| MPSEM-package | Modeling Phylogenetic Signals using Eigenvector Maps |
| add.edge | Graph creation and manipulation functions |
| add.vertex | Graph creation and manipulation functions |
| as.data.frame.PEM | Class and methods for Phylogenetic Eigenvector Maps (PEM) |
| collapse.vertex | Graph creation and manipulation functions |
| EvolveOptimMarkovTree | Simulates the evolution of a quantitative trait. |
| getAncGraphLocations | Phylogenetic Eigenvector Map |
| getGraphLocations | Phylogenetic Eigenvector Map |
| graph-class | Graph class and methods |
| graph-functions | Graph creation and manipulation functions |
| lmforwardsequentialAICc | Linear modelling utility functions |
| lmforwardsequentialsidak | Linear modelling utility functions |
| Locations2PEMscores | Phylogenetic Eigenvector Map |
| MPSEM | Modeling Phylogenetic Signals using Eigenvector Maps |
| OUvar | Simulates the evolution of a quantitative trait. |
| PEM-class | Class and methods for Phylogenetic Eigenvector Maps (PEM) |
| PEM.build | Phylogenetic Eigenvector Map |
| PEM.fitSimple | Phylogenetic Eigenvector Map |
| PEM.forcedSimple | Phylogenetic Eigenvector Map |
| PEM.updater | Phylogenetic Eigenvector Map |
| PEMInfluence | Phylogenetic Eigenvector Map |
| PEMvar | Simulates the evolution of a quantitative trait. |
| PEMweights | Phylogenetic Eigenvector Map |
| Phylo2DirectedGraph | Graph creation and manipulation functions |
| pop.graph | Graph creation and manipulation functions |
| predict.PEM | Class and methods for Phylogenetic Eigenvector Maps (PEM) |
| print.graph | Graph class and methods |
| print.PEM | Class and methods for Phylogenetic Eigenvector Maps (PEM) |
| rm.edge | Graph creation and manipulation functions |
| rm.vertex | Graph creation and manipulation functions |
| trait-simulator | Simulates the evolution of a quantitative trait. |
| TraitOUsimTree | Simulates the evolution of a quantitative trait. |
| TraitVarGraphSim | Simulates the evolution of a quantitative trait. |