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 morphometrics analyses and other morphometrics approaches should be easy to plug in, or develop from, on top of this canvas.
github.com/MomX/Momocs
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.grindr
rationale and use.andnow
and andnow_method
class tells you what to do with this object, and which classes are supported by this function/method.coo_*
methods: coo_range
, coo_range_enlarge
, coo_diffrange
, coo_template_relatively
. The latter will prepare ground for proper size handling, notably for morphospaces.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
.pal_manual
, pal_qual_solarized
and pal_seq_grey
.dispatch_fac
is now behind all fac
argumentsfgProcrustes
now accepts listsefourier
with default norm=TRUE
now messages about how wrong it may bedplyr::data_frame
everywhere pertinentis.*
aliases for is_*
methodsclassify
for a whilecalibrate_*(..., method)
have been renamed to calibrate_*_method
. See ?calibrate_reconstructions
and friends.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 ownplot.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 schemeis_clockwise
is deprecated, now coo_likely_clockwise
; same for is_anticlockwise
now coo_likely_anticlockwise
. Better reflect the incertainty and gather with coo_*
friendsrename
(handled by select
anyway)table
(poor shortcut anyway and avoid this boring startup message)stack2
and panel2
before their rewritingas_Out
, that should have been efourier_i.OutCoe
anyway.panel.OutCoe
method that was additionnaly the only Coe
method. May be back in further versions..
, eg .is.error
(try Momocs:::. + <Tab>
for a complete list).function_foo
renamed to .function_foo
): .coo_angle_edge1
, .vecs_param
, .refactor
NEWS
is now a decent NEWS filereshape2
, plyr
dependenciesRColorBrewer
, progress
::
. A nice side effect is to remove annoying messages when attaching Momocs. Another is the removal of most importFrom
.subset
is now subsetize
...LDA
when retain=1
(#e7704eb)options("verbose")
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.nsfishes
and charring
to comply R CMD CHECK.coo_slice
now suports ldk
argumentMANOVA_PW
now returns p-valuesnsfishes
testthat
sfourier
family implementationapodemus
and mouse
plot2.PCA
deprecated due to ggplot2 2.2.0 breaking changes0.2.6
(the one from the JSS paper.NEWS
)Out
, Opn
and Ldk
to handle
(closed) outlines, open outlines and configuration of landmarks. Coo
becomes a "super class" encompassing the three others.MANOVA
, MANOVA_PW
, LDA
, KMEANS
, CLUST
.panel
, stack
, plot.PCA
chaff
, flowers
, oak
, olea
, molars
, shapes
, wings
,browseVignette("Momocs")
is available