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multi.ace to be more modular and handle both
continuous and/or discrete characters. Changes include a change
in argument name from castor.options to the
generic options.args (the options can be provided the same
way as before though); and a change in default
arguments for models which can now be left missing
(previously was "ER") and applies "ER" and
"BM" for respectively discrete and continuous characters by
default.dist.helper
now allows to save distance matrices in the cache, saving a lot of RAM
and speeding up calculations. You can use the helper using
dispRity(..., dist.helper = my_distance_function) or
dispRity(..., dist.helper = my_distance_matrix).dispRity, custom.subsets and
chrono.subsets option: these three functions can now
use dist.data = TRUE to specify that the input data is a
distance matrix (and handle it accordingly).boot.by
to specify whether bootstrap the rows (previous behaviour), the columns
or both (for distance matrices).set.root.time to add a
root time to a tree ("phylo"), list of trees
("multiPhylo") or dispRity object with
trees.remove.dispRity to
cleanly remove specific parts of a "dispRity" object.count.neighbours to count the
number of neighbours for each elements within a certain radius (thanks
to Rob MacDonald for the suggestion).custom.subsets can now take a logical vector for the
group argument.custom.subsets now recycles node names when using a
tree to create clade groups.plot functions doing scatter plot now centers them
without changing the scale of both axes.tree.age:
the number of digits output by tree.age is now changed from
3 to 4 by default.reduce.space are now
drawn from the input data distribution which speeds up the function
significantly.match.tip.edges can now just work for colouring edges
connecting a vector of tips.boot.matrix.make.metric (now uses the
largest requestable subset rather than the whole data for testing).scale.dispRity now correctly ignores NAs
when scaling.multi.ace now correctly handles invariant characters
when looking for NAs.dispRity objects with a $covar component
are not interpreted as bootstrapped by boot.matrix
anymore.dimensions argument from boot.matrix
is now removed: it has been redundant with the dimensions
argument in the dispRity since v0.3!custom.subsets,
chrono.subsets, boot.matrix and
dispRity. This change is not affecting the user level
appart from now allowing to bypass some error messages (thanks to Mario
Corio for that obvious suggestion).name.subsets for
directly accessing the subsets names of a dispRity object
(basically doing names(my_dispRity$subsets)).MCMCglmm.variance for
calculating the variance for specific terms in a "MCMCglmm"
model.pgls.dispRity to run
PGLS test on a dispRity object with a level-2 metric and a
tree (using excellent phylolm
algorithm). The new test comes with its own S3 print, summary and plot
functions if the input dispRity data contains multiple
trees or multiple matrices (running and handling the output of multiple
phylolm).get.tree utility function to
get the trees in each subsets (thanks to Jack Hadfield for this
suggestion and help with implementation).roundness to measure the roundness
of a variance-covariance matrix.custom.subsets, chrono.subsets,
boot.matrix and dispRity functions: the
tree, FADLAD, prob and
dimensions arguments is now NULL by default
(instead of missing).projections function. The defaults are now
scale = TRUE, centre = FALSE (previously
TRUE) and abs = FALSE (previously
TRUE). The default arguments for
dispRity.covar.projections remain unchanged though
(scale = TRUE, centre = TRUE,
abs = TRUE).randtest.dispRity function’s subsets
argument now can take a list of arguments of subsets to compare is
data is a dispRity object. The call message
has also been updated to be much more verbose and clear of what has been
tested.projections.*
functions for speed.test.metric now also adds the slope coefficient if the
option model is used.plot/summary on test.metric
results are now more easy to interpret.reduce.space has now 25 times less chances to be stuck
on a local optimum.match.tip.edges now also works on nodes and on
"multiPhylo" objects and has a added an option
use.parsimony (default is TRUE) to propagate
the matching down the tree (i.e. if two nodes have the same unique
ancestor and variable value, the ancestor is consider to have that
variable value as well).covar.plot.clean.data can now also handle a list of
"phylo" objects as tree input (i.e. it does
not need to be specifically classed as "multiPhylo").spptest to GET.space.maker can now generate specific row names and be
replicated to generate a bunch of spaces (via the new optional arguments
elements.names and replicates
respectively).add.tree utility function now has an optional
argument to override any existing trees (replace = TRUE) or
not (replace = FALSE; which remains the default previous
behaviour).print.dispRity now recognises and highlights simulated
data from the treats
package.NA management for S3
functions.covar.plot
making the figures more aesthetic.remove.zero.brlen now also removes negative branch
lengths and works on "multiPhylo" objects (thanks to Thomas
Johnson for this suggestion).fill.dispRity has now an extra argument
check to toggle the data checking on and off (more for
developers).multi.ace is now described in details in the
