*New*function:`multi.ace`

for performing fast ancestral character estimations on multiple matrices (based on`castor::asr_mk_model`

).*New*function:`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).*New*function:`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.- the
`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. *New*metric:`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)`

).*New*metric:`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.

- The
`dispRity`

package now depends on`R (>= 4.0.0)`

. - Many updates to the
`dispRity`

manual. - Many minor speed improvements across the package
- Simplified syntax for the internal
`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: **removed**option in`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`

.**removed**option in`plot.dispRity`

: the`ylim`

,`ylab`

,`xlab`

and`col`

options have now been removed. They are now handled through`...`

as normal generic`plot(...)`

arguments.**removed**option in`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)`

).**removed**option in`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.*New*option in`dtt.dispRity`

:`scale.time`

allowing to scale the time axis (like in`geiger::dtt`

) or not.- when plotting
`chrono.subsets`

`dispRity`

objects, the x label ticks are now rounded if possible (for nicer looking plots!). - when using automatic
`chrono.subsets`

time slices, the name of the time slices (their age) is now rounded for aesthetics.

- Updated all calls to the
`Claddis`

package to match version 0.6 (thanks to Graeme Lloyd for fixing this one!) - Updated
`Claddis.ordination`

function to be compatible with the new`ape`

version`5.4`

(thanks to Emmanuel Paradis for the pointing that out). - Fixed a bug in
`chrono.subsets`

where ladder trees with no tip branch lengths an`method = "continuous"`

option would get stuck in an infinite loop. - Fixed a bug in
`chrono.subsets`

where the`"*.split"`

methods would bug if the last slice is through a single edge.

*New*metric:`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).*New*metric:`deviations`

, a dimension level 2 metric that measures the deviation of each element from a hyperplane.- Completely rewritten
`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"`

). - all
`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.

- update
`reduce.matrix`

to work with`vegan::vegdist`

version 2.5-6 (thanks to Jari Oksanen for the fix). - updated class evaluations throughout the package for
`R`

version`4.0.0`

:`class(.) == *`

is now`is(., *)`

. - updated
`...`

argument bug PR#16223. - In
`make.metric`

the argument`...`

is now ignored if any`names(...)`

is`"tree"`

or`"phy"`

. - fixed bug in
`neighbours`

and`span.tree.length`

when feeding “distance” like metrics (thanks to Ashley Reaney for finding that one).

- greatly improved speed of
`chrono.subsets`

with`method = "continuous`

(now > 1000 times faster!). - minor warning message fix for
`plot.dispRity`

with time slices. - removed
`paleotree`

package dependency (though the links to this excellent package are still there!). - increased
`R`

version requirement to`3.5`

. `...`

in`summary.dispRity`

are now directly passed to`cent.tend`

(e.g.`na.rm = TRUE`

).- added some time improvements in several phylo functions based on the
`castor`

package. - updated all the package demo data to fit the new
`dispRity`

object architecture (see above). Note that this might effect the exact results of calculations using these demo datasets. - you can now specify the dimensions of the matrix to make a disparity metric in
`make.metric`

through the`data.dim`

option. - metrics passed in
`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.

*New*metric:`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).*New*metric:`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.).*New*metric:`quantiles`

, a dimension level 2 metric that measures the*n*th quantile range per axis (a good alternative to the`ranges`

function!).*New*metric:`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).*New*metric:`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).*Updated*metric:`span.tree.length`

now outputs the length of each edges (c.f. the sum of the length) and becomes a level 2 metric.- The
`chrono.subsets`

can now take`multiPhylo`

objects for slicing through multiple trees at once! *New*utility function:`reduce.matrix`

for optimising data overlap in a matrix with missing data.*New*utility function:`slide.nodes`

for sliding specific nodes on a tree.*New*utility function:`remove.zero.brlen`

for stochastically removing zero branch lengths on a tree (using the`slide.nodes`

function).**New argument**in`plot.dispRity`

: the`type`

argument can now be`"preview"`

to have a glimpse at two of the dimensions of the trait-space.- The
`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. - Added a “Other functionalities” section to the manual describing miscellaneous functions.

