Momocs1.4.1 package

Calculate orthogonal polynomial fits on open outlines

Builds an Out object

Builds an OutCoe object

Data: Outline coordinates of cephalic outlines of trilobite

Data: Landmarks coordinates of mosquito wings

Defines new landmarks on Out and Opn objects

Add new landmarks based on angular positions

Define tips as new landmarks

Defines links between landmarks

Defines sliding landmarks matrix

Builds an Opn object

Builds an OpnCoe object

Discrete cosinus transform

Investe discrete cosinus transform

Calculates and draws 'dfourier' shapes

Dissolve Coe objects

Adds new landmarks on Out and Opn objects

Arrange rows by variables

Turn Momocs objects into tydy data_frames

Retain groups with at least n shapes

Convert (x; y) coordinates to chaincoded coordinates

Calculates Bezier coefficients from a shape

Calculates a shape from Bezier coefficients

Boxplot of morphometric coefficients

Boxplot on PCA objects

Jitters Coe (and others) objects

Convert between different classes

Quantitative calibration, through deviations, for Out and Opn objects

Quantitative calibration, through harmonic power, for Out and Opn obje...

Quantitative r2 calibration for Opn objects

Calibrate using reconstructed shapes

Split to several objects based on a factor

Calculate classification metrics on a confusion matrix

Hierarchical clustering

Coe "super" class

Rearrange a matrix of (typically Fourier) coefficients

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

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

Some color palettes

Transparency helpers and palettes

Combine several objects

Convert complex to/from cartesian coordinates

Coo "super" class

Aligns coordinates

Aligns shapes along their 'calliper length'

Aligns shapes using their shortest radius

Aligns shapes along the x-axis

Calculates the angle of every edge of a shape

Calculates the tangent angle along the perimeter of a shape

Calculates the area of a shape

Plots (lollipop) differences between two configurations

Register new baselines

Register Bookstein's coordinates

Calculates coordinates of the bounding box

Calculates the calliper length

Returns the distance between everypoints and the centroid

Centers coordinates

Calculate centroid coordinates

Calculates centroid size

Checks shapes

Calculates the (recursive) convex hull of a shape

Calculates the Haralick's circularity of a shape

Closes/uncloses shapes

Calculates the convexity of a shape

coo_down Retains coordinates with negative y-coordinates

Adds a shape to the current plot

Draw radii to the current plot

Calculate abscissa and ordinate on a shape

Calculates the eccentricity of a shape

Calculates the elongation of a shape

Extract coordinates from a shape

Flips shapes

Forces shapes to close

Interpolates coordinates

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

Nearest intersection between a shape and a segment

Test if shapes are closed

Jitters shapes

Defines landmarks interactively

Retains coordinates with negative x-coordinates

Calculates the length of a shape

Tests if shapes are (likely) developping clockwise or anticlockwise

Plots sets of shapes.

Plots (lollipop) differences between two configurations

Calculates length and width of a shape

Counts coordinates

Momocs' 'oscilloscope' for Fourier-based approaches

Calculates perimeter and variations

Plots a single shape

Calculate coordinates range

Calculates the rectangularity of a shape

Calculates the rectilinearity of a shape

Reverses coordinates

Retains coordinates with positive x-coordinates

Rotates coordinates

Rotates shapes with a custom center

Plots differences as (colored) segments aka a ruban

Sample coordinates (among points)

Sample a proportion of coordinates (among points)

Samples coordinates (regular radius)

Calculates all scalar descriptors of shape

Scales coordinates

Shears shapes

Slices shapes between successive coordinates

Slides coordinates

Slides coordinates in a particular direction

Slides coordinates using the widest gap

Smoothes coordinates

Smoothes coordinates on curves

Calculates the solidity of a shape

Calculates the total absolute curvature of a shape

'Templates' shapes

Translates coordinates

Trims both ends coordinates from shape

Trims bottom coordinates from shape

Trims top coordinates from shape

Truss measurement

Removes rotation so that the centroid and a given point are parallel t...

Retains coordinates with positive y-coordinates

Calculates the width of a shape

A wrapper to calculates euclidean distances between two points

Data: Outline coordinates of Apodemus (wood mouse) mandibles

Data: Outline coordinates of beer and whisky bottles.

Data: Landmark and semilandmark coordinates on cereal glumes

Data: Outline coordinates from an experimental charring on cereal grai...

Data: Measurement of iris flowers

Data: Outline coordinates of hand-drawn hearts

Data: Outline coordinates of 360 molars

Data: Outline coordinates of mosquito wings.

