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dispRity (version 1.5.0)

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 (Guillerme (2018) ). The package also provides functions for looking at disparity in a serial way (e.g. disparity through time - Guillerme and Cooper (2018) ) 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

1.5.0

License

GPL-3 | file LICENSE

Issues

3

Pull Requests

1

Stars

26

Forks

12

Maintainer

Thomas Guillerme

Last Published

September 25th, 2020

Functions in dispRity (1.5.0)

adonis.dispRity

adonis dispRity (from vegan::adonis)
bhatt.coeff

Bhattacharrya Coefficient
chrono.subsets

Separating data in chronological subsets.
boot.matrix

Bootstraps and rarefies data.
check.morpho

Check a morphological matrix consistency levels.
Claddis.ordination

Imports data from Claddis
apply.NA

Apply inapplicable characters to a matrix.
BeckLee_disparity

BeckLee_disparity
BeckLee

Beck and Lee 2014 datasets
char.diff

Character differences
dispRity-package

Measuring Disparity in R
combine.subsets

Combines or cleans subsets.
clean.data

Cleaning phylogenetic data
crown.stem

Separates stem and crown species
custom.subsets

Separating data into custom subsets.
get.bin.ages

Get time bins ages
dispRity.per.group

Disparity in different groups.
get.contrast.matrix

Generates a contrast matrix.
dispRity.metric

Disparity metrics
make.dispRity

Creates a dispRity object.
get.subsets

Extracts subsets from a dispRity object.
dispRity

Calculates disparity from a matrix.
dispRity.through.time

Disparity through time.
disparity

disparity
dtt.dispRity

dtt dispRity (from geiger::dtt)
extract.dispRity

Extracting disparity values.
pair.plot

Plots pairwise comparisons
get.ancestors

Get ancestors
fill.dispRity

Fills a dispRity object.
geomorph.ordination

Imports data from geomorph
matrix.dispRity

Fetching a matrix from a dispRity object.
slice.tree

Time slicing a tree.
model.test.wrapper

Model test wrapper
make.metric

Creating disparity metrics
size.subsets

Size subsets.
multi.ace

Ancestral states estimations with multiple trees
nodes.coordinates

Nodes coordinates
model.test.sim

Simulate Model Test
extinction.subsets

Getting the time subsets from at and after an extinction event
model.test

Model Test
summary.dispRity

dispRity object summary
space.maker

Creating multidimensional spaces
reduce.space

Reduce space
remove.zero.brlen

Remove zero branch length
reduce.matrix

Reduce a matrix
slide.nodes

Stretching a tree
random.circle

Random circle
sort.dispRity

Sorting or ordering a dispRity object.
plot.dispRity

dispRity object plotting
print.dispRity

Prints a dispRity object.
tree.age

Calculating the age of nodes and tips in a tree.
plot.char.diff

Plots character differences
null.test

Testing a null hypothesis on multidimensional data.
sim.morpho

Simulates morphological data.
rescale.dispRity

Rescaling and centering disparity results.
test.dispRity

Testing disparity hypotheses
test.metric

Test disparity metric