• Check the tutorial there or with browseVignettes("Momocs")
• You're welcome to implement ideas, propose new ones, review the code, the helpfiles or the vignettes, report bugs, ask for help: here on GitHub or there: [email protected].

Momocs

• is a complete toolkit for morphometrics, from data extraction to multivariate analyses.
• includes most common 2D morphometrics approaches : outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout.
• allows reproducible, pipeable, complex morphometric analyses and 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.
• hinges on the core functions developed in the must-have book Morphometrics with R by Julien Claude (2008).

Use it

From CRAN: install.packages("Momocs")

But I recommend using the last version:

if (!requireNamespace("devtools")) install.packages("devtools")
devtools::install_github('vbonhomme/Momocs')

You can cite it with: citation("Momocs")

Features

Matrices of xy-coordinates

• ~100 generic tools like centering, scaling, rotating, calculating area, perimeter, etc. Full list with apropos("coo_")
• generic plotters: coo_plot and g (work in progress)

Data acquisition + Babel

• Outline extraction from black mask/silhouettes .jpgs
• Landmark definition on outlines (def_ldk or via StereoMorph)
• Open curves digitization with bezier curves (via StereoMorph)
• Import/Export from/to .nts, .tps, PAST, .txt, etc.

Outline analysis

• Elliptical Fourier analysis (efourier)
• Radii variation (rfourier)
• Radii variation - curvilinear abscissa (sfourier)
• Tangent Angle Fourier analysis (tfourier)

Open-outlines

• Natural (raw) polynomials (npoly)
• Orthogonal (Legendre) polynomials (opoly)
• Discrete Cosinus Transform (dfourier)
• bezier core functions

Configuration of landmarks

• Full Generalized Procrustes Adjustment (fgProcrustes)
• Sliding semi-landmarks (fgsProcrustes)

Traditional morphometrics and global shape descriptors

• Facilities for multivariate analysis (see flowers)
• A long list of shape scalars (eg. coo_eccentricity, coo_rectilinearity, etc.)

Data handling

• Easy data manipulation with filter, select, slice, mutate and other verbs ala dplyr
• New verbs useful for morphometrics such as combine and chop, to handle several 2D views
• Permutation methods to resample data (perm, breed)

Multivariate analysis

• Mean shape (groupwise) calculations (mshapes)
• Principal component analysis (PCA)
• Multivariate analysis of variance (MANOVA + pairwise testing MANOVA_PW)
• Linear discriminant analysis and screening (LDA)
• Hierarchical clustering (CLUST)
• K-means (KMEANS)

Graphical methods

• Family pictures and quick inspection of whole datasets (stack and panel)
• Some ggplot2 plots, when useful (and convet Momocs' objects into data.frames it with as_df`)
• Morphological spaces for PCA
• Thin plate splines and variation around deformation grids

Misc

• Datasets for all types of data (bot, trilo, mosquito, hearts, olea, shapes, wings, oak, molars, flower, chaff, charring)
• Shiny demonstrators/helpers. See Momecs
• Online documentation