Measuring Disparity


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Documentation for package ‘dispRity’ version 1.6.0

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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, 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