manual.slice.tree has now a keep.all.ancestors
option to do exactly that.test.metric.get.disparity now correctly concatenates one
dimensional results into a "numeric" (rather than a
"matrix").make.metric now internally handles covar
object correctly (i.e. as distance matrices).ellipse.volume has been changed to
ellipsoid.volume to more accurately reflect what it is
measuring.rescale.dispRity has been changed to
scale.dispRity and correctly registered as a S3
method.randtest.dist has been changed to
distance.randtest to avoid conflict with
*.dist S3 methods.select.axes for selecting
and analysing the number of axes required to contain an arbitrary amount
of variance.randtest.dist for
measuring the distance between the observed statistic and a specific
quantile of the simulated statistic (thanks to Frane Babarovic for the
inspiration).dispRity objects can now contain covariance matrices as
a $covar object. The covar part can be
directly used for some specific metrics (usually
my_metric.covar) and are handled by the
dispRity function (and plot,
summary, etc…) in a specific way. $covar
contains a list of two elements VCV the variance covariance
matrix and loc the coordinates of the centre of the
VCV in space (can be left empty). $covar
matrices are effectively treated as bootstraps.covar.plot for plotting the
covar content of dispRity objects (this is
separated from plot.dispRity because of the many different
options).MCMCglmm.subsets is a function
that allows to convert a MCMCglmm object into a
dispRity object.projections.between a between
group metric for applying the projections metric between
the major covariance axis of two matrices.disalignment: the (dis)alignment
of a group compared to another one (i.e. the rejection from group B’s
centre on the group A’s major axis). a between group metric for applying
the projections metric between the major covariance axis of
two matrices.dispRity.fast function for the fastest disparity
calculations at the expanses of pretty much everything this package
does. This is a really situational function.MCMCglmm objects: MCMCglmm.traits for
extracting the number of traits, MCMCglmm.levels for
extracting the level names, MCMCglmm.sample for sampling
posterior IDs and MCMCglmm.covars for extracting
variance-covariance matricesdispRity objects
with covar matrices: get.covar to extract the
VCV matrices (or a subsample of them); axes.covar to
extract the major axes of the VCV matrices and as.covar to
transform dispRity metric function to use a covar
object.match.tip.edge for
matching tip labels as factors/characters/integer to tree edges.dispRity.covar.projections for covariance projections
analyses (with its associated S3 sub-class).charadriiformes, a
data.frame and a phylo object of 359
Charadriiformes species (gulls, plovers and sandpipers) from Cooney et al
2017 along with a MCMCglmm model with each clade as a
random term.... in all the
dispRity plotting functions can now be targeted to a
specific plotting element. When multiple elements are plot by default
(e.g. lines, legend, points, etc…) it is now possible to pass a specific
... argument to the specific plotted element using the
syntax <element>.<argument>
(e.g. points.col = "blue" will only apply the argument
col = "blue" to the points).projections and projections.tree metrics: the
default "position" output is now scaled, centred and
absolute (see ?projections for details).custom.subsets and
select.axes. This can create some minor user level changes
namely: warning messages for empty subsets now correctly mentions
“subsets” (rather than subsamples); groups with incorrect elements are
now always flagged as errors (rather than just ignored). The changes at
the developer level is that the logic is now made smoother and exported
in custom.subsets_fun.R.function.index.csv list (and updater) to help
developers find internal functions locations easily.test.dispRity to only occur when using a test of class
"htest".custom.subsets can now group elements using a
"factor" vector.MCMCglmm objects, dispRity objects
in general, dispRity objects with subsets, ect…). It should
now be much easier to find these sometimes overlooked functions.dispRity manual,
including a section on covar and
between.groups specific analyses.test.metric (using the new
official dispRity.fast function).data$disparity now don’t
have dimension names anymore (significantly reducing the size of
disparity objects). However, you can always retrieve the
dimensions names using get.disparity.ellipse.volume, you
can now directly specify one of the following methods:
"pca" to calculate the eigen values from the ordinated
matrix; "eigen" to directly do an eigen decomposition of
the matrix (new); or "axes" to directly measure the axes
(new); or directly provide the eigen values.check.subsets now handles the
checking of "dispRity" objects much faster making most
functions relying on it slightly faster (this function is typically not
called more than once per function).adonis.dispRity to the newest
vegan::adonis2 code (thanks to Jari Oksanen for the
notification).geiger for
dtt.dispRity to avoid package maintenance errors. This
leads to no changes at the user level and geiger::dtt is
still acknowledged in the manual.tree.age function’s manual now makes it clear it does
not estimate tree ages.plot.dispRity(..., type = "preview"),
group’s colour attribution and plotting is now made so that the groups
