# Measuring Disparity

## Documentation for package ‘dispRity’ version 1.6.0

- DESCRIPTION file.

## 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, get or remove tree
adonis.dispRity | adonis dispRity (from 'vegan::adonis')
ancestral.dist | Disparity metrics
angles | Disparity metrics
apply.NA | Apply inapplicable characters to a matrix.

## -- 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 | Bhattacharrya Coefficient
boot.matrix | Bootstraps and rarefies data.

## -- C --

centroids | Disparity metrics
char.diff | Character differences
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 | Combines or cleans subsets.
convhull.surface | Disparity metrics
convhull.volume | Disparity metrics
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
disparity | disparity
displacements | Disparity metrics
dispRity | Calculates disparity from a matrix.
dispRity.metric | Disparity metrics
dispRity.per.group | Disparity in different groups.
dispRity.through.time | Disparity through time.
dtt.dispRity | dtt dispRity (from 'geiger::dtt')

## -- E --

edge.length.tree | Disparity metrics
ellipse.volume | Disparity metrics
extinction.subsets | Getting the time subsets from at and after an extinction event
extract.dispRity | Extracting disparity values.

## -- F --

fetch.matrix | Fetching a matrix from a 'dispRity' object.
fill.dispRity | Fills a 'dispRity' object.
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.dispRity, | Extracts subsets from a dispRity object.
get.subsets | Extracts subsets from a dispRity object.
get.subsets.dispRity | Extracts subsets from a dispRity object.
get.tree | Add, get or remove tree
group.dist | Disparity metrics

## -- M --

make.dispRity | Creates a 'dispRity' object.
make.metric | Creating disparity metrics
matrix.dispRity | Fetching a matrix from a 'dispRity' object.
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 | Number of subsets.
neighbours | Disparity metrics
null.test | Testing a null hypothesis on multidimensional data.

## -- P --

pair.plot | Plots pairwise comparisons
pairwise.dist | Disparity metrics
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.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.tree | Add, get or remove tree
remove.zero.brlen | Remove zero branch length
rescale.dispRity | Rescaling and centering disparity results.

## -- S --

sim.morpho | Simulates morphological data.
size.subsets | Size subsets.
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 | Calculating the age of nodes and tips in a tree.

## -- V --

variances | Disparity metrics