Morphometrics using R

The goal of Momocs is to provide a complete, convenient, reproducible and open-source toolkit for 2D morphometrics. It includes most common 2D morphometrics approaches on outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout. It allows reproducible, complex morphometric analyses and other morphometrics approaches should be easy to plug in, or develop from, on top of this canvas.


News

Momocs 1.2.5

Preamble

  • Started a general review of Momocs (including #184) to prepare for MomX. For my convenience, all changes will stack on 1.2.5 on GitHub but will appear, in the end, as 1.9.0 on CRAN to both reflect proximity with 2.0 and the huge quantity if changes since 1.2
  • Moved everything to github.com/MomX/Momocs
  • ongoing complete review of code
  • ongoing complete review of manual pages: lots of grouping, more and better
  • graphics is not dead (aka grindr): pipe-friendly base layers for biplots and shape drawing on cartesian coordinates. Is used to replace all multivariate plotters (eg plot.PCA), family pictures (eg stack will be replace by pile and remove an annoying conflict with utils::stack, panel) and single shape plotters (eg ldk_plot, coo_plot). This strategy is faster, much more generic and will ease further development and maintenance compared to previous Momocs graphs.
  • A vignette details grindr rationale and use.

New

  • new functions: andnow and andnow_method class tells you what to do with this object, and which classes are supported by this function/method.
  • new coo_* methods: coo_range, coo_range_enlarge, coo_diffrange, coo_template_relatively. The latter will prepare ground for proper size handling, notably for morphospaces.
  • Many coo functions ported to methods and now supporting .Coo directly: coo_angle_edges, coo_angle_tangent, coo_boundingbox, coo_calliper, coo_chull, coo_chull_onion, coo_circularity, coo_circularityharalick, coo_circularity_norm, coo_convexity, coo_dxy, coo_eccentricityboundingbox, coo_eccentricityeigen, coo_elongation, coo_intersect_angle, coo_intersect_direction, coo_intersect_segment, coo_perim, coo_perimcum, coo_perimpts, coo_rectangularity, coo_rectilinearity, coo_scalex, coo_scaley, coo_solidity, coo_truss.
  • Palettes are now those colorblind-friendly from RColorBrewer and those, state of the art, virids palettes. See also pal_manual, pal_qual_solarized and pal_seq_grey.
  • dispatch_fac is now behind all fac arguments
  • fgProcrustes now accepts lists
  • efourier with default norm=TRUE now messages about how wrong it may be
  • dplyr::data_frame everywhere pertinent

Deprecated

  • All is.* aliases for is_* methods
  • Deprecated classify for a while
  • All calibrate_*(..., method) have been renamed to calibrate_*_method. See ?calibrate_reconstructions and friends.
  • Deprecated plot3.PCA (will be replaced in further versions)
  • Ntable now splitted into of plot_table + table
  • coo_tangle now in coo_angle_tangent
  • coo_theta3 now in coo_angle_edges
  • truss now in coo_truss and a method of its own
  • plot.Coo is now inspect
  • pos.shapes is now morphospace_positions
  • is_closed is deprecated, now coo_is_closed; same for is_open now coo_is_open, to comply with all coo_* friends naming scheme
  • is_clockwise is deprecated, now coo_likely_clockwise; same for is_anticlockwise now coo_likely_anticlockwise. Better reflect the incertainty and gather with coo_* friends
  • Deprecated rename (handled by select anyway)
  • Deprecated table (poor shortcut anyway and avoid this boring startup message)
  • Deprecated stack2 and panel2 before their rewriting
  • Deprecated as_Out, that should have been efourier_i.OutCoe anyway.
  • Consequently deprecated panel.OutCoe method that was additionnaly the only Coe method. May be back in further versions.
  • Some non-exported functions (ie internals) now homegeneously begin with a ., eg .is.error (try Momocs:::. + <Tab> for a complete list).
  • Some previously exported functions are now internals (function_foo renamed to .function_foo): .coo_angle_edge1, .vecs_param, .refactor
  • NEWS is now a decent NEWS file
  • Online doc has been moved to [http://momx.github.io/Momocs/]

Dependencies

  • Released reshape2, plyr dependencies
  • Now depends RColorBrewer, progress
  • Proper indications of external functions with ::. A nice side effect is to remove annoying messages when attaching Momocs. Another is the removal of most importFrom.

