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Momocs (version 1.4.1)

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

746

Version

1.4.1

License

GPL-2 | GPL-3

Issues

Pull Requests

Stars

Forks

Repository

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

Homepage

http://momx.github.io/Momocs/

Maintainer

Vincent Bonhomme

Last Published

November 13th, 2023

Functions in Momocs (1.4.1)

Mean shape calculation for Coo, Coe, etc.

Boxplot on PCA objects

Boxplot of morphometric coefficients

Calculates Bezier coefficients from a shape

Arrange rows by variables

(Metric) multidimensional scaling

Turn Momocs objects into tydy data_frames

coo_angle_edges

Calculates the angle of every edge of a shape

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

Calculates a shape from Bezier coefficients

Aligns shapes along the x-axis

Principal component analysis on Coe objects

calibrate_deviations

Quantitative calibration, through deviations, for Out and Opn objects

coeff_rearrange

Rearrange a matrix of (typically Fourier) coefficients

Builds an OutCoe object

Combine several objects

Transparency helpers and palettes

Ptolemaic ellipses and illustration of efourier

Calculates the calliper length

calibrate_harmonicpower

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

Traditional morphometrics class

Quantitative r2 calibration for Opn objects

Multivariate analysis of (co)variance on Coe objects

Builds an Ldk object

coo_aligncalliper

Aligns shapes along their 'calliper length'

calibrate_reconstructions

Calibrate using reconstructed shapes

Adds new landmarks on Out and Opn objects

Non metric multidimensional scaling

Builds an Opn object

coo_alignminradius

Aligns shapes using their shortest radius

Builds an OpnCoe object

Retain groups with at least n shapes

Builds an Out object

Returns the distance between everypoints and the centroid

Convert (x; y) coordinates to chaincoded coordinates

Aligns coordinates

Convert complex to/from cartesian coordinates

Split to several objects based on a factor

Calculate centroid coordinates

Centers coordinates

classification_metrics

Calculate classification metrics on a confusion matrix

Calculates the convexity of a shape

coo_force2close

Forces shapes to close

coo_interpolate

Interpolates coordinates

Closes/uncloses shapes

coo_eccentricity

Calculates the eccentricity of a shape

Calculates the elongation of a shape

Calculates the length of a shape

Register new baselines

Plots (lollipop) differences between two configurations

Register Bookstein's coordinates

Draw radii to the current plot

Calculate abscissa and ordinate on a shape

Test if shapes are closed

coo_boundingbox

Calculates coordinates of the bounding box

Plots sets of shapes.

Plots (lollipop) differences between two configurations

Calculates centroid size

coo_likely_clockwise

Tests if shapes are (likely) developping clockwise or anticlockwise

Plots differences as (colored) segments aka a ruban

Convert between different classes

Jitters Coe (and others) objects

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

Adds a shape to the current plot

coo_angle_tangent

Calculates the tangent angle along the perimeter of a shape

coo_down Retains coordinates with negative y-coordinates

Some color palettes

Calculates the area of a shape

Extract coordinates from a shape

coo_intersect_angle

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

Defines landmarks interactively

Momocs' 'oscilloscope' for Fourier-based approaches

Calculates perimeter and variations

Sample coordinates (among points)

Calculates all scalar descriptors of shape

Rotates coordinates

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

Slides coordinates

Truss measurement

coo_rotatecenter

Rotates shapes with a custom center

coo_slidedirection

Slides coordinates in a particular direction

Plots a single shape

coo_intersect_segment

Nearest intersection between a shape and a segment

Calculate coordinates range

Retains coordinates with positive y-coordinates

Calculates the width of a shape

Counts coordinates

Calculates length and width of a shape

Samples coordinates (regular radius)

coo_sample_prop

Sample a proportion of coordinates (among points)

Scales coordinates

Calculates the (recursive) convex hull of a shape

coo_rectilinearity

Calculates the rectilinearity of a shape

coo_rectangularity

Calculates the rectangularity of a shape

Slices shapes between successive coordinates

coo_circularity

Calculates the Haralick's circularity of a shape

Calculates euclidean distance between two points.

Calculates euclidean intermediate between two points.

Data: Outline coordinates of mosquito wings.

grindr drawers for shape plots

Dissolve Coe objects

Data: Outline coordinates of mouse molars

Data: Outline coordinates of North Sea fishes

'Templates' shapes

Data: Landmark and semilandmark coordinates on cereal glumes

Calculates the total absolute curvature of a shape

Data: Outline coordinates of beer and whisky bottles.

Reverses coordinates

Retains coordinates with negative x-coordinates

Translates coordinates

Trims both ends coordinates from shape

coo_smoothcurve

Smoothes coordinates on curves

Plots a .jpg image

Data: Outline coordinates of hand-drawn hearts

Data: Outline coordinates of various shapes

Data: Outline coordinates of olive seeds open outlines.