Data: Outline coordinates of mouse molars

Data: Outline coordinates of North Sea fishes

Data: Configuration of landmarks of oak leaves

Data: Outline coordinates of olive seeds open outlines.

Data: Outline coordinates of various shapes

grindr drawers for shape plots

Calculates euclidean distance between two points.

Calculates euclidean intermediate between two points.

Calculates euclidean distance every pairs of points in two matrices.

Calculates the shortest euclidean distance found for every point of on...

Elliptical Fourier transform (and its normalization)

Inverse elliptical Fourier transform

Calculates and draw 'efourier' shapes.

Exports Coe objects and shapes

Brew and serve fac from Momocs object

Full Generalized Procrustes alignment between shapes

Full Generalized Procrustes alignment between shapes with sliding land...

Subset based on conditions

Flips PCA axes

Full Procrustes alignment between two shapes

Calculates convex hull area/volume of PCA scores

Retrieves landmarks coordinates

Get paired individual on a Coe, PCA or LDA objects

Extracts sliding landmarks coordinates

Harmonic contribution to shape

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

Plots a .jpg image

Extract outlines coordinates from an image silhouette

Extract outline coordinates from multiple .jpg files

Extract outline coordinates from a single .jpg file

Import files creates by StereoMorph into Momocs

Import a tps file

Import coordinates from a .txt file

Graphical inspection of shapes

Class and component testers

Tests if coordinates likely have equally spaced radii

KMEANS on PCA objects

KMEDOIDS

grindr layers for multivariate plots

Morphospace layers

Linear Discriminant Analysis on Coe objects

Builds an Ldk object

Checks 'ldk' shapes

Draws convex hulls around landmark positions

Draws confidence ellipses for landmark positions

Draws kernel density contours around landmark

Add landmarks labels

Draws links between landmarks

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

Creates links (all pairwise combinations) between landmarks

Creates links (Delaunay triangulation) between landmarks

Multivariate analysis of (co)variance on Coe objects

Pairwise Multivariate analyses of variance

(Metric) multidimensional scaling

Measures shape descriptors

Momocs

Calculates nice positions on a plane for drawing shapes

Plots mosaics of shapes.

Mean shape calculation for Coo, Coe, etc.

Add new variables

Non metric multidimensional scaling

Calculate natural polynomial fits on open outlines

Color palettes

Family picture of shapes

grindr papers for shape plots

Principal component analysis on Coe objects

Shape variation along PC axes

Permutes and breed Coe (and others) objects

Graphical pile of shapes

Plots Linear Discriminant Analysis

Plots Principal Component Analysis

Plots a cross-validation table as an heatmap

Plots a cross-correlation table

Draws colored segments from a matrix of coordinates.

LDA plot using grindr layers

Pairwise comparison of a list of shapes

NMDS plot unsing grindr layers

PCA plot using grindr layers

Silhouette plot

Plots confusion matrix of sample sizes within $fac

Calculates shape from a polynomial model

Partial Procrustes alignment between two shapes

Ptolemaic ellipses and illustration of efourier

Rearrange, (select and reorder) landmarks to retain

Objects exported from other packages

"Redo" a LDA on new data

Rename columns by name

"Redo" a PCA on a new Coe

Rescale coordinates from pixels to real length units

Radii variation Fourier transform (equally spaced radii)

Inverse radii variation Fourier transform

Calculates and draw 'rfourier' shapes.

Removes asymmetric and symmetric variation on OutCoe objects

Removes harmonics from Coe objects

Remove shapes with missing data in fac

Remove shapes with incomplete slices

Renames levels on Momocs objects

Sample a fraction of shapes

Sample n shapes

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

Select columns by name

Radii variation Fourier transform (equally spaced curvilinear abscissa...

Inverse radii variation Fourier transform

Calculates and draw 'sfourier' shapes.

Subset based on positions

Extracts partitions of sliding coordinates

Family picture of shapes

Subsetize various Momocs objects

Calcuates symmetry indices on OutCoe objects

Tangent angle Fourier transform

Inverse tangent angle Fourier transform

Calculates and draws 'tfourier' shapes.

Binds .jpg outlines from .txt landmarks taken on them

Deformation 'vector field' using Thin Plate Splines

Deformation grids using Thin Plate Splines

Deformation isolines using Thin Plate Splines.

Vanilla Thin Plate Splines

Thin Plate Splines for 2D data

Traditional morphometrics class

Validates Coo objects

Identify outliers