Man pages for motmot.2.0
Models of Trait Macroevolution on Trees
| addFossilToPhy | add a fossil to an interior branch of a time-scaled phylogeny |
| allCladeMembers | allCladeMembers (internal function) |
| ancState | Extimate ancestral state (internal function) |
| anolis.data | Anolis phenotype 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... |
| contemporaryPhy | prune tree and data to lineages present in a time bin in the... |
| dropTipPartial | Drop tips from a phylogenetic tree while preserving deleted... |
| 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 |
| name.check | Name check (internal function) |
| node.descendents | Identify nodes and tips descended from a node (internal... |
| nodeTimes | Get times for nodes and tips |
| optim.likRatePhylo | Maximum likelihood rate estimation for traits and phylogenies |
| phyloCovar | Calculation of Brownian (co)variance using independent... |
| phyloMean | Calculation of phylogenetically corrected mean. |
| phyloVar | Calculation of Brownian variance. |
| pic.motmot | Phylogenetically independent contrasts (internal) |
| plotPhylo.motmot | Tree plotting for rates Plots trees with colours based on... |
| RatePhylo.allCI | Confidence intervals for rate parameters |
| RatePhylo.CI | Confidence intervals for rate parameters |
| removeNonBin | remove species occuring before time in the past (internal... |
| sampleHiddenSp | Sample hidden speciation events along branches of a tree... |
| sliceTree | Slice tree (internal function) |
| sortTraitData | Sort data and remove missing entries for tree and trait data |
| timeSliceSummary | Identify shifts in the rate of trait diversification through... |
| timeTravelPhy | timeTravelPhy (internal function) |
| traitData.plot | plot a univariate continuous trait data on a phylogeny |
| traitMedusaSummary | Identify shifts in the rate of trait diversification |
| transformPhylo | Phylogenetic tree transformations |
| transformPhylo.ll | Log-likelhood for models of trait evolution. |
| transformPhylo.MCMC | Bayesian MCMC for models of trait evolution |
| transformPhylo.ML | Maximum likelihood for models of trait evoluion |
| transformPhylo.sim | Phylogenetic tree transformations |
| transformRateMatrix | Conversion among data and phylogeny objects |