larger groups are plotted in the background and the smaller in the
foreground.NAs are now better handled in internal checking
functions.dispRity when selecting a specific
number of dimensions (old warning artefact).plot.dispRity when using
type = "preview" on bootstrapped data and for
type = "box" when the subsets to plot are from different
sizes (now plots all the data correctly).chrono.subsets with
"continuous" method a FADLAD data containing
only node values (now correctly taken into account; thanks to Peng-Wei
Li for noticing it) and when using chrono.subsets with
"gradual.*" models on empty subsets.standardGeneric functions are now correctly interpreted
as functions throughout the package.observed = TRUE is now used as the
default).test.metric plots with
save.steps options with more than two types of shifts.null.test which is now correctly
managing the number of dimensions inherited from dispRity
objects (thanks to Alex Slavenko for spotting this one and the two
above).is(data, c("array", "matrix"))
to is.array(data) for R 4.1.2.matrix.dispRity and extract.dispRity are
now deprecated. You should now use respectively get.matrix
and get.disparity instead (the arguments don’t change
though).projections that allows to measure
elements’ projection on an arbitrary axis (or their distance from this
axis with measure = "distance").projections.tree that allows to
measure elements’ projection on axis between elements of a given
tree.edge.length.tree the edge length
from each element given a tree (with the option
to.root = TRUE/FALSE to measure the edge length from the
element to the root of the tree (default = TRUE) or the nearest ancestor
(FALSE).test.metric with
save.steps and then visualise them with
plot.dispRity along side the disparity metric test
results.n.subsets to directly get
the number of subsets in a dispRity object.randtest.dispRity that
is a wrapper for ade4::randtest applied to
dispRity objects (not dissimilar from
null.test).dispRity objects now have a reserved $tree
component that contain any number of trees attached to the data. This
allows any function to use the reserved argument name tree
to extract directly the relevant tree from the dispRity
object, for functions like chrono.subsets or metrics like
ancestral.dist! To help manipulate the tree
component of the dispRity object, you can now use the new
utility functions add.tree, get.tree and
remove.tree.4.0 back to
3.6 following Joseph Brown’s
issue and fix.reduce.space "random" algorithm now
outputs a named logical vector (like the other algorithms!)."only" text when printing
dispRity objects that contains “only” matrices (even though
that can be 10k matrices!).summary.dispRity for
"dispRity" "randtest" objects to output
“ready-to-publish” result tables.estimation.details argument to
multi.ace allowing to also return specific arguments from
the ancestral states estimation (thanks to Armin Elsler for the
suggestion).inc.nodes to clean.data
whether to check if the nodes in the tree match the labels in the
matrix.make.metric with the option silent = TRUE
now outputs a list of info rather than only the level of the metric. You
can reproduce the old behaviour using
make.metric(..., silent = TRUE)$type).plot using preview when the
given argument pch did not match the number of groups (the
different pch arguments are now used correctly).ancestral.dist metric. The
function is now much faster and much easier to use (due to the new
dispRity object structure). The options
nodes.coords has been removed and the option
full is now changed by to.root. If you still
really want to use the older version of ancestral.dist
using ancestral.dist.deprecated though.dimensions option throughout the package (e.g. in
the dispRity function) can now also be a vector of
dimensions to take into consideration (e.g. c(1,2,5)).chrono.subsets now automatically detects the number of
digits to round for the internal time slicing functions (thanks to Mario Corio for finding this
one).test.metric plots that now display
correctly the “top” and “bottom” changes for the “position” shift.test.metric plots that now display the R^2
values correctly.tree.age when the tree tips/node labels
vector is longer than the actual number of tips/nodes in the tree.ancestral.dist (see NEW
FEATURES above).node.coordinates function (no replacement; you
must use a package version prior 1.5.10 to use this function).get.ancestors function (no replacement; you
must use a package version prior 1.5.10 to use this function).multi.ace for performing fast
ancestral character estimations on multiple matrices (based on
castor::asr_mk_model).reduce.space, a function to
modify trait spaces imported from the moms shiny
app. This function comes with a new reduction algorithm: the
“evenness” algorithm for flattening the curve (thanks to Gavin Thomas for the
suggestion).test.metric (and associated
plot, print and summary
functions), to apply the reduce.space function on a
specific space and metric to test whether a metric is picking up
specific changes in trait space.dispRity function can now use
"between.groups" metrics to calculate disparity between
groups rather than within groups. The make.metric function
is now modified to allow detection of metrics that can be applied
between groups.group.dist, a dimension level 1
metric for between groups that measures the distance between two groups.
