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Momocs (version 1.3.2)

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 morphometrics 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

538

Version

1.3.2

License

GPL-2 | GPL-3

Issues

Pull Requests

Stars

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Repository

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

Maintainer

Vincent Bonhomme

Last Published

October 6th, 2020

Functions in Momocs (1.3.2)

Pairwise Multivariate analyses of variance

(Metric) multidimensional scaling

Ptolemaic ellipses and illustration of efourier

Builds an OpnCoe object

calibrate_deviations

Quantitative calibration, through deviations, for Out and Opn objects

calibrate_harmonicpower

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

Builds an Out object

Linear Discriminant Analysis on Coe objects

Builds an OutCoe object

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

Shape variation along PC axes

Boxplot on PCA objects

Centers coordinates

Calculates the calliper length

Principal component analysis on Coe objects

coo_likely_clockwise

Tests if shapes are (likely) developping clockwise or anticlockwise

Closes/uncloses shapes

Returns the distance between everypoints and the centroid

Convert (x; y) coordinates to chaincoded coordinates

Retain groups with at least n shapes

Defines landmarks interactively

coeff_rearrange

Rearrange a matrix of (typically Fourier) coefficients

Aligns coordinates

Convert complex to/from cartesian coordinates

Mean shape calculation for Coo, Coe, etc.

Hierarchical clustering

coo_aligncalliper

Aligns shapes along their 'calliper length'

Extract coordinates from a shape

Coe "super" class

Calculate centroid coordinates

Adds a shape to the current plot

Plots a single shape

Calculates Bezier coefficients from a shape

Calculates the convexity of a shape

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

Calculates a shape from Bezier coefficients

Builds an Ldk object

coo_sample_prop

Sample a proportion of coordinates (among points)

Some color palettes

coo_down Retains coordinates with negative y-coordinates

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

Retains coordinates with negative x-coordinates

coo_slidedirection

Slides coordinates in a particular direction

Boxplot of morphometric coefficients

coo_alignminradius

Aligns shapes using their shortest radius

Rotates coordinates

Data: Outline coordinates of cephalic outlines of trilobite

Quantitative r2 calibration for Opn objects

coo_boundingbox

Calculates coordinates of the bounding box

classification_metrics

Calculate classification metrics on a confusion matrix

Slides coordinates

Calculate coordinates range

grindr layers for multivariate plots

Register Bookstein's coordinates

Calculates perimeter and variations

calibrate_reconstructions

Calibrate using reconstructed shapes

Calculates the (recursive) convex hull of a shape

Coo "super" class

coo_eccentricity

Calculates the eccentricity of a shape

Calculates the elongation of a shape

Calculates the length of a shape

Plots a .jpg image

coo_angle_tangent

Calculates the tangent angle along the perimeter of a shape

Calculates centroid size

Calculates the area of a shape

Trims bottom coordinates from shape

Full Generalized Procrustes alignment between shapes with sliding landmarks

Test if shapes are closed

Truss measurement

Momocs' 'oscilloscope' for Fourier-based approaches

Smoothes coordinates

coo_circularity

Calculates the Haralick's circularity of a shape

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

Plots sets of shapes.

Data: Measurement of iris flowers

Plots differences as (colored) segments aka a ruban

grindr drawers for shape plots

coo_rotatecenter

Rotates shapes with a custom center

Data: Outline coordinates of beer and whisky bottles.

Samples coordinates (regular radius)

Sample coordinates (among points)

Exports Coe objects and shapes

Plots (lollipop) differences between two configurations

Get paired individual on a Coe, PCA or LDA objects

Turn Momocs objects into tydy data_frames

Extract outline coordinates from multiple .jpg files

Reverses coordinates

Trims top coordinates from shape

Define tips as new landmarks

Split to several objects based on a factor

Multivariate analysis of (co)variance on Coe objects

Traditional morphometrics class

coo_rectangularity

Calculates the rectangularity of a shape

coo_interpolate

Interpolates coordinates

Extract outline coordinates from a single .jpg file

coo_rectilinearity

Calculates the rectilinearity of a shape

Slides coordinates using the widest gap

coo_angle_edges

Calculates the angle of every edge of a shape

Plots (lollipop) differences between two configurations

Adds new landmarks on Out and Opn objects

coo_smoothcurve

Smoothes coordinates on curves

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

Aligns shapes along the x-axis

Retains coordinates with positive y-coordinates

Inverse radii variation Fourier transform

Data: Outline coordinates of North Sea fishes

Retains coordinates with positive x-coordinates

Builds an Opn object

Jitters Coe (and others) objects

Data: Outline coordinates from an experimental charring on cereal grains

Calculates the width of a shape

Data: Landmarks coordinates of mosquito wings

Inverse elliptical Fourier transform

Data: Landmark and semilandmark coordinates on cereal glumes

Elliptical Fourier transform (and its normalization)

Defines links between landmarks

Removes rotation so that the centroid and a given point are parallel to the x-axis

Extracts sliding landmarks coordinates

Scales coordinates

Draws kernel density contours around landmark

Calculates euclidean distance every pairs of points in two matrices.

