![[R logo]](../../../doc/html/logo.jpg){kind=logo}
![[Up]](../../../doc/html/left.jpg){kind=small}
![[Top]](../../../doc/html/up.jpg){kind=small}
| motmot-package | Models of trait macroevolution on trees |
| anolis.data | Anolis data |
| anolis.tree | Anolis phylogeny |
| as.rateData | Conversion among data and phylogeny objects |
| as.rateMatrix | Conversion among data and phylogeny objects |
| cladeIdentity | Identify branches (including tips) descended from a node (internal function). |
| fairProportions | Calculate fair proportions phylogenetic diversity metric |
| likRatePhylo | Log-likelihood rate estimation for traits and phylogenies |
| likTraitPhylo | Log-likelihood rate estimation for traits and phylogenies |
| make.anc | Create design matrix (internal function) |
| make.likRatePhylo | Internal function |
| ML.RatePhylo | Maximum likelihood rate estimation for traits and phylogenies |
| motmot | Models of trait macroevolution on trees |
| node.descendents | Identify nodes and tips descended from a node (internal function). |
| optim.likRatePhylo | Maximum likelihood rate estimation for traits and phylogenies |
| phyloCovar | Calculation of Brownian (co)variance using independent contrasts. |
| phyloMean | Calculation of phylogenetically corrected mean. |
| phyloVar | Calculation of Brownian variance. |
| pic.motmot | Phylogenetically independent contrasts (internal) |
| plotPhylo.motmot | Tree plotting for rates |
| RatePhylo.allCI | Confidence intervals for rate parameters |
| RatePhylo.CI | Confidence intervals for rate parameters |
| traitMedusaSummary | Identify shifts in the rate of trait diversification |
| transformPhylo | Phylogenetic tree transformations |
| transformPhylo.ll | Log-likelhood for models of trait evoluion. |
| transformPhylo.ML | Maximum likelhood for models of trait evoluion. |
| transformPhylo.sim | Simulate trait data |
| transformRateMatrix | Conversion among data and phylogeny objects |