Calculates the solidity of a shape

Data: Outline coordinates of 360 molars

Data: Configuration of landmarks of oak leaves

Full Procrustes alignment between two shapes

A wrapper to calculates euclidean distances between two points

Extract outlines coordinates from an image silhouette

Brew and serve fac from Momocs object

Inverse elliptical Fourier transform

Harmonic contribution to shape

Calculates and draws 'dfourier' shapes

Elliptical Fourier transform (and its normalization)

Class and component testers

Full Generalized Procrustes alignment between shapes with sliding landmarks

Investe discrete cosinus transform

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

Measures shape descriptors

is_equallyspacedradii

Tests if coordinates likely have equally spaced radii

Full Generalized Procrustes alignment between shapes

Calculates convex hull area/volume of PCA scores

Retains coordinates with positive x-coordinates

Creates links (Delaunay triangulation) between landmarks

Retrieves landmarks coordinates

Graphical inspection of shapes

Checks 'ldk' shapes

Import coordinates from a .txt file

Draws convex hulls around landmark positions

Slides coordinates using the widest gap

Get paired individual on a Coe, PCA or LDA objects

Defines sliding landmarks matrix

Trims top coordinates from shape

Data: Outline coordinates of cephalic outlines of trilobite

Add new variables

Data: Outline coordinates from an experimental charring on cereal grains

Data: Landmarks coordinates of mosquito wings

Trims bottom coordinates from shape

Smoothes coordinates

Data: Measurement of iris flowers

Add new landmarks based on angular positions

Data: Outline coordinates of Apodemus (wood mouse) mandibles

Defines new landmarks on Out and Opn objects

Calculate natural polynomial fits on open outlines

NMDS plot unsing grindr layers

Discrete cosinus transform

Pairwise comparison of a list of shapes

Draws confidence ellipses for landmark positions

Draws kernel density contours around landmark

Family picture of shapes

Define tips as new landmarks

plot_silhouette

Silhouette plot

Defines links between landmarks

Calculates euclidean distance every pairs of points in two matrices.

LDA plot using grindr layers

Plots a cross-correlation table

PCA plot using grindr layers

grindr layers for multivariate plots

Exports Coe objects and shapes

Plots mosaics of shapes.

morphospace_positions

Calculates nice positions on a plane for drawing shapes

Calculates and draw 'efourier' shapes.

layers_morphospace

Morphospace layers

Inverse radii variation Fourier transform

Extract outline coordinates from multiple .jpg files

"Redo" a LDA on new data

Calculates shape from a polynomial model

Calculates and draw 'rfourier' shapes.

Extracts sliding landmarks coordinates

import_StereoMorph_curve1

Import files creates by StereoMorph into Momocs

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

grindr papers for shape plots

Creates links (all pairwise combinations) between landmarks

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

plot_devsegments

Draws colored segments from a matrix of coordinates.

Plots confusion matrix of sample sizes within $fac

Permutes and breed Coe (and others) objects

Objects exported from other packages

Sample a fraction of shapes

Renames levels on Momocs objects

Rename columns by name

Plots Linear Discriminant Analysis

Graphical pile of shapes

Radii variation Fourier transform (equally spaced radii)

Removes asymmetric and symmetric variation on OutCoe objects

Family picture of shapes

Subsetize various Momocs objects

Rescale coordinates from pixels to real length units

Deformation 'vector field' using Thin Plate Splines

Deformation grids using Thin Plate Splines

Remove shapes with missing data in fac

Remove shapes with incomplete slices

Subset based on conditions

Removes harmonics from Coe objects

Subset based on positions

slidings_scheme

Extracts partitions of sliding coordinates

Select columns by name

Import a tps file

Extract outline coordinates from a single .jpg file

Binds .jpg outlines from .txt landmarks taken on them

Thin Plate Splines for 2D data

Draws links between landmarks

Add landmarks labels

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

Sample n shapes

Plots Principal Component Analysis

Calculate orthogonal polynomial fits on open outlines

Partial Procrustes alignment between two shapes

Radii variation Fourier transform (equally spaced curvilinear abscissa)

Plots a cross-validation table as an heatmap

Inverse radii variation Fourier transform

Rearrange, (select and reorder) landmarks to retain

Calculates and draw 'sfourier' shapes.

Calculates and draws 'tfourier' shapes.

Inverse tangent angle Fourier transform

"Redo" a PCA on a new Coe

Calcuates symmetry indices on OutCoe objects

Tangent angle Fourier transform

Validates Coo objects

Deformation isolines using Thin Plate Splines.

Identify outliers

Vanilla Thin Plate Splines

Coe "super" class

Coo "super" class

Hierarchical clustering

Linear Discriminant Analysis on Coe objects

Pairwise Multivariate analyses of variance

KMEANS on PCA objects

Shape variation along PC axes