Register new baselines

Calculates length and width of a shape

Counts coordinates

Calculates all scalar descriptors of shape

Objects exported from other packages

Translates coordinates

Dissolve Coe objects

Inverse radii variation Fourier transform

KMEANS on PCA objects

Data: Outline coordinates of mouse molars

Calculates the solidity of a shape

Data: Outline coordinates of mosquito wings.

Rename columns by name

A wrapper to calculates euclidean distances between two points

Data: Outline coordinates of Apodemus (wood mouse) mandibles

Removes harmonics from Coe objects

Arrange rows by variables

Non metric multidimensional scaling

Trims both ends coordinates from shape

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

Calculates and draws 'dfourier' shapes

Data: Outline coordinates of 360 molars

Data: Outline coordinates of olive seeds open outlines.

Data: Configuration of landmarks of oak leaves

Import coordinates from a .txt file

Binds .jpg outlines from .txt landmarks taken on them

Calculate natural polynomial fits on open outlines

Full Generalized Procrustes alignment between shapes

Data: Outline coordinates of hand-drawn hearts

Creates links (Delaunay triangulation) between landmarks

Investe discrete cosinus transform

Data: Outline coordinates of various shapes

Combine several objects

Calculates and draw 'rfourier' shapes.

Radii variation Fourier transform (equally spaced curvilinear abscissa)

Convert between different classes

Transparency helpers and palettes

Calculate abscissa and ordinate on a shape

Defines new landmarks on Out and Opn objects

Calculates and draw 'efourier' shapes.

Measures shape descriptors

Calculates the total absolute curvature of a shape

Calculates euclidean distance between two points.

grindr papers for shape plots

Calculates euclidean intermediate between two points.

Extract outlines coordinates from an image silhouette

import_StereoMorph_curve1

Import files creates by StereoMorph into Momocs

Permutes and breed Coe (and others) objects

Subset based on conditions

Draw radii to the current plot

Graphical inspection of shapes

coo_force2close

Forces shapes to close

Family picture of shapes

'Templates' shapes

Brew and serve fac from Momocs object

layers_morphospace

Morphospace layers

Add new variables

Checks 'ldk' shapes

Slices shapes between successive coordinates

Class and component testers

Harmonic contribution to shape

Draws confidence ellipses for landmark positions

Inverse tangent angle Fourier transform

Creates links (all pairwise combinations) between landmarks

plot_silhouette

Silhouette plot

Plots Principal Component Analysis

Thin Plate Splines for 2D data

Family picture of shapes

Draws convex hulls around landmark positions

Plots Linear Discriminant Analysis

Plots confusion matrix of sample sizes within $fac

morphospace_positions

Calculates nice positions on a plane for drawing shapes

Subset based on positions

Remove shapes with missing data in fac

Plots a cross-validation table as an heatmap

slidings_scheme

Extracts partitions of sliding coordinates

Remove shapes with incomplete slices

is_equallyspacedradii

Tests if coordinates likely have equally spaced radii

NMDS plot unsing grindr layers

Pairwise comparison of a list of shapes

Calcuates symmetry indices on OutCoe objects

Calculate orthogonal polynomial fits on open outlines

"Redo" a PCA on a new Coe

PCA plot using grindr layers

Partial Procrustes alignment between two shapes

plot_devsegments

Draws colored segments from a matrix of coordinates.

Rearrange, (select and reorder) landmarks to retain

Radii variation Fourier transform (equally spaced radii)

Graphical pile of shapes

Plots a cross-correlation table

Rescale coordinates from pixels to real length units

Full Procrustes alignment between two shapes

How many axes to retain this much of variance or trace ?

Sample n shapes

LDA plot using grindr layers

Deformation isolines using Thin Plate Splines.

Calculates and draw 'sfourier' shapes.

Vanilla Thin Plate Splines

Calculates shape from a polynomial model

Validates Coo objects

Identify outliers

"Redo" a LDA on new data

Add new landmarks based on angular positions

Plots mosaics of shapes.

Removes asymmetric and symmetric variation on OutCoe objects

Select columns by name

Calculates and draws 'tfourier' shapes.

Discrete cosinus transform

Tangent angle Fourier transform

Defines sliding landmarks matrix

Deformation 'vector field' using Thin Plate Splines

Calculates convex hull area/volume of PCA scores

Retrieves landmarks coordinates

Import a tps file

Sample a fraction of shapes

Add landmarks labels

Draws links between landmarks

Renames levels on Momocs objects

Subsetize various Momocs objects

Deformation grids using Thin Plate Splines