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Momocs (version 1.0.0)

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

1.0.0

License

GPL-2 | GPL-3

Issues

Pull Requests

Stars

Forks

Repository

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

Maintainer

Vincent Bonhomme

Last Published

March 18th, 2016

Functions in Momocs (1.0.0)

Coo "super" class

Builds an Opn object

Convert an OutCoe object into an Out object

Plots confusion matrix of sample sizes within $fac

Coe "super" class

Pairwise Multivariate analyses of variance

Principal component analysis on Coe objects

coo_down ----------------- Retains coordinates with negative y-coordinates

Linear Discriminant Analysis on Coe objects

Combines Momocs objects

Plots sets of shapes.

Momocs_lastversion

Install and load the last version of Momocs

Samples coordinates (regular radius)

Jitters Coe (and others) objects

Defines landmarks interactively

coo_circularityharalick

Calculates the Haralick's circularity of a shape

Centers coordinates

Builds an Ldk object

Retains coordinates with positive x-coordinates

Reverses coordinates

Calculates the convexity of a shape

coo_interpolate

Interpolates coordinates

Retains group with at least a certain number of individuals

Classify using LDA

Multivariate analysis of variance on Coe objects

Adds a shape to the current plot

Hierarchical clustering

calibrate_deviations

Quantitative calibration, through deviations, for Out and Opn objects

Calculates the convex hull of a shape

Plots differences as (colored) segments aka a ruban

Boxplot on PCA objects

Confidence ellipses

Calculates centroid size

Momocs' 'oscilloscope' for Fourier-based approaches

Converts Momocs objects to data.frames

Counts coordinates

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

A wrapper to calculates euclidean distances between two points

Builds an Out object

Register new baselines

Calculates the cumulative chordal distance along a shape.

Data: Landmark and semilandmark coordinates on cereal glumes

Binds with a database

Aligns coordinates

Calculates shape from a polynomial model

Converts a matrix of coordinates to an array of coordinates

coo_smoothcurve

Smoothes coordinates on curves

Closes/uncloses shapes

KMEANS on PCA objects

Sample coordinates (among points)

Calculates the calliper length

Converts an array of coordinates to a matrix

Scales coordinates

Calculates the angle of every edge of a shape

Discrete cosinus transform

Browse Momocs online doc

Calculates the elongation of a shape

Calculates the chordal distance along a shape.

Calculates Bezier coefficients from a shape

Data: Outline coordinates of mosquito wings.

calibrate_reconstructions

Calibrate using reconstructed shapes

Arranges (ala dplyr) on Momocs objects

coo_eccentricityboundingbox

Calculates the eccentricity (bounding box) of a shape

Data: Outline coordinates of beer and whisky bottles.

Calculate abscissa and ordinate on a shape

Data: Outline coordinates of olive seeds open outlines.

Builds an OutCoe object

Calculates the area of a shape

Slides coordinates

Investe discrete cosinus transform

Defines landmarks on Out and Opn objects

Calculates euclidean intermediate between two points.

Quantitative r2 calibration for Opn objects

Calculates the perimeter

Ptolemaic ellipses and illustration of efourier

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

Calculates and draw 'rfourier' shapes.

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

Transparency helpers and palettes

Get Momocs version

Builds an OpnCoe object

Calculates a shape from Bezier coefficients

Calculates the tangent angle along the perimeter of a shape

coo_rectangularity

Calculates the rectangularity of a shape

Chops (rough slicing) Momocs objects

Calculates the length of a shape

Shape variation along PC axes

Shrinks coordinates in one direction

Imports .nef to Coe objects

Dissolves Coe objects

Calculates the solidity of a shape

coo_circularitynorm

Calculates the 'normalized' circularity of a shape

coo_eccentricityeigen

Calculates the eccentricity (using eigenvalues) of a shape

Smoothes coordinates

Extract coordinates from a shape

Elliptical Fourier transform

Traditional morphometrics class

Family picture of shapes

Slides coordinates using the widest gap

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

Calculates convex hull area/volume of PCA scores

Retains coordinates with negative x-coordinates

Exports Coe objects and shapes

Extracts structure from filenames

Tests if shapes are closed

Harmonic contribution to shape

Retains coordinates with positive y-coordinates

Trims coordinates from shape

Renames levels on Momocs objects

Translates coordinates

Data: Configuration of landmarks of oak leaves

Retrieves landmarks coordinates

Add landmarks labels

import_StereoMorph_curve1

Imports files creates by StereoMorph into Momocs

Extracts outlines coordinates from an image silhouette

Subsets on Momocs objects

Various class/component testers

Extracts sliding landmarks coordinates

Histogram of morphometric coefficients

Normalizes harmonic coefficients.