Breaking changes

  • Besides deprecated/renamed functions there should be no breaking changes.
  • Future breaking changes are announced within concerned functions.

Minor

  • Waiting for a cleaner fix, subset is now subsetize...
  • Fixed a bug in LDA when retain=1 (#e7704eb)
  • Messages homogeneity
  • Internals have been lightened
  • verbosity and progress bar are now handled via options("verbose")
  • Various minor bugs fixes, see GitHub

Momocs 1.2.4 (GitHub)

  • New functions/methods: coo_intersect_segment, coo_intersect_direction, coo_intersect_angle, def_ldk_direction, def_ldk_angle, def_ldk, def_ldk_tips, coo_sample_prop
  • coo_slice.Opn now supports ldk argument.
  • Now depends rgeos for intersecting methods.
  • Lightened nsfishes and charring to comply R CMD CHECK.
  • Various minor bugs fixes, see GitHub

Momocs 1.2.3 (GitHub)

  • Built with R 3.4.3
  • coo_slice now suports ldk argument
  • Various minor bugs fixes, see GitHub

Momocs 1.2.2 (CRAN + GitHub)

  • MANOVA_PW now returns p-values
  • New dataset nsfishes
  • minor debugging, see GitHub

Momocs 1.2.1 (GitHub)

  • Introduced testing with testthat
  • Minor debugging, see GitHub

Momocs 1.1.6 (GitHub + CRAN)

  • sfourier family implementation
  • new datasets: apodemus and mouse

Momocs 1.1.0 (GitHub + CRAN)

  • plot2.PCA deprecated due to ggplot2 2.2.0 breaking changes
  • Few minor changes that can be followed on GitHub commits

Momocs 1.0 (CRAN + GitHub)

  • Release on CRAN that replaces the now completely obsolete 0.2.6 (the one from the JSS paper.
  • It consists of the last version pushed to CRAN.

Momocs 0.9 (Github)

  • Started to routinely use GitHub (and NEWS)
  • a complete rewriting of the package, and the inclusion of new morphometrics approches (open outlines, configuration of landmarks, global shape descriptors).
  • New design with classes Out, Opn and Ldk to handle (closed) outlines, open outlines and configuration of landmarks. Coo becomes a "super class" encompassing the three others.
  • S4 -> S3 rewriting. Maybe less orthodox but much more easy to understand, code, extend which is probably the most required for Momocs at this step.
  • Renaming of functions/methods in a more consistent scheme
  • New/partial rewriting of multivariate methods: MANOVA, MANOVA_PW, LDA, KMEANS, CLUST.
  • Graphics have been refreshed: panel, stack, plot.PCA
  • New datasets: chaff, flowers, oak, olea, molars, shapes, wings,
  • General review of the helpfiles
  • Many issues fixed, see GitHub
  • Momocs speed dating: a tutorial as a vignette (see browseVignette("Momocs") is available

Reference manual

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install.packages("Momocs")

1.2.9 by Vincent Bonhomme, 10 months ago


https://github.com/MomX/Momocs/


Report a bug at https://github.com/MomX/Momocs/issues


Browse source code at https://github.com/cran/Momocs


Authors: Vincent Bonhomme [aut, cre] , Julien Claude [aut]


Documentation:   PDF Manual  


GPL-2 | GPL-3 license


Imports ape, dplyr, magrittr, graphics, geometry, geomorph, ggplot2, grDevices, jpeg, MASS, progress, RColorBrewer, rgeos, sp, utils

Suggests devtools, knitr, rmarkdown, testthat, covr, roxygen2


See at CRAN