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Momocs (version 1.4.0)

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

577

Version

1.4.0

License

GPL-2 | GPL-3

Issues

Pull Requests

Stars

Forks

Repository

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

Maintainer

Vincent Bonhomme

Last Published

April 4th, 2022

Functions in Momocs (1.4.0)

Coe "super" class

KMEANS on PCA objects

Pairwise Multivariate analyses of variance

Multivariate analysis of (co)variance on Coe objects

Hierarchical clustering

Coo "super" class

Builds an Ldk object

(Metric) multidimensional scaling

Linear Discriminant Analysis on Coe objects

Builds an OutCoe object

Mean shape calculation for Coo, Coe, etc.

Arrange rows by variables

Jitters Coe (and others) objects

Convert between different classes

Turn Momocs objects into tydy data_frames

Boxplot on PCA objects

Split to several objects based on a factor

Boxplot of morphometric coefficients

Aligns shapes along the x-axis

classification_metrics

Calculate classification metrics on a confusion matrix

Traditional morphometrics class

Principal component analysis on Coe objects

Retain groups with at least n shapes

Builds an OpnCoe object

Builds an Out object

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

Some color palettes

Adds new landmarks on Out and Opn objects

Centers coordinates

coo_angle_edges

Calculates the angle of every edge of a shape

Calculate centroid coordinates

Closes/uncloses shapes

Calculates the convexity of a shape

Ptolemaic ellipses and illustration of efourier

Calculates a shape from Bezier coefficients

Calculates Bezier coefficients from a shape

Shape variation along PC axes

coeff_rearrange

Rearrange a matrix of (typically Fourier) coefficients

coo_boundingbox

Calculates coordinates of the bounding box

Register Bookstein's coordinates

Convert (x; y) coordinates to chaincoded coordinates

Calculates the calliper length

Quantitative r2 calibration for Opn objects

Test if shapes are closed

Calculates the length of a shape

coo_likely_clockwise

Tests if shapes are (likely) developping clockwise or anticlockwise

Returns the distance between everypoints and the centroid

Calculate abscissa and ordinate on a shape

Extract coordinates from a shape

Draw radii to the current plot

Non metric multidimensional scaling

calibrate_reconstructions

Calibrate using reconstructed shapes

coo_down Retains coordinates with negative y-coordinates

Defines landmarks interactively

Retains coordinates with negative x-coordinates

Reverses coordinates

calibrate_harmonicpower

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

Transparency helpers and palettes

Builds an Opn object

Combine several objects

calibrate_deviations

Quantitative calibration, through deviations, for Out and Opn objects

Aligns coordinates

Convert complex to/from cartesian coordinates

Plots a single shape

Calculate coordinates range

coo_eccentricity

Calculates the eccentricity of a shape

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

Data: Landmark and semilandmark coordinates on cereal glumes

Data: Outline coordinates of beer and whisky bottles.

Calculates the elongation of a shape

Register new baselines

coo_aligncalliper

Aligns shapes along their 'calliper length'

Plots (lollipop) differences between two configurations

coo_alignminradius

Aligns shapes using their shortest radius

Calculates centroid size

Rotates coordinates

Plots (lollipop) differences between two configurations

Plots sets of shapes.

coo_angle_tangent

Calculates the tangent angle along the perimeter of a shape

Calculates the area of a shape

Momocs' 'oscilloscope' for Fourier-based approaches

coo_force2close

Forces shapes to close

coo_interpolate

Interpolates coordinates

Adds a shape to the current plot

Calculates perimeter and variations

coo_rotatecenter

Rotates shapes with a custom center

Calculates all scalar descriptors of shape

Retains coordinates with positive x-coordinates

Scales coordinates

Truss measurement

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

Add new landmarks based on angular positions

Investe discrete cosinus transform

Defines new landmarks on Out and Opn objects

Calculates and draws 'dfourier' shapes

Calculates the total absolute curvature of a shape

Slices shapes between successive coordinates

Calculates the (recursive) convex hull of a shape

coo_circularity

Calculates the Haralick's circularity of a shape

Data: Outline coordinates from an experimental charring on cereal grains

'Templates' shapes

Define tips as new landmarks

Data: Measurement of iris flowers

Plots differences as (colored) segments aka a ruban

Sample coordinates (among points)

coo_intersect_segment

Nearest intersection between a shape and a segment

Calculates length and width of a shape

Counts coordinates

coo_intersect_angle

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

coo_rectangularity

Calculates the rectangularity of a shape

Slides coordinates

coo_slidedirection

Slides coordinates in a particular direction

coo_sample_prop

Sample a proportion of coordinates (among points)

Samples coordinates (regular radius)

Data: Outline coordinates of cephalic outlines of trilobite

Extract outlines coordinates from an image silhouette

Plots a .jpg image

Exports Coe objects and shapes

Calculates and draw 'efourier' shapes.

grindr layers for multivariate plots

Data: Landmarks coordinates of mosquito wings

Translates coordinates

Data: Outline coordinates of hand-drawn hearts

Data: Outline coordinates of North Sea fishes

Trims both ends coordinates from shape

Data: Outline coordinates of 360 molars

Calculates the solidity of a shape

coo_smoothcurve

Smoothes coordinates on curves

A wrapper to calculates euclidean distances between two points

Calculates euclidean intermediate between two points.

