Measuring Disparity

Documentation for package ‘dispRity’ version 1.8

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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
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 --

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, 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
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 --

Disparity metrics