Man pages for Hackout3/saphy
Sequential Analysis of Phylogenies
| branchLengthMetrics | Produces a dataframe of tree branch length statistics |
| compute.distance.matrix | Computes a pairwise distance matrix |
| expand.distance.matrix | Updates a pre-existing distance matrix |
| imbalanceMetrics | Produces a dataframe of tree imbalance statistics |
| imbalanceThreshold | Produces a list of a confidence intervals given a tree... |
| pairwise.distance | Calculate pairwise distance between two sequences |
| permuteTrees | Produces a list of permuted trees with the same tip and... |
| plot.branch.lengths | Plots the average branch lengths over time |
| prunePermute | Produces a list of a list of sequentially growing trees given... |
| simulatetree | Simulate tree and sequences in two-population SIR-model |
| timeprune | Prune tree in time order |
| tiplength | Extracts the length of a tip from a tree |