By default, this is the minimum distance but the function takes the
probs argument allowing the distance to be between, says,
the 95% CI (probs = c(0.025, 0.975))) or between the
centroids (probs = c(0.5)).point.dist, a dimension level 2
metric for between groups that measures the distance between the rows in
matrix to a point in matrix2. That point is
the centroid by default but the point argument can take any
function.dispRity package now depends on
R (>= 4.0.0).dispRity manual.plot.dispRity S3
methods (for a potential ggpRity?). These changes should
not be apparent at the user level but see the two removed options
below:plot.dispRity: the
chrono.subsets option
(TRUE/FALSE) has now been removed. The
time-slicing-ness is now automatically detected or can be specified by
the user normally through xlab.plot.dispRity: the
ylim, ylab, xlab and
col options have now been removed. They are now handled
through ... as normal generic plot(...)
arguments.plot.dispRity: the
elements.pch option has now been removed. The
pch of the plotted elements can now be passed like other
options directly to elements
(e.g. elements = list(pch = 15)).plot.dispRity: the
dimensions, matrix, nclass and
coeff options have now been removed. Any options for dual
class plots (randtest, dtt,
model.test, type = "preview" etc…) are now
handled through the generic specific.args argument.dtt.dispRity:
scale.time allowing to scale the time axis (like in
geiger::dtt) or not.chrono.subsets dispRity
objects, the x label ticks are now rounded if possible (for nicer
looking plots!).chrono.subsets time slices, the
name of the time slices (their age) is now rounded for aesthetics.Claddis package to match
version 0.6 (thanks to Graeme
Lloyd for fixing this
one!)Claddis.ordination function to be compatible
with the new ape version 5.4 (thanks to Emmanuel Paradis for the
pointing that out).chrono.subsets where ladder trees with
no tip branch lengths an method = "continuous" option would
get stuck in an infinite loop.chrono.subsets where the
"*.split" methods would bug if the last slice is through a
single edge.dispRity where some 1D matrices could
loose their class for certain metrics.angles, a dimension level 2 metric
that measures the angle of the main axis of each dimension in a matrix
(in slopes, angles or degrees).deviations, a dimension level 2
metric that measures the deviation of each element from a
hyperplane.char.diff function. It now uses a
way faster bitwise comparison architecture and comes with different
distance methods as well as modular optional arguments on how to treat
various special tokens ("?", "-",
"&", etc.). This also allows many more distance methods
(now including "hamming", "manhattan",
"comparable", "euclidean",
"maximum" and "mord").dispRity functions can now intake a single
"matrix" or a "list" of matrices with the same
row names and dimensions. The disparity is then calculated directly on
all the matrices and summarised as before through
summary.dispRity. This option can be used to add
uncertainty to disparity calculations. For example in
chrono.subsets you can now provide a list of trees and a
list of associated ancestral state estimates; or for
custom.subsets you can provide a list of matrices with
different values representing different estimations of the traits.reduce.matrix to work with
vegan::vegdist version 2.5-6 (thanks to Jari Oksanen for
the fix).R
version 4.0.0: class(.) == * is now
is(., *).... argument bug PR#16223.make.metric the argument ... is now
ignored if any names(...) is "tree" or
"phy".neighbours and
span.tree.length when feeding “distance” like metrics
(thanks to Ashley Reaney for finding that one).chrono.subsets with
method = "continuous (now > 1000 times faster!).plot.dispRity with time
slices.paleotree package dependency (though the links
to this excellent package are still there!).R version requirement to
3.5.... in summary.dispRity are now directly
passed to cent.tend (e.g. na.rm = TRUE).castor package.dispRity object architecture (see above). Note that this
might effect the exact results of calculations using these demo
datasets.make.metric through the data.dim
option.dispRity are now tested using the
input data dimensions.chrono.subsets with multiple trees now stretches the
root edges length to match the oldest tree.displacements, a dimension level 2
metric that measures the position of elements in space (i.e. their
distance from the centre relative to their distance to their
centroid).neighbours, a dimension level 2
