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dispRity (version 1.8)

Measuring Disparity

Description

A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.

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Install

install.packages('dispRity')

Monthly Downloads

914

Version

1.8

License

GPL-3 | file LICENSE

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Maintainer

Thomas Guillerme

Last Published

December 11th, 2023

Functions in dispRity (1.8)

charadriiformes

Charadriiformes
boot.matrix

Bootstraps and rarefies data.
crown.stem

Separates stem and crown species
check.morpho

Check a morphological matrix consistency levels.
char.diff

Character differences
chrono.subsets

Separating data in chronological subsets.
covar.plot

covar.plot
covar.utilities

Utilities for a dispRity object with covariance matrices
custom.subsets

Separating data into custom subsets.
clean.data

Cleaning phylogenetic data
dispRity.metric

Disparity metrics
distance.randtest

Randtest distance
dispRity.fast

Fast dispRity
dispRity.per.group

Disparity in different groups.
dispRity.through.time

Disparity through time.
demo_data

Demo datasets
dispRity.covar.projections

Covar projection analyses wrapper
dispRity-package

Measuring Disparity in R
dispRity

Calculates disparity from a matrix.
disparity

disparity
match.tip.edge

Match tips or nodes edge vector
get.matrix

Extract elements from a dispRity object.
make.metric

Creating disparity metrics
get.contrast.matrix

Generates a contrast matrix.
extinction.subsets

Getting the time subsets before and after an extinction event
geomorph.ordination

Imports data from geomorph
get.bin.ages

Get time bins ages
make.dispRity

Make and fill dispRity.
dtt.dispRity

dtt dispRity (from geiger::dtt)
get.subsets

Extracts or modify subsets from a dispRity object.
null.test

Testing a null hypothesis on multidimensional data.
pgls.dispRity

phylolm dispRity (from phylolm::phylolm)
plot.dispRity

dispRity object plotting
print.dispRity

Prints a dispRity object.
pair.plot

Plots pairwise comparisons
multi.ace

Ancestral states estimations with multiple trees
model.test.wrapper

Model test wrapper
model.test.sim

Simulate Model Test
random.circle

Random circle
remove.zero.brlen

Remove zero branch length
model.test

Model Test
reduce.matrix

Reduce a matrix
sim.morpho

Simulates morphological data.
select.axes

Selects ordination axes
reduce.space

Reduce space
plot.char.diff

Plots character differences
randtest.dispRity

Random (permutation) test
slice.tree

Time slicing a tree.
scale.dispRity

Rescaling and centering disparity results.
test.dispRity

Testing disparity hypotheses
slide.nodes

Stretching a tree
summary.dispRity

dispRity object summary
tree.age

Extracting the age of nodes and tips in a tree.
test.metric

Test disparity metric
space.maker

Creating multidimensional spaces
sort.dispRity

Sorting or ordering a dispRity object.
bhatt.coeff

Bhattacharyya Coefficient
as.covar

as.covar
Claddis.ordination

Imports data from Claddis
MCMCglmm.utilities

MCMCglmm object utility functions
add.tree

Add, remove or get trees (or subtrees)
apply.NA

Apply inapplicable characters to a matrix.
adonis.dispRity

adonis dispRity (from vegan::adonis2)
BeckLee

Beck and Lee 2014 datasets
BeckLee_disparity

BeckLee_disparity
MCMCglmm.subsets

MCMCglmm.subsets