# Measuring Disparity

## Documentation for package ‘dispRity’ version 1.9

- DESCRIPTION file
- Package NEWS

## Help Pages

A B C D E F G M N P Q R S T V

dispRity-package | Measuring Disparity in R

## -- A --

add.tree | Add, remove or get trees (or subtrees)
adonis.dispRity | adonis dispRity (from 'vegan::adonis2')
ancestral.dist | Disparity metrics
angles | Disparity metrics
apply.NA | Apply inapplicable characters to a matrix.
as.covar | as.covar
axis.covar | Utilities for a dispRity object with covariance matrices

## -- B --

BeckLee | Beck and Lee 2014 datasets
BeckLee_ages | Beck and Lee 2014 datasets
BeckLee_disparity | BeckLee_disparity
BeckLee_mat50 | Beck and Lee 2014 datasets
BeckLee_mat99 | Beck and Lee 2014 datasets
BeckLee_tree | Beck and Lee 2014 datasets
between.groups.fun | Disparity metrics
bhatt.coeff | Bhattacharyya Coefficient
boot.matrix | Bootstraps and rarefies data.

## -- C --

centroids | Disparity metrics
char.diff | Character differences
charadriiformes | Charadriiformes
check.morpho | Check a morphological matrix consistency levels.
chrono.subsets | Separating data in chronological subsets.
Claddis.ordination | Imports data from Claddis
clean.data | Cleaning phylogenetic data
combine.subsets | Extracts or modify subsets from a 'dispRity' object.
convhull.surface | Disparity metrics
convhull.volume | Disparity metrics
count.neighbours | Disparity metrics
covar.plot | covar.plot
covar.utilities | Utilities for a dispRity object with covariance matrices
crown.stem | Separates stem and crown species
cust.series | Separating data into custom subsets.
cust.subsets | Separating data into custom subsets.
custom.series | Separating data into custom subsets.
custom.subsets | Separating data into custom subsets.

## -- D --

demo_data | Demo datasets
deviations | Disparity metrics
diagonal | Disparity metrics
dimension.level1.fun | Disparity metrics
dimension.level2.fun | Disparity metrics
dimension.level3.fun | Disparity metrics
disalignment | Disparity metrics
disparity | disparity
displacements | Disparity metrics
dispRity | Calculates disparity from a matrix.
dispRity.covar.projections | Covar projection analyses wrapper
dispRity.fast | Fast dispRity
dispRity.metric | Disparity metrics
dispRity.per.group | Disparity in different groups.
dispRity.through.time | Disparity through time.
distance.randtest | Randtest distance
dtt.dispRity | dtt dispRity (from 'geiger::dtt')

## -- E --

edge.length.tree | Disparity metrics
ellipse.volume | Disparity metrics
ellipsoid.volume | Disparity metrics
extinction.subsets | Getting the time subsets before and after an extinction event
extract.dispRity | Extract elements from a 'dispRity' object.

## -- F --

fill.dispRity | Make and fill 'dispRity'.
func.div | Disparity metrics
func.eve | Disparity metrics

## -- G --

geomorph.ordination | Imports data from geomorph
get.bin.ages | Get time bins ages
get.contrast.matrix | Generates a contrast matrix.
get.covar | Utilities for a dispRity object with covariance matrices
get.disparity | Extract elements from a 'dispRity' object.
get.matrix | Extract elements from a 'dispRity' object.
get.subsets | Extracts or modify subsets from a 'dispRity' object.
get.tree | Add, remove or get trees (or subtrees)
group.dist | Disparity metrics

## -- M --

make.dispRity | Make and fill 'dispRity'.
make.metric | Creating disparity metrics
match.tip.edge | Match tips or nodes edge vector
matrix.dispRity | Extract elements from a 'dispRity' object.
MCMCglmm.covars | MCMCglmm object utility functions
MCMCglmm.levels | MCMCglmm object utility functions
MCMCglmm.sample | MCMCglmm object utility functions
MCMCglmm.subsets | MCMCglmm.subsets
MCMCglmm.traits | MCMCglmm object utility functions
MCMCglmm.utilities | MCMCglmm object utility functions
MCMCglmm.variance | MCMCglmm object utility functions
mode.val | Disparity metrics
model.test | Model Test
model.test.sim | Simulate Model Test
model.test.wrapper | Model test wrapper
multi.ace | Ancestral states estimations with multiple trees

## -- N --

n.ball.volume | Disparity metrics
n.subsets | Extracts or modify subsets from a 'dispRity' object.
name.subsets | Extracts or modify subsets from a 'dispRity' object.
neighbours | Disparity metrics
null.test | Testing a null hypothesis on multidimensional data.

## -- P --

pair.plot | Plots pairwise comparisons
pairwise.dist | Disparity metrics
pgls.dispRity | phylolm dispRity (from 'phylolm::phylolm')
plot.char.diff | Plots character differences
plot.dispRity | dispRity object plotting
point.dist | Disparity metrics
print.dispRity | Prints a 'dispRity' object.
projections | Disparity metrics
projections.between | Disparity metrics
projections.tree | Disparity metrics

## -- Q --

quantiles | Disparity metrics

## -- R --

radius | Disparity metrics
random.circle | Random circle
randtest.dispRity | Random (permutation) test
ranges | Disparity metrics
reduce.matrix | Reduce a matrix
reduce.space | Reduce space
remove.dispRity | Make and fill 'dispRity'.
remove.tree | Add, remove or get trees (or subtrees)
remove.zero.brlen | Remove zero branch length
rescale.dispRity | Rescaling and centering disparity results.
roundness | Disparity metrics

## -- S --

sauron.plot | covar.plot
scale.dispRity | Rescaling and centering disparity results.
select.axes | Selects ordination axes
set.root.time | Adds root time to a tree
sim.morpho | Simulates morphological data.
size.subsets | Extracts or modify subsets from a 'dispRity' object.
slice.tree | Time slicing a tree.
slide.nodes | Stretching a tree
sort.dispRity | Sorting or ordering a 'dispRity' object.
space.maker | Creating multidimensional spaces
span.tree.length | Disparity metrics
summary.dispRity | dispRity object summary

## -- T --

test.dispRity | Testing disparity hypotheses
test.metric | Test disparity metric
time.series | Separating data in chronological subsets.
time.subsets | Separating data in chronological subsets.
tree.age | Extracting the age of nodes and tips in a tree.

## -- V --

variances | Disparity metrics