metric that measures the distance from an element to its neighbour
(e.g. the nearest neighbour, the furthest, the median, etc.).quantiles, a dimension level 2
metric that measures the nth quantile range per axis (a good
alternative to the ranges function!).func.eve, a dimension level 1
metric that measures the functional evenness (i.e. the spread along the
minimum spanning tree; from Villéger et al. 2008).func.div, a dimension level 1
metric that measures the functional divergence (i.e. the ratio of
deviation from the centroid; from Villéger et al. 2008).span.tree.length now outputs
the length of each edges (c.f. the sum of the length) and becomes a
level 2 metric.chrono.subsets can now take multiPhylo
objects for slicing through multiple trees at once!reduce.matrix for
optimising data overlap in a matrix with missing data.slide.nodes for sliding
specific nodes on a tree.remove.zero.brlen for
stochastically removing zero branch lengths on a tree (using the
slide.nodes function).plot.dispRity: the
type argument can now be "preview" to have a
glimpse at two of the dimensions of the trait-space.Claddis.ordination can now directly take a matrix’s
path as input (leaving the function to read and transform the matrix
into Claddis format. The function can thus now also be used
to convert matrices into Claddis format.centroids and ancestral.dist functions can
now take the method option for "euclidean" or
"manhattan" distances.switch.dispRity are more verbose when input
the wrong metric(s).scree option in space.maker does not
require to sum up to one anymore.cor.matrix option in space.maker does not
require to have a valid Choleski decomposition (an approximation is used
instead).clean.data that did not output dropped
tips correctly when applied on multiPhylo objects.chrono.subsets for funky
time slices/bins (e.g. with negative values).time.slice function.NA as na.rm or
na.omit.dispRity objects now contain a metric argument (if a
metric was applied). This argument can now be recycled by the
appropriate functions (e.g. in null.test).plot.dispRity argument observed can now
take a list of arguments to be passed points().boot.matrix now makes a error warning message when
bootstrapping distance matrices (as suggested by Dave Bapst!).geomorph.ordination can now be used to simply create
coordinates matrices (no ordination!) with ordinate = FALSE
argument.faster eigen value estimations in
ellipse.volume when the argument is left missing.Claddis.ordination
function. This function now uses the brand new version of the
Claddis package on CRAN (0.3).plot.dispRity with option "box" now
correctly display plot ranges when disparity is an observed
distribution.test.dispRity handles errors messages more efficiently
when disparity is an observed distribution.summary.dispRity handles non-bootstrapped distributions
display properly.geomorph.ordination now converts
"character" vectors into "factors".adonis.dispRity now properly handles complex formulas
(with arithmetic signs).... are now properly handled by internal metric testing
functions for more accurate error messages.char.diff names are now properly protected in the
C implementation to comply with new rcheck
requirements.model.test,
model.test.sim and model.test.wrapper for
fitting models of disparity evolution through time (with associated
manuals, vignettes and S3 methods! Thanks to Mark Puttick).boot.matrix:
prob for passing probabilities of sampling for specific
elements.print method for objects of class "dtt"
and "dispRity" (from dtt.dispRity).dtt.dispRity now allows to specify the alternative
hypothesis (if nsim > 0).ellipse.volume can now take an explicit eigen value
vector (the eigen values are still automatically estimated correctly for
PCO and MDS).make.metric when
dealing with optional arguments.plot.dispRity.dtt.char.diff to properly reflect the probability
of different splits between characters (thanks to Abigail Pastore).Claddis.ordination
function.Claddis.ordination
function (with add = TRUE).C symbols properly.S3 methods.scale.dispRity is now
rescale.dispRity.merge.subsets is now
combine.subsets.time.subsets is now
chrono.subsets - time.subsets can still be
called as an alias for the same function.Claddis.ordination function to comply with the
CRAN requirement (this function is still live in the GitHub version
1.1).custom.subset can now automatically create clade-based
groups if a phylo object is passed to
group.extinction.subsets, to
get the list to be passed to test.dispRity for testing the
effect of extinction.dtt.dispRity, a wrapper for
geiger::dtt.
