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Momocs (version 1.1.0)

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

669

Version

1.1.0

License

GPL-2 | GPL-3

Issues

Pull Requests

Stars

Forks

Repository

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

Maintainer

Vincent Bonhomme

Last Published

October 25th, 2016

Functions in Momocs (1.1.0)

Convert an OutCoe object into an Out object

Binds with a database

Arranges (ala dplyr) on Momocs objects

Adds new landmarks on Out and Opn objects

Calculates a shape from Bezier coefficients

Retains group with at least a certain number of individuals

Converts Momocs objects to data.frames

Converts an array of coordinates to a matrix

Converts an array of coordinates to a list of matrices

Calculates Bezier coefficients from a shape

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

Quantitative r2 calibration for Opn objects

calibrate_reconstructions

Calibrate using reconstructed shapes

Boxplot on PCA objects

calibrate_harmonicpower

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

Converts chain-coded coordinates to Out object

calibrate_deviations

Quantitative calibration, through deviations, for Out and Opn objects

Boxplot of morphometric coefficients

Chops (rough slicing) Momocs objects

Jitters Coe (and others) objects

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

Some color palettes

Aligns coordinates

Hierarchical clustering

Coe "super" class

Transparency helpers and palettes

Confidence ellipses

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

Combines Momocs objects

Classify using LDA

Centers coordinates

Aligns shapes along the x-axis

Calculates the area of a shape

coo_aligncalliper

Aligns shapes along their 'calliper length'

Plots (lollipop) differences between two configurations

Returns the distance between everypoints and the centroid

Calculates the calliper length

Register new baselines

Register Bookstein's coordinates

coo_alignminradius

Aligns shapes using their shortest radius

Calculates centroid size

coo_circularity

Calculates the circularity of a shape

Calculate centroid coordinates

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

Calculates the convexity of a shape

Calculates the convex hull of a shape

coo_circularityharalick

Calculates the Haralick's circularity of a shape

coo_circularitynorm

Calculates the 'normalized' circularity of a shape

Closes/uncloses shapes

Adds a shape to the current plot

coo_force2close

Forces shapes to close

Calculates the cumulative chordal distance along a shape.

Calculate abscissa and ordinate on a shape

Calculates the chordal distance along a shape.

Plots a single shape

Calculates the perimeter

Smoothes coordinates

coo_smoothcurve

Smoothes coordinates on curves

Plots sets of shapes.

Calculates the length of a shape

coo_interpolate

Interpolates coordinates

Plots differences as (colored) segments aka a ruban

coo_eccentricityboundingbox

Calculates the eccentricity (bounding box) of a shape

Scales coordinates

Sample coordinates (among points)

Samples coordinates (regular radius)

coo_eccentricityeigen

Calculates the eccentricity (using eigenvalues) of a shape

Defines landmarks interactively

Retains coordinates with negative x-coordinates

Slices shapes between successive coordinates

Slides coordinates

Calculates the angle of every edge of a shape

Calculates the width of a shape

Calculates the tangent angle along the perimeter of a shape

Calculates the solidity of a shape

Translates coordinates

Data: Landmarks coordinates of mosquito wings

Coo "super" class

Calculates and draw 'efourier' shapes.

Extracts outline coordinates from a single .jpg file

Filters (ala dplyr) on Momocs objects

Extracts outline coordinates from multiple .jpg files

Full Generalized Procrustes alignment between shapes with sliding landmarks

Elliptical Fourier transform

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

'Templates' shapes

Data: Measurement of iris flowers

Data: Outline coordinates of hand-drawn hearts

Investe discrete cosinus transform

Inverse elliptical Fourier transform

Calculates and draws 'dfourier' shapes

Full Procrustes alignment between two shapes

Normalizes harmonic coefficients.

Calculates convex hull area/volume of PCA scores

Linear Discriminant Analysis on Coe objects

Checks 'ldk' shapes

Creates links (Delaunay triangulation) between landmarks

Get Momocs version

Converts a matrix of coordinates to an array of coordinates

Builds an Opn object

Builds an OpnCoe object

Plots Linear Discriminant Analysis

Graphical inspection of shapes

Counts coordinates

Momocs' 'oscilloscope' for Fourier-based approaches

Reverses coordinates

Retains coordinates with positive x-coordinates

A wrapper to calculates euclidean distances between two points

Data: Outline coordinates of olive seeds open outlines.

Data: Outline coordinates of beer and whisky bottles.

Data: Configuration of landmarks of oak leaves

Harmonic contribution to shape

Histogram of morphometric coefficients

Various class/component testers

KMEANS on PCA objects

Converts a matrix of coordinates into a list of matrices

Pairwise Multivariate analyses of variance

Plots Principal Component Analysis

Plots Principal Component Analysis ala ggplot2

Mean shape calculation for Coo, Coe, etc.