`centroids`

and`ancestral.dist`

functions can now take the`method`

option for`"euclidean"`

or`"manhattan"`

distances.- All functions methods selection have now been sped up using
`switch`

. - Error messages in
`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).- Updated all tests and functions to be compatible with R 3.6.
- Fixed bug in
`clean.data`

that did not output dropped tips correctly when applied on`multiPhylo`

objects. - Improved error messages in
`chrono.subsets`

for funky time slices/bins (e.g. with negative values). - Speed improvements for the
`time.slice`

function. - Better internal handling of distance matrices for the disparity metrics.
- Most functions handles
`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.- better internal handling of error messages.
`faster`

eigen value estimations in`ellipse.volume`

when the argument is left missing.- removed internal handling of the
`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.

*New*functions:`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).**New argument**in`boot.matrix`

:`prob`

for passing probabilities of sampling for specific elements.- S3
`print`

method for objects of class`"dtt"`

and`"dispRity"`

(from`dtt.dispRity`

).

- tydiversed most of the error messages.
`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).- Improved metric checking messages from
`make.metric`

when dealing with optional arguments. - Removed cascade of warnings triggered by
`plot.dispRity.dtt`

.

- Corrected
`char.diff`

to properly reflect the probability of different splits between characters (thanks to Abigail Pastore).

- CRAN release 1 with the additional
`Claddis.ordination`

function.

- Added default Cailliez correction to
`Claddis.ordination`

function (with`add = TRUE`

). - Improved test coverage.

- First CRAN release

- Registered
`C`

symbols properly. - Overall improvement for the
`S3`

methods. **Changed name**:`scale.dispRity`

is now`rescale.dispRity`

.**Changed name**:`merge.subsets`

is now`combine.subsets`

.**Changed name**:`time.subsets`

is now`chrono.subsets`

-`time.subsets`

can still be called as an alias for the same function.

- Minor bug fixes and typos in various error messages and in the manual.

- Removed
`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`

.*New*utility function:`extinction.subsets`

, to get the list to be passed to`test.dispRity`

for testing the effect of extinction.*New*test function:`dtt.dispRity`

, a wrapper for`geiger::dtt`

. This version is slower that`geiger::dtt`

but allows any univariate disparity metric!*New*test function:`adonis.dispRity`

, a wrapper for`vegan::adonis`

.*New*utility function:`crown.stem`

for separating a tree into crown and stem groups.*New*disparity metric:`span.tree.length`

the length of the minimum spanning tree.*New*disparity metric:`pairwise.dist`

: the element’s pairwise distances.*New*disparity metric:`radius`

: the radius of each dimensions.*New*disparity metric:`n.ball.volume`

: the*n*-dimensional sphere or ellipsoid volume.**New argument**in`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`

.

- Changed calls to
`stats::dist`

to`vegan::vegdist`

to allow more distances to be passed through`methods`

arguments. `slice.tree`

can now slice through a single edge.- Various minor speed improvements.

- Correct behaviour in
`tree.age`

to estimate ages for trees with fossils only.

**Change name**throughout the package,`subsample`

is now replaced by`subset`

(e.g.`time.subsamples`

is now renamed`time.subsets`

,`data$subsamples`

is now`data$subsets`

, etc…).**Changed argument**in`time.subsets`

,`model = "gradual"`

is now replaced by`model = "proximity"`

and`model = "punctuated"`

is now replaced by`model = "random"`

.

*New*disparity metric:`ancestral.distance`

to get the distance from taxa/nodes to their ancestors.*New*function:`random.circle`

for generating random circle coordinates (see example in`space.maker`

for creating doughnut spaces!).*New*function:`get.bin.ages`

for getting the geological timescale of a tree (based on`geoscale`

).