This version is slower that geiger::dtt but allows any
univariate disparity metric!adonis.dispRity, a wrapper
for vegan::adonis.crown.stem for
separating a tree into crown and stem groups.span.tree.length the
length of the minimum spanning tree.pairwise.dist: the
element’s pairwise distances.radius: the radius of
each dimensions.n.ball.volume: the
n-dimensional sphere or ellipsoid volume.time.subsets,
model = "equal.split" and
model = "gradual.split" that retain the probability of
being either the descendant or the ancestor. This probability is passed
to boot.matrix .stats::dist to
vegan::vegdist to allow more distances to be passed through
methods arguments.slice.tree can now slice through a single edge.tree.age to estimate ages for
trees with fossils only.subsample is now replaced by subset
(e.g. time.subsamples is now renamed
time.subsets, data$subsamples is now
data$subsets, etc…).time.subsets,
model = "gradual" is now replaced by
model = "proximity" and model = "punctuated"
is now replaced by model = "random".ancestral.distance to
get the distance from taxa/nodes to their ancestors.random.circle for generating
random circle coordinates (see example in space.maker for
creating doughnut spaces!).get.bin.ages for getting the
geological timescale of a tree (based on geoscale).t0 argument to time.subsamples
allowing to set the start age of the first subsample.slice.tree.Claddis.ordination and
geomorph.ordination for automatically ordinating data from
Claddis and geomorph packages!char.diff for calculating
character differences and associated plot function
(plot.char.diff)merge.subsamples for…
merging subsamples.size.subsamples for
getting the size of subsamples in a disparity object.dispRity.through.time
and dispRity.per.group now runs easy default disparity
analysis.n*(n-1). Bigger matrices now only trigger a warning.dimensions optional argument to
dispRity to overwrite the number of dimensions generated by
boot.matrix.variances, ranges and
centroids are now simplified for speed. The optional
arguments for data cleaning are now passed to
make.metric.space.maker now allows to approximate the dimensions
variance distribution with the scree option.hyper.volume metric for
dependencies reasons,parallel option from
boot.matrix (the new architecture is already super fast:
<2sec for 5k taxa and 10k bootstraps!).series as a part of
dispRity objects is now changed to subsamples
throughout the whole package.time.series is now
renamed time.subsamples, if dates are provided and method
is discrete, this function doesn’t need a phylogeny any
more.get.subsamples.dispRity
is now renamed get.subsamples.cust.series is now
renamed custom.subsamples (to avoid confusion with
custard.subsamples!). Its factor argument as
been changed to groups and can now take a simple list.dispRity object
architecture.sim.morpho can now use model = "mixed" for
using both HKY-binary and Mk in characters
simulation.dispRity object utilities are now all grouped under the
?dispRity.utilities manual with appropriate S3
methods.rm.last.axis argument in
boot.matrix. It is now replaced by
dimensions.plot.dispRity,
type = "lines" is now replaced by
type = "line".merge.time.series for
cleaning or merging time series,.dispRity-simulate_data on how to
simulate morphological characters in dispRity.sim.morpho generates
morphological matrices.check.morpho for checking how
“realistic” the simulate morphological matrices are.get.contrast.matrix and
apply.inapplicable functions for morphological
matrices.pair.plot,
scale.dispRity and sort.dispRity.space.maker for creating some
multidimensional spaces!convhull.surface,
convhull.volume and hyper.volume.null.test.plot.dispRity arguments:
density for controlling the polygons density and
add for adding plots.dispRity, test.dispRity,
plot.dispRity, and summary.dispRity can now
intake one or more distribution rather than just one or more single
values of disparity; whether the data is bootstrapped or not).dispRity can now intake dispRity objects
with level 2 disparity metrics.boot.matrix and dispRity can now run in
parallel.centroids disparity metric can now use a
centroid argument for fixing the centroid point value.variances and ranges disparity metrics can
now intake a k.root argument for scaling the results.type_discrete argument in
plot.dispRity and type argument can now be:
continuous disparity curves.box for real boxplots.lines for the distribution vertical lines.polygon for the distribution boxes.get.dispRity for subsampling
dispRity objects.extract.dispRity for extracting
disparity results.test.dispRity for applying tests
to dispRity objects.make.metric for helping creating
your very own disparity metric.hyper.volume for measuring the
morphospace hyper-ellipsoid volume.metric argument from dispRity can now
intake up two three functions (see dispRity.metric and
make.metric).plot.dispRity options improved (rarefaction +
default).cust.series can now intake multiple factors
columns.boot.matrix, dispRity,
summary and plot now also include observed
values.plot now has an observed option to plot
the observed disparity.taxa to elements.plot option diversity has been renamed
elements.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.