Calculates euclidean distance between two points.

Data: Outline coordinates of Apodemus (wood mouse) mandibles

Full Generalized Procrustes alignment between shapes

Dissolve Coe objects

Data: Outline coordinates of olive seeds open outlines.

Data: Outline coordinates of various shapes

grindr drawers for shape plots

Slides coordinates using the widest gap

coo_rectilinearity

Calculates the rectilinearity of a shape

Smoothes coordinates

Full Generalized Procrustes alignment between shapes with sliding landmarks

Data: Configuration of landmarks of oak leaves

Elliptical Fourier transform (and its normalization)

Defines links between landmarks

layers_morphospace

Morphospace layers

Inverse elliptical Fourier transform

Calculates convex hull area/volume of PCA scores

Family picture of shapes

Graphical inspection of shapes

Import coordinates from a .txt file

Defines sliding landmarks matrix

Creates links (Delaunay triangulation) between landmarks

Measures shape descriptors

Calculates shape from a polynomial model

"Redo" a LDA on new data

grindr papers for shape plots

Pairwise comparison of a list of shapes

Permutes and breed Coe (and others) objects

Brew and serve fac from Momocs object

Full Procrustes alignment between two shapes

Plots confusion matrix of sample sizes within $fac

NMDS plot unsing grindr layers

plot_silhouette

Silhouette plot

Remove shapes with missing data in fac

Retrieves landmarks coordinates

Discrete cosinus transform

Get paired individual on a Coe, PCA or LDA objects

Extracts sliding landmarks coordinates

Class and component testers

Family picture of shapes

Deformation isolines using Thin Plate Splines.

Subsetize various Momocs objects

is_equallyspacedradii

Tests if coordinates likely have equally spaced radii

Creates links (all pairwise combinations) between landmarks

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

Plots a cross-correlation table

Vanilla Thin Plate Splines

Rename columns by name

Objects exported from other packages

LDA plot using grindr layers

Calculates and draw 'rfourier' shapes.

Inverse radii variation Fourier transform

Extract outline coordinates from a single .jpg file

Harmonic contribution to shape

Tangent angle Fourier transform

Deformation grids using Thin Plate Splines

Calcuates symmetry indices on OutCoe objects

Validates Coo objects

Inverse radii variation Fourier transform

Deformation 'vector field' using Thin Plate Splines

Calculates and draw 'sfourier' shapes.

Identify outliers

Remove shapes with incomplete slices

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

Extract outline coordinates from multiple .jpg files

import_StereoMorph_curve1

Import files creates by StereoMorph into Momocs

Trims bottom coordinates from shape

Retains coordinates with positive y-coordinates

Trims top coordinates from shape

Calculates the width of a shape

Checks 'ldk' shapes

Draws convex hulls around landmark positions

Import a tps file

Data: Outline coordinates of mosquito wings.

Data: Outline coordinates of mouse molars

Draws confidence ellipses for landmark positions

Calculate orthogonal polynomial fits on open outlines

Draws kernel density contours around landmark

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.

morphospace_positions

Calculates nice positions on a plane for drawing shapes

Add landmarks labels

Draws links between landmarks

Subset based on conditions

Partial Procrustes alignment between two shapes

Graphical pile of shapes

Plots mosaics of shapes.

Plots Linear Discriminant Analysis

Removes asymmetric and symmetric variation on OutCoe objects

Add new variables

PCA plot using grindr layers

plot_devsegments

Draws colored segments from a matrix of coordinates.

Calculate natural polynomial fits on open outlines

Rearrange, (select and reorder) landmarks to retain

"Redo" a PCA on a new Coe

Removes harmonics from Coe objects

slidings_scheme

Extracts partitions of sliding coordinates

Calculates and draws 'tfourier' shapes.

Inverse tangent angle Fourier transform

Subset based on positions

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

Sample n shapes

Select columns by name

Plots Principal Component Analysis

Radii variation Fourier transform (equally spaced curvilinear abscissa)

Plots a cross-validation table as an heatmap

Radii variation Fourier transform (equally spaced radii)

Rescale coordinates from pixels to real length units

Renames levels on Momocs objects

Sample a fraction of shapes

Binds .jpg outlines from .txt landmarks taken on them

Thin Plate Splines for 2D data