- Momocs version 1.0 "Mataa" ๐ฟ will be released on CRAN in March 2016
- Momocs' online documentation lives there
Momocs, morphometrics using R
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, 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.
- hinges on the core functions developed in the must-have book Morphometrics with R by Julien Claude (2008).
CRAN version
install.packages("Momocs")
Last version
That's always a good idea to use the last version.
Be sure to have devtools
installed (install.packages("devtools")
), then:
devtools::install_github("vbonhomme/Momocs", build_vignettes= TRUE)
How to cite it
citation("Momocs")
You are welcome to
- propose ideas and report bugs
- offer your published data to the world
- ask for hotline and/or collaborate and/or hire me:
[email protected]
(* = on its way)
Data acquisition + Babel
- Outline extraction
- Landmark definition on outlines (via StereoMorph)
- Open curves digitization with bezier curves (via StereoMorph)
- Import/Export from/to
.nts
,.tps
,PAST
,.txt
, etc.*
Outline analysis
- Elliptical Fourier analysis
- Radius Variation Fourier analysis
- Tangent Angle Fourier analysis
- Calibration for all methods
Open-outlines
- Natural (raw) polynomials (
npoly
) - Orthogonal (Legendre) polynomials (
opoly
) - Discrete Cosinus Transform (
dfourier
) - Calibration for all methods
bezier
core functions
Configuration of landmarks
- Full Generalized Procrustes Adjustment (
fgProcrustes
) - Resistant Fit Procrustes Adjustments*
- Sliding semi-landmarks
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
filter
,select
,slice
,mutate
and other verbs ala dplyr- New verbs useful for morphometrics such as
combine
andchop
, 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 testingMANOVA_PW
) - Linear discriminant analysis and screening (
LDA
) - Hierarchical clustering (
CLUST
) - K-means (
KMEANS
)
Graphical methods
- Family pictures and quick inspection of whole datasets
- Some ggplot2 plots, when useful
- Morphological spaces for PCA
- Thin plate splines and variation around deformation grids
Various
- Datasets for all types of data (
bot
,trilo
,mosquito
,hearts
,olea
,shapes
,wings
,oak
,molars
,flower
,chaff
,charring
) - Vignettes (
browseVignettes("Momocs")
) - Shiny demonstrators/helpers. See Momecs
- Online documentation