Phylogenetic Ridge Regression Methods for Comparative Studies
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Documentation for package ‘RRphylo’ version 3.0.0
Help Pages
| RRphylo-package | Phylogenetic Ridge Regression Methods for Comparative Studies |
| addShift | Graphical representation of search.shift results |
| angle.matrix | Ontogenetic shape vectors analysis |
| colorbar | Draw colorbar on a plot |
| compRates | Comparing average absolute rates between clades |
| conv.map | Mapping morphological convergence on 3D surfaces |
| cutPhylo | Cut the phylogeny at a given age or node |
| DataApes | Example dataset |
| DataCetaceans | Example dataset |
| DataFelids | Example dataset |
| DataOrnithodirans | Example dataset |
| DataSimians | Example dataset |
| DataUng | Example dataset |
| distNodes | Finding distance between nodes and tips |
| evo.dir | Phylogenetic vector analysis of phenotypic change |
| fix.poly | Resolving polytomies to non-zero length branches |
| getGenus | Taxonomic inspection of the tree at the genus level |
| getMommy | Upward tip or node to root path |
| getSis | Get sister clade |
| lollipoPlot | Lollipop charts |
| makeFossil | Make fossil species on a phylogeny |
| makeL | Matrix of branch lengths along root-to-tip paths |
| makeL1 | Matrix of branch lengths along a root-to-node path |
| move.lineage | Move tips or clades |
| namesCompare | Checking species names for misspelling and synonyms |
| node.paths | Tracing nodes along paths |
| overfitPGLS | Testing PGLS_fossil overfit |
| overfitRR | Testing RRphylo overfit |
| overfitSC | Testing search.conv overfit |
| overfitSS | Testing search.shift overfit |
| overfitST | Testing search.trend overfit |
| PGLS_fossil | Phylogenetic Generalized Least Square with phylogenies including fossils |
| phyloclust | Test for phylogenetic clustering |
| plotConv | Graphical representation of search.conv results |
| plotRates | Plot RRphylo rates at a specified node |
| plotRR | Plot the RRphylo output onto the phylogenetic tree |
| plotShift | Graphical representation of search.shift results |
| plotTrend | Graphical representation of search.trend results |
| random.evolvability.test | Randomization test for phylogenetic structuring in evolvability |
| rate.map | Mapping rate and direction of phenotypic change on 3D surfaces. |
| rateHistory | Computing historical rates |
| resampleTree | Altering phylogenetic trees |
| rescaleRR | Rescaling phylogenetic trees |
| retrieve.angles | Extracting a user-specified subset of the evo.dir results |
| RRphylo | Evolutionary rates computation along phylogenies |
| RRphylo-defunct | Defunct functions in Package RRphylo |
| RRphylo-deprecated | Deprecated functions in Package RRphylo |
| scaleTree | Phylogenetic tree calibration |
| search.conv | Searching for morphological convergence among species and clades |
| search.shift | Locating shifts in phenotypic evolutionary rates |
| search.trend | Searching for evolutionary trends in phenotypes and rates |
| setBM | Producing simulated phenotypes with trends |
| sig2BM | Brownian Motion rate computation |
| sizedsubtree | Find a node subtending to a clade of desired size |
| StableTraitsR | Run StableTraits from within R |
| swap.phylo | Defunct functions in Package RRphylo |
| swapONE | Create alternative phylogenies from a given tree |
| tips | Get descending tips |
| tree.merger | Fast construction of phylogenetic trees |
| treeCompare | Visualize the difference between phylogenetic trees |
| treedataMatch | Cross-reference tree and data |