Measuring Disparity
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Documentation for package ‘dispRity’ version 1.7.0
Help Pages
| dispRity-package | Measuring Disparity in R |
-- A --
| add.tree | Add, get or remove tree |
| adonis.dispRity | adonis dispRity (from 'vegan::adonis2') |
| ancestral.dist | Disparity metrics |
| angles | Disparity metrics |
| apply.NA | Apply inapplicable characters to a matrix. |
| as.covar | as.covar |
| axis.covar | Utilities for a dispRity object with covariance matrices |
-- 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 |
| charadriiformes | Charadriiformes |
| 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 | Extracts or modify subsets from a 'dispRity' object. |
| convhull.surface | Disparity metrics |
| convhull.volume | Disparity metrics |
| covar.plot | covar.plot |
| covar.utilities | Utilities for a dispRity object with covariance matrices |
| 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 |
| disalignment | Disparity metrics |
| disparity | disparity |
| displacements | Disparity metrics |
| dispRity | Calculates disparity from a matrix. |
| dispRity.covar.projections | Covar projection analyses wrapper |
| dispRity.fast | Fast dispRity |
| 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 | Extract elements from a 'dispRity' object. |
-- F --
| fill.dispRity | Make and fill 'dispRity'. |
| 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.covar | Utilities for a dispRity object with covariance matrices |
| get.disparity | Extract elements from a 'dispRity' object. |
| get.matrix | Extract elements from a 'dispRity' object. |
| get.subsets | Extracts or modify subsets from a 'dispRity' object. |
| get.tree | Add, get or remove tree |
| group.dist | Disparity metrics |
-- M --
| make.dispRity | Make and fill 'dispRity'. |
| make.metric | Creating disparity metrics |
| match.tip.edge | Match tips edge vector |
| matrix.dispRity | Extract elements from a 'dispRity' object. |
| MCMCglmm.covars | MCMCglmm object utility functions |
| MCMCglmm.levels | MCMCglmm object utility functions |
| MCMCglmm.sample | MCMCglmm object utility functions |
| MCMCglmm.subsets | MCMCglmm.subsets |
| MCMCglmm.traits | MCMCglmm object utility functions |
| MCMCglmm.utilities | MCMCglmm object utility functions |
| 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 | Extracts or modify subsets from a 'dispRity' object. |
| 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.between | Disparity metrics |
| projections.tree | Disparity metrics |
-- Q --
| quantiles | Disparity metrics |
-- R --
| radius | Disparity metrics |
| random.circle | Random circle |
| randtest.dispRity | Random (permutation) test |
| randtest.dist | Randtest distance |
| 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 --
| sauron.plot | covar.plot |
| select.axes | Selects ordination axes |
| sim.morpho | Simulates morphological data. |
| size.subsets | Extracts or modify subsets from a 'dispRity' object. |
| 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 | Extracting the age of nodes and tips in a tree. |
-- V --
| variances | Disparity metrics |