plot_PCA
and plot_LDA
did not consistently work within eg pdf()
. Thanks to Bill fof pointing this. (214)return
for return()
to please R CMD checkas_df
now uses tibble
verbs everywheredplyr::as_data_frame
for tibble::as_tibble
KMEDOIDS
on top of cluster::pam
. Added a plot_silhouette
to go with this friend. Now depends cluster
.NMDS
on top of vegan::metaMDS
; use plot_NMDS
to plot it and vegan::stressplot
for a Shepard plot. Now depends vegan
.MDS
on top of cmdscale
; use plot_MDS
to plot it.mshapes
is now MSHAPES
to stick with other capitalized "multivariate" methods. mshapes
now just announces its future deprecation.MSHAPES
now just returns data_frame of PCs or LDs when used on PCA
or LDA
objects.plot_MSHAPES
is the new method for plotting it. Works on lists and on the result of MSHAPES
.plot_CV
has been refreshed, and is better now at plotting either small or very big matrices.fac_dispatcher
supports NULL
which eases a lot multivariate plots (notably Momecs side)rm_missing
to deal with missing data in $fac
boxplot
methods on Coe have been refreshedhist
methods on Coe deprecatedcoo_plot
no longer a method and gains a cex.first.point
argumentcoo_scalars
that gather all scalar descriptors of shapeTraCoe
class properly data_frame
ize fac when build from TraCoe()
CLUST
methods have been rewrote and now wraps around dendextend
.ape
dependency.list
s which is more elegant when working with chop
+combine
LDA
methods have been partly rewritten and now handles constant and collinear variables by dropping them and storing them in the returned listcoo_untiltx
now removes (residual) rotational biases after coo_slidedirection
and should be used after it.plot_LDA
now on. Pretty much the same as plot_PCA
(which was expected yet nice)..layerize_LDA
as an internal to prepare the previousMomocs_coo
and Momocs_FAQ
; others refreshed.morphospace_position
and chullfilled
in plot_PCA
now properly workingverify
replaces validate
to avoid conflict with shiny::validate
(for Momecs)subsetize
now exported (again)def_ldk
gains a close
and points
argumentdata.frame
rather than data_frame
Coo
builders gain a .data.frame
method, notably to ease compatibility with Momitas_df
now returns more useful data_frame
everywhere and gain a retain
argumentcoo_angle_edge1
and friends, now in coo_angle_edges
see 1.2.9.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::tibble()
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_*
friendstable
(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
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