Mutates (ala dplyr) on Momocs objects

Methods for PCA eigen values

Samples n shapes on Momocs objects

Selects (ala dplyr) on Momocs objects

Slices (ala dplyr) on Momocs objects

Deformation isolines using Thin Plate Splines.

Vanilla Thin Plate Splines

Draws kernel density contours around landmark

Add landmarks labels

Validates Coo objects

Truss measurement

Draws links between landmarks

Builds an Ldk object

Momocs_lastversion

Install and load the last version of Momocs

Browse Momocs online doc

Family picture of shapes (ggplot2)

Principal component analysis on Coe objects

"Redo" a PCA on a new Coe

Plots a cross-correlation table

plot_devsegments

Draws colored segments from a matrix of coordinates.

Rescale coordinates from pixels to real length units

Removes shapes with incomplete slices

Removes harmonics from Coe objects

Family picture of shapes

slidings_scheme

Extracts partitions of sliding coordinates

Traditional morphometrics class

Rotates coordinates

coo_rotatecenter

Rotates shapes with a custom center

Shrinks coordinates in one direction

Data: Outline coordinates of 360 molars

Retains coordinates with positive y-coordinates

Trims top coordinates from shape

Defines new landmarks on Out and Opn objects

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.

Extracts sliding landmarks coordinates

Imports coordinates from a .txt file

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

Converts a list of coordinates to a matrix of coordinates.

Converts a list of coordinates to an array of coordinates

Tests if shapes are closed

Converts a matrix of coordinates to a data.frame

Plots confusion matrix of sample sizes within $fac

Converts a matrix of coordinates to a list of coordinates.

Imports .nts to Coo objects

Transmutes (ala dplyr) on Momocs objects

Data: Outline coordinates of mosquito wings.

Data: Outline coordinates of various shapes

Calculates euclidean distance between two points.

Data: Outline coordinates of cephalic outlines of trilobite

Calculates euclidean intermediate between two points.

Exports Coe objects and shapes

import_StereoMorph_curve1

Imports files creates by StereoMorph into Momocs

Full Generalized Procrustes alignment between shapes

Imports a tps file

Calculates the elongation of a shape

Extract coordinates from a shape

Plots (lollipop) differences between two configurations

coo_rectangularity

Calculates the rectangularity of a shape

Calculates length and width of a shape

coo_slidedirection

Slides coordinates in a particular direction

coo_rectilinearity

Calculates the rectilinearity of a shape

Slides coordinates using the widest gap

Trims both ends coordinates from shape

Draws convex hulls around landmark positions

Draws confidence ellipses for landmark positions

Measures shape descriptors

Family picture of shapes

Builds an OutCoe object

Multivariate analysis of (co)variance on Coe objects

Permutes and breed Coe (and others) objects

Shape variation along PC axes

Trims bottom coordinates from shape

Data: Outline coordinates from an experimental charring on cereal grains

Data: Landmark and semilandmark coordinates on cereal glumes

Discrete cosinus transform

Defines sliding landmarks matrix

Defines links between landmarks

Get paired individual on a Coe, PCA or LDA objects

Retrieves landmarks coordinates

Dissolves Coe objects

Plots a .jpg image

Ptolemaic ellipses and illustration of efourier

Objects exported from other packages

Radii variation Fourier transform

Cross-tabulates objects

Calcuates symmetry indices on OutCoe objects

Removes asymmetric and symmetric variation on OutCoe objects

Extracts structure from filenames

Extracts outlines coordinates from an image silhouette

Deformation grids using Thin Plate Splines

Deformation 'vector field' using Thin Plate Splines

Creates links (all pariwise combinations) between landmarks

Imports .nef to Coe objects

Calculate natural polynomial fits on open outlines

Calculate orthogonal polynomial fits on open outlines

Renames levels on Momocs objects

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

Calculates shape from a polynomial model

Plots a cross-validation table as an heatmap

Converts (x; y) coordinates to chaincoded coordinates

Samples a fraction of shapes in Momocs objects

Some vector utilities.

Calculates and draws 'tfourier' shapes.

Inverse tangent angle Fourier transform

Calculates nice positions on a plane for drawing shapes

Partial Procrustes alignment between two shapes

Tangent angle Fourier transform

Calculates and draw 'rfourier' shapes.

Binds .jpg outlines from .txt landmarks taken on them

"Redo" a LDA on new data

Builds an Out object

Remove outliers on Coe

Inverse radii variation Fourier transform

Renames (ala dplyr) on Momocs objects

Family picture of shapes (ggplot2)

Subsets on Momocs objects

Thin Plate Splines for 2D data

Reads a single tps-like shape as lines