| MPSEM-package | Modelling Phylogenetic Signals using Eigenvector Maps | 
| add.edge | MPSEM graph Manipulation Functions | 
| add.vertex | MPSEM graph Manipulation Functions | 
| as.data.frame.PEM | Class and Methods for Phylogenetic Eigenvector Maps (PEM) | 
| collapse.vertex | MPSEM graph Manipulation Functions | 
| dstGraph | Distance-Based Directed Graph | 
| EvolveOptimMarkovTree | Simulate the Evolution of a Quantitative Trait | 
| getAncGraphLocations | Phylogenetic Eigenvector Maps | 
| getGraphLocations | Phylogenetic Eigenvector Maps | 
| graph | Class and Method for Directed Graphs | 
| graph-class | Class and Method for Directed Graphs | 
| graph-functions | MPSEM graph Manipulation Functions | 
| InflMat | Phylogenetic Eigenvector Maps | 
| lm-utils | Linear Modelling Utility Functions | 
| lmforwardsequentialAICc | Linear Modelling Utility Functions | 
| lmforwardsequentialsidak | Linear Modelling Utility Functions | 
| Locations2PEMscores | Phylogenetic Eigenvector Maps | 
| OUvar | Simulate the Evolution of a Quantitative Trait | 
| PEM | Class and Methods for Phylogenetic Eigenvector Maps (PEM) | 
| PEM-class | Class and Methods for Phylogenetic Eigenvector Maps (PEM) | 
| PEM-functions | Phylogenetic Eigenvector Maps | 
| PEM.build | Phylogenetic Eigenvector Maps | 
| PEM.fitSimple | Phylogenetic Eigenvector Maps | 
| PEM.forcedSimple | Phylogenetic Eigenvector Maps | 
| PEM.updater | Phylogenetic Eigenvector Maps | 
| PEMvar | Simulate the Evolution of a Quantitative Trait | 
| PEMweights | Phylogenetic Eigenvector Maps | 
| Phylo2DirectedGraph | MPSEM graph Manipulation Functions | 
| pop.graph | MPSEM graph Manipulation Functions | 
| predict.PEM | Class and Methods for Phylogenetic Eigenvector Maps (PEM) | 
| print.graph | Class and Method for Directed Graphs | 
| print.PEM | Class and Methods for Phylogenetic Eigenvector Maps (PEM) | 
| rm.edge | MPSEM graph Manipulation Functions | 
| rm.vertex | MPSEM graph Manipulation Functions | 
| simulation | Simulate the Evolution of a Quantitative Trait | 
| trait | Simulate the Evolution of a Quantitative Trait | 
| trait-simulator | Simulate the Evolution of a Quantitative Trait | 
| TraitOUsimTree | Simulate the Evolution of a Quantitative Trait | 
| TraitVarGraphSim | Simulate the Evolution of a Quantitative Trait | 
| utils | Linear Modelling Utility Functions |