Package: dispRity 1.9

Thomas Guillerme

dispRity: Measuring Disparity

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.

Authors:Thomas Guillerme [aut, cre, cph], Mark Puttick [aut, cph], Jack Hatfield [aut, cph]

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dispRity.pdf |dispRity.html✨
dispRity/json (API)
NEWS

# Install 'dispRity' in R:
install.packages('dispRity', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/tguillerme/disprity/issues

Datasets:

On CRAN:

disparityecologymultidimensionalitypalaeobiology

8.56 score 25 stars 1 packages 202 scripts 973 downloads 6 mentions 108 exports 93 dependencies

Last updated 2 days agofrom:dd044e1ca4. Checks:OK: 1 WARNING: 8. Indexed: no.

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Doc / VignettesOKDec 20 2024
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Exports:add.treeadonis.dispRityancestral.distanglesapply.NAas.covaraxis.covarbhatt.coeffboot.matrixcentroidschar.diffcheck.morphochrono.subsetsCladdis.ordinationclean.datacombine.subsetsconvhull.surfaceconvhull.volumecount.neighbourscovar.plotcrown.stemcustom.subsetsdeviationsdiagonaldimension.level1.fundimension.level2.fundimension.level3.fundisalignmentdisplacementsdispRitydispRity.covar.projectionsdispRity.fastdispRity.per.groupdispRity.through.timedistance.randtestdtt.dispRityedge.length.treeellipse.volumeellipsoid.volumeextinction.subsetsfill.dispRityfunc.divfunc.evegeomorph.ordinationget.bin.agesget.contrast.matrixget.covarget.disparityget.matrixget.subsetsget.treegroup.distmake.dispRitymake.metricmatch.tip.edgeMCMCglmm.covarsMCMCglmm.levelsMCMCglmm.sampleMCMCglmm.subsetsMCMCglmm.traitsMCMCglmm.variancemode.valmodel.testmodel.test.simmodel.test.wrappermulti.acen.ball.volumen.subsetsname.subsetsneighboursnull.testpair.plotpairwise.distpgls.dispRityplot.char.diffplot.dispRitypoint.distprint.dispRityprojectionsprojections.betweenprojections.treequantilesradiusrandom.circlerandtest.dispRityrangesreduce.matrixreduce.spaceremove.dispRityremove.treeremove.zero.brlenrescale.dispRityroundnessscale.dispRityselect.axesset.root.timesim.morphosize.subsetsslice.treeslide.nodessort.dispRityspace.makerspan.tree.lengthsummary.dispRitytest.dispRitytest.metrictree.agevariances

Dependencies:abindade4apecastorCladdisclicliprclusterclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdigestdoParallelellipseexpmfansifarverforeachfuturefuture.applygenericsgeometrygeoscaleGETggplot2globalsgluegmpgridExtragtableigraphisobanditeratorsjsonlitelabelinglatticelifecyclelinproglistenvlpSolvemagicmagrittrmapsMASSmathjaxrMatrixmgcvmnormtmulticoolmunsellnaturalsortnlmenumDerivoptimParallelparallellypartitionspbapplypermutephangornphyclustphylolmphytoolspillarpixmappkgconfigpolynomquadprogR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppProgressRdpackrlangRSpectrascalesscatterplot3dsetsspstraptibbleutf8vctrsveganviridisLitewithrzoo

Readme and manuals

Help Manual

Help pageTopics
Measuring Disparity in RdispRity-package
Add, remove or get trees (or subtrees)add.tree get.tree remove.tree
adonis dispRity (from 'vegan::adonis2')adonis.dispRity
Apply inapplicable characters to a matrix.apply.NA
as.covaras.covar
Beck and Lee 2014 datasetsBeckLee BeckLee_ages BeckLee_mat50 BeckLee_mat99 BeckLee_tree
BeckLee_disparityBeckLee_disparity
Bhattacharyya Coefficientbhatt.coeff
Bootstraps and rarefies data.boot.matrix
Character differenceschar.diff
Charadriiformescharadriiformes
Check a morphological matrix consistency levels.check.morpho
Separating data in chronological subsets.chrono.subsets time.series time.subsets
Imports data from CladdisCladdis.ordination
Cleaning phylogenetic dataclean.data
covar.plotcovar.plot sauron.plot
Utilities for a dispRity object with covariance matricesaxis.covar covar.utilities get.covar
Separates stem and crown speciescrown.stem
Separating data into custom subsets.cust.series cust.subsets custom.series custom.subsets
Demo datasetsdemo_data
disparitydisparity
Calculates disparity from a matrix.dispRity
Covar projection analyses wrapperdispRity.covar.projections
Fast dispRitydispRity.fast
Disparity metricsancestral.dist angles between.groups.fun centroids convhull.surface convhull.volume count.neighbours deviations diagonal dimension.level1.fun dimension.level2.fun dimension.level3.fun disalignment displacements dispRity.metric edge.length.tree ellipse.volume ellipsoid.volume func.div func.eve group.dist mode.val n.ball.volume neighbours pairwise.dist point.dist projections projections.between projections.tree quantiles radius ranges roundness span.tree.length variances
Disparity in different groups.dispRity.per.group
Disparity through time.dispRity.through.time
Randtest distancedistance.randtest
dtt dispRity (from 'geiger::dtt')dtt.dispRity
Getting the time subsets before and after an extinction eventextinction.subsets
Imports data from geomorphgeomorph.ordination
Get time bins agesget.bin.ages
Generates a contrast matrix.get.contrast.matrix
Extract elements from a 'dispRity' object.extract.dispRity get.disparity get.matrix matrix.dispRity
Extracts or modify subsets from a 'dispRity' object.combine.subsets get.subsets n.subsets name.subsets size.subsets
Make and fill 'dispRity'.fill.dispRity make.dispRity remove.dispRity
Creating disparity metricsmake.metric
Match tips or nodes edge vectormatch.tip.edge
MCMCglmm.subsetsMCMCglmm.subsets
MCMCglmm object utility functionsMCMCglmm.covars MCMCglmm.levels MCMCglmm.sample MCMCglmm.traits MCMCglmm.utilities MCMCglmm.variance
Model Testmodel.test
Simulate Model Testmodel.test.sim
Model test wrappermodel.test.wrapper
Ancestral states estimations with multiple treesmulti.ace
Testing a null hypothesis on multidimensional data.null.test
Plots pairwise comparisonspair.plot
phylolm dispRity (from 'phylolm::phylolm')pgls.dispRity
Plots character differencesplot.char.diff
dispRity object plottingplot.dispRity
Prints a 'dispRity' object.print.dispRity
Random circlerandom.circle
Random (permutation) testrandtest.dispRity
Reduce a matrixreduce.matrix
Reduce spacereduce.space
Remove zero branch lengthremove.zero.brlen
Rescaling and centering disparity results.rescale.dispRity scale.dispRity
Selects ordination axesselect.axes
Adds root time to a treeset.root.time
Simulates morphological data.sim.morpho
Time slicing a tree.slice.tree
Stretching a treeslide.nodes
Sorting or ordering a 'dispRity' object.sort.dispRity
Creating multidimensional spacesspace.maker
dispRity object summarysummary.dispRity
Testing disparity hypothesestest.dispRity
Test disparity metrictest.metric
Extracting the age of nodes and tips in a tree.tree.age