Removes asymmetric and symmetric variation on OutCoe objects

Rotates coordinates

Calculates nice positions on a plane for drawing shapes

Inverse elliptical Fourier transform

Mutates (ala dplyr) on Momocs objects

Inverse radii variation Fourier transform

Plots a single shape

Plots Principal Component Analysis

Data: Outline coordinates of various shapes

Imports coordinates from a .txt file

Defines links between landmarks

Graphical inspection of shapes

Plots a .jpg image

Calculates euclidean distance every pairs of points in two matrices.

Plots (lollipop) differences between two configurations

Extracts outline coordinates from multiple .jpg files

Filters (ala dplyr) on Momocs objects

Permutes and breed Coe (and others) objects

Calculates and draw 'efourier' shapes.

Calculates and draws 'tfourier' shapes.

Calculates the width of a shape

Truss measurement

Deformation grids using Thin Plate Splines

Samples a fraction of shapes in Momocs objects

coo_rotatecenter

Rotates shapes with a custom center

"Redo" a LDA on new data

Draws kernel density contours around landmark

Converts a matrix of coordinates to a list of coordinates.

Slices shapes between successive coordinates

Data: Measurement of iris flowers

Family picture of shapes (ggplot2)

Methods for PCA eigen values

Boxplot of morphometric coefficients

Partial Procrustes alignment between two shapes

Checks 'ldk' shapes

Full Procrustes alignment between two shapes

Draws convex hulls around landmark positions

Some color palettes

Plots Principal Component Analysis ala ggplot2

Calculate centroid coordinates

Renames (ala dplyr) on Momocs objects

Data: Outline coordinates of cephalic outlines of trilobite

Removes shapes with incomplete slices

Data: Outline coordinates of hand-drawn hearts

Creates links (all pariwise combinations) between landmarks

Data: Outline coordinates of 360 molars

Full Generalized Procrustes alignment between shapes with sliding landmarks

Family picture of shapes (ggplot2)

Plots a cross-correlation table

Deformation 'vector field' using Thin Plate Splines

Data: Landmarks coordinates of mosquito wings

Full Generalized Procrustes alignment between shapes

Calculate orthogonal polynomial fits on open outlines

plot_devsegments

Draws colored segments from a matrix of coordinates.

Reads a single tps-like shape as lines

Measures shape descriptors

Register Bookstein's coordinates

"Redo" a PCA on a new Coe

Extracts outline coordinates from a single .jpg file

Converts a matrix of coordinates to a data.frame

Rescale coordinates from pixels to real length units

Converts a list of coordinates to an array of coordinates

Tangent angle Fourier transform

Binds .jpg outlines from .txt landmarks taken on them

Draws confidence ellipses for landmark positions

Converts a matrix of coordinates into a list of matrices

Removes harmonics from Coe objects

Deformation isolines using Thin Plate Splines.

slidings_scheme

Extracts partitions of sliding coordinates

Vanilla Thin Plate Splines

Slices (ala dplyr) on Momocs objects

Imports .nts to Coo objects

Converts a list of coordinates to a matrix of coordinates.

Cross-tabulates objects

Converts an array of coordinates to a list of matrices

coo_rectilinearity

Calculates the rectilinearity of a shape

Remove outliers on Coe

coo_force2close

Forces shapes to close

Thin Plate Splines for 2D data

Family picture of shapes

Radii variation Fourier transform

coo_aligncalliper

Aligns shapes along their 'calliper length'

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

coo_alignminradius

Aligns shapes using their shortest radius

Calcuates symmetry indices on OutCoe objects

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

'Templates' shapes

Calculates and draws 'dfourier' shapes

Defines sliding landmarks matrix

Plots Linear Discriminant Analysis

#' @describeIn plot.PCA #' @export mplot <- plot.PCA Plots a combination of the three first PCs

Objects exported from other packages

Samples n shapes on Momocs objects

Inverse tangent angle Fourier transform

Data: Outline coordinates from an experimental charring on cereal grains

Calculates length and width of a shape

Validates Coo objects

Converts chain-coded coordinates to Out object

Plots (lollipop) differences between two configurations

Calculate natural polynomial fits on open outlines

coo_circularity

Calculates the circularity of a shape

coo_slidedirection

Slides coordinates in a particular direction

Calculates euclidean distance between two points.

Get paired individual on a Coe, PCA or LDA objects

Imports a tps file

Creates links (Delaunay triangulation) between landmarks

Draws links between landmarks

Plots a cross-validation table as an heatmap

Transmutes (ala dplyr) on Momocs objects

calibrate_harmonicpower

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

Aligns shapes along the x-axis

Mean shape calculation for Coo, Coe, etc.

Returns the distance between everypoints and the centroid

Converts (x; y) coordinates to chaincoded coordinates

Selects (ala dplyr) on Momocs objects

Some vector utilities.