Index | tree.merger tool | tree.merger basics | Merging trees: input tree and data | Merging trees: Attaching individual tips to the backbone tree | Merging trees: Attaching clades to the backbone tree | Building a new tree | Guided examples | scaleTree tool | Guided examples | move.lineage tool | cutPhylo tool | fix.poly tool | References

Index | swapONE | Swapping species positions | Shifting node ages | Guided examples | resampleTree | References

Index | overfit- functions basics | overfitRR | Guided examples | overfitSS | overfitST | overfitSC | overfitPGLS

Index | plotting RRphylo outputs onto the tree | plotting RRphylo rates | plotting search.trend results | plotting search.shift results | plotting search.conv results

Index | RRphylo Basics | RRphylo phylogenetic ridge regression | Accounting for the effect of a covariate | Multiple regression framework | Setting values at internal nodes | Guided examples | References

Index | search.conv basics | Morphological convergence between clades | Morphological convergence within/between categories | Guided examples | References

Index | search.trend basics | Temporal trends on the entire tree | Temporal trends at clade level | Multivariate data and multiple RRphylo output | Guided examples | References

Index | search.shift basics | Clade condition | Sparse condition | Guided examples | References