⚠️There's a newer version (1.8) of this package.Take me there.

dispRity (version 1.7.0)

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.

Copy Link

Version

Install

install.packages('dispRity')

Monthly Downloads

730

Version

1.7.0

License

GPL-3 | file LICENSE

Issues

Pull Requests

Stars

Forks

Last Published

August 9th, 2022

Functions in dispRity (1.7.0)

as.covar

as.covar
BeckLee_disparity

BeckLee_disparity
MCMCglmm.utilities

MCMCglmm object utility functions
BeckLee

Beck and Lee 2014 datasets
add.tree

Add, get or remove tree
apply.NA

Apply inapplicable characters to a matrix.
adonis.dispRity

adonis dispRity (from vegan::adonis2)
Claddis.ordination

Imports data from Claddis
MCMCglmm.subsets

MCMCglmm.subsets
bhatt.coeff

Bhattacharrya Coefficient
custom.subsets

Separating data into custom subsets.
boot.matrix

Bootstraps and rarefies data.
crown.stem

Separates stem and crown species
covar.utilities

Utilities for a dispRity object with covariance matrices
covar.plot

covar.plot
clean.data

Cleaning phylogenetic data
chrono.subsets

Separating data in chronological subsets.
charadriiformes

Charadriiformes
check.morpho

Check a morphological matrix consistency levels.
char.diff

Character differences
dispRity

Calculates disparity from a matrix.
demo_data

Demo datasets
extinction.subsets

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

Imports data from geomorph
dispRity-package

Measuring Disparity in R
get.subsets

Extracts or modify subsets from a dispRity object.
get.matrix

Extract elements from a dispRity object.
dispRity.through.time

Disparity through time.
match.tip.edge

Match tips edge vector
dispRity.per.group

Disparity in different groups.
model.test

Model Test
dispRity.fast

Fast dispRity
dispRity.covar.projections

Covar projection analyses wrapper
make.metric

Creating disparity metrics
make.dispRity

Make and fill dispRity.
dtt.dispRity

dtt dispRity (from geiger::dtt)
disparity

disparity
dispRity.metric

Disparity metrics
multi.ace

Ancestral states estimations with multiple trees
randtest.dispRity

Random (permutation) test
random.circle

Random circle
null.test

Testing a null hypothesis on multidimensional data.
pair.plot

Plots pairwise comparisons
slide.nodes

Stretching a tree
plot.char.diff

Plots character differences
sort.dispRity

Sorting or ordering a dispRity object.
get.contrast.matrix

Generates a contrast matrix.
model.test.sim

Simulate Model Test
model.test.wrapper

Model test wrapper
get.bin.ages

Get time bins ages
reduce.matrix

Reduce a matrix
randtest.dist

Randtest distance
space.maker

Creating multidimensional spaces
summary.dispRity

dispRity object summary
plot.dispRity

dispRity object plotting
print.dispRity

Prints a dispRity object.
select.axes

Selects ordination axes
rescale.dispRity

Rescaling and centering disparity results.
remove.zero.brlen

Remove zero branch length
tree.age

Extracting the age of nodes and tips in a tree.
reduce.space

Reduce space
test.dispRity

Testing disparity hypotheses
sim.morpho

Simulates morphological data.
slice.tree

Time slicing a tree.
test.metric

Test disparity metric