Momocs 1.4.1
- Removed rgeos dependency so that Momocs can resurect on CRAN
Momocs 1.4.0
- Fixed several minor bugs, mostly with plotting.
- coo_slide duplicated the initial point in some cases. Now
fixed.
- coo_likely_clockwise (and friends) now uses complex numbers and is
much more robust.
- removed some annoying messages.
- slice(…, 1) now returns a matrix for $coe, not a numeric
([,,drop=FALSE])
- I’m currently out of academia and I’m looking for funding to develop
MomX. I plan to give some of my time in 2022 and after but if you have
any ideas, either directly or through hiring me for consulting, ring my
bell!
Momocs 1.3.3
plot_PCA and plot_LDA did not consistently
work within eg pdf(). Thanks to Bill fof pointing this.
(214)
- coo_shearx/y did not return the Coo. Fixed.
Momocs 1.3.2
- Turned remaining
return for return() to
please R CMD check
as_df now uses tibble verbs
everywhere
- printing Coo is faster now at the price of sampling 100 shapes on
which to calculate the mean number of coordinates and their sd.
- Removed the (quite) annoying startup message. I will not have time
for MomX until 2021 anyway
Momocs 1.3.1
- Changed all
dplyr::as_data_frame for
tibble::as_tibble
Momocs 1.3.0
- This version will be the last major one released on CRAN.
Momocs is now retired and will no longer be maintained. See
momx.github.io. As of April 15, 2020 it satisifies all available testing
approaches.
- new multivariate method:
KMEDOIDS on top of
cluster::pam. Added a plot_silhouette to go
with this friend. Now depends cluster.
- new multivariate method:
NMDS on top of
vegan::metaMDS; use plot_NMDS to plot it and
vegan::stressplot for a Shepard plot. Now depends
vegan.
- new multivariate method:
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.
- Consequently,
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)
- new handling method
rm_missing to deal with missing
data in $fac
boxplot methods on Coe have been refreshed
hist methods on Coe deprecated
coo_plot no longer a method and gains a
cex.first.point argument
- new method:
coo_scalars that gather all scalar
descriptors of shape
TraCoe class properly data_frameize fac
when build from TraCoe()
CLUST methods have been rewrote and now wraps around
dendextend.
- Consequently released
ape dependency.
- all morphometrics methods now accepts
lists 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 list
- morphospace on LDAs are (finally) back, yet still quite
experimental.
coo_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
previous
- new vignettes:
Momocs_coo and Momocs_FAQ;
others refreshed.
morphospace_position and chullfilled in
plot_PCA now properly working
verify replaces validate to avoid conflict
with shiny::validate (for Momecs)
subsetize now exported (again)
def_ldk gains a close and
points argument
- no more printing of Coo errors that was due to some forgotten
data.frame rather than data_frame
- all
Coo builders gain a .data.frame
method, notably to ease compatibility with Momit
as_df now returns more useful data_frame
everywhere and gain a retain argument
- deprecated
coo_angle_edge1 and friends, now in
coo_angle_edges see 1.2.9.
- fixed minor bugs (see GitHub history of commits)
Momocs 1.2.9
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 of 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::tibble() 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
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