- Added a
`t0`

argument to`time.subsamples`

allowing to set the start age of the first subsample. - Allowing subsamples to contain less than three elements (up to 0!).

- Fixed fuzzy match issues in
`slice.tree`

.

- Entirely rewritten manual (in GitBook)!
*New*function:`Claddis.ordination`

and`geomorph.ordination`

for automatically ordinating data from`Claddis`

and`geomorph`

packages!*New*function:`char.diff`

for calculating character differences and associated plot function (`plot.char.diff`

)*New*utility function:`merge.subsamples`

for… merging subsamples.*New*utility function:`size.subsamples`

for getting the size of subsamples in a disparity object.*New*wrapping functions:`dispRity.through.time`

and`dispRity.per.group`

now runs easy default disparity analysis.

- Input ordinated matrices do not need to be of maximum size
`n*(n-1)`

. Bigger matrices now only trigger a warning. - Added
`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.

**Removed**`hyper.volume`

metric for dependencies reasons,**Removed**`parallel`

option from`boot.matrix`

(the new architecture is already super fast: <2sec for 5k taxa and 10k bootstraps!).**Changed name**:`series`

as a part of`dispRity`

objects is now changed to`subsamples`

throughout the whole package.**Changed name**:`time.series`

is now renamed`time.subsamples`

, if dates are provided and method is`discrete`

, this function doesn’t need a phylogeny any more.**Changed name**:`get.subsamples.dispRity`

is now renamed`get.subsamples`

.**Modified function**:`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.

- Complete change of the
`dispRity`

object architecture (see more here).

`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.

**Removed**`rm.last.axis`

argument in`boot.matrix`

. It is now replaced by`dimensions`

.**Changed argument**in`plot.dispRity`

,`type = "lines"`

is now replaced by`type = "line"`

.

*New*utility function:`merge.time.series`

for cleaning or merging time series,.*New*vignette:`dispRity-simulate_data`

on how to simulate morphological characters in`dispRity`

.*New*function:`sim.morpho`

generates morphological matrices.*New*function:`check.morpho`

for checking how “realistic” the simulate morphological matrices are.*New*utility functions:`get.contrast.matrix`

and`apply.inapplicable`

functions for morphological matrices.

- Minor updates for the graphical functions.

*New*utility functions:`pair.plot`

,`scale.dispRity`

and`sort.dispRity`

.*New*function:`space.maker`

for creating some multidimensional spaces!*New*disparity metrics:`convhull.surface`

,`convhull.volume`

and`hyper.volume`

.*New*disparity test`null.test`

.*New*`plot.dispRity`

arguments:`density`

for controlling the polygons density and`add`

for adding plots.

- Many updates to the functions manual and vignettes.
- Some algorithm are now greatly improved for speed.
- Disparity can now be calculated as a distribution (i.e.
`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.

- Minor functions corrections for specific optional arguments combinations.

**Removed**`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.

*New*function:`get.dispRity`

for subsampling dispRity objects.*New*function:`extract.dispRity`

for extracting disparity results.*New*function:`test.dispRity`

for applying tests to`dispRity`

objects.*New*function:`make.metric`

for helping creating your very own disparity metric.*New*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`

).- Many improved functions manuals and examples!
- Improved vignettes:
*dispRity palaeo demo*a quick demo aimed more for palaeobiologist.*dispRity ecology demo*a quick demo aimed more for ecologists.*dispRity manual*for people that want to know the package in details.*dispRity metrics*for explaining how the disparity metric implementation works.

`plot.dispRity`

options improved (rarefaction + default).`cust.series`

can now intake multiple factors columns.- Added example for ecological data.
`boot.matrix`

,`dispRity`

,`summary`

and`plot`

now also include observed values.`plot`

now has an`observed`

option to plot the observed disparity.

- Fixed many error/warning messages.

- Changed
`taxa`

to`elements`

. `plot`

option`diversity`

has been renamed`elements`

.

- First release!