- CRAN release 2 (v.1.2) with the additional
`Claddis.ordination`

function.

*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!