliding coordinates

Calculate orthogonal polynomial fits on open outlines

Sample a fraction of shapes

Sample n shapes

"Redo" a PCA on a new Coe

Family picture of shapes

Partial Procrustes alignment between two shapes

Binds .jpg outlines from .txt landmarks taken on them

Inverse tangent angle Fourier transform

Plots a cross-correlation table

Thin Plate Splines for 2D data

Plots confusion matrix of sample sizes within $fac

Multivariate plots using grindr layers

Calculates and draws 'tfourier' shapes.

Validates Coo objects

Calculates shape from a polynomial model

Rearrange, (select and reorder) landmarks to retain

Deformation 'vector field' using Thin Plate Splines

Identify outliers

Removes asymmetric and symmetric variation on OutCoe objects

Objects exported from other packages

Deformation grids using Thin Plate Splines

Removes harmonics from Coe objects

Calculates and draw 'sfourier' shapes.

Radii variation Fourier transform (equally spaced curvilinear abscissa)

Subset based on positions

Inverse radii variation Fourier transform

Methods for PCA eigen values

Calcuates symmetry indices on OutCoe objects

Select and rename columns by name

Tangent angle Fourier transform

Deformation isolines using Thin Plate Splines.

Vanilla Thin Plate Splines