| kernel.dist* |
Kaphi |
The kernel distance between two trees. |
nLTT |
Kaphi |
Does not currently work |
| sackin |
Kaphi |
Sackin index. |
| colless |
Kaphi |
Colless imbalance number. |
| cophenetic.index |
Kaphi |
Cophenetic index. |
| ladder.length |
Kaphi |
Max ladder length. |
| IL.nodes |
Kaphi |
Number of internal nodes with one leaf. |
| tree.width |
Kaphi |
Max width divided by max depth. |
| max.delta.width |
Kaphi |
Max difference in in width between two levels. |
| n.cherries |
Kaphi |
Number of cherries(node with two leaves). |
| prop.unbalanced |
Kaphi |
Proportion of unbalanced subtrees. |
| avg.unbalance |
Kaphi |
Average ratio of unbalanced subtrees. |
| pybus.gamma |
Kaphi |
Pybus' gamma statistic |
| internal.terminal.ratio |
Kaphi |
Ratio of internal to terminal branches. |
| cophenetic.phylo.met |
Kaphi |
Wrapper of ape::cophenetic.phylo, computes pairwise distances between the pairs of tips from a phylogenetic tree using its branch lengths. |
| dist.nodes.met |
Kaphi |
Wrapper of ape::dist.nodes, similar to cophenetic.phylo, but includes internal nodes. |
| dist.topo |
ape |
Topological distance between two trees using the method from Penny & Hendy (1985). |
| avgladder |
phyloTop |
Mean size of ladders in the tree. |
| getDepths.met |
Kaphi |
Wrapper of phyloTop::getDepths, originally returns a list of two vectors: tipDepths and nodeDepths, but given metric will output non-scalar values of type 'tips' or type 'nodes' specified by user. |
| pitchforks |
phyloTop |
Number of clades with three tips. |
| RF.dist |
phangorn |
Robinson-Foulds distance: number of clades not shared. |
| KF.dist |
phangorn |
RF with branch lengths: sums of differences in branch lengths. |
| path.dist |
phangorn |
Path distance metric: nodal distance ("NODE") with k=2. |
| Trip |
Kaphi |
Critchlow et al. (1996), Proportion of triplets not shared between trees. |
| TripL |
Kaphi |
Kuhner & Yamato (2014), Trip distance using branch lengths |
| MAST |
Kaphi |
Gordon (1980), Number of tips in the Maximum Agreement SubTree of given subtrees. |
| Align |
Kaphi |
Nye et al. (2006), Calculates dissimilarity of of all one-to-one mapping of branches between 2 trees and determines most optimal mapping of branches |
| Sim |
Kaphi |
Hein et al. (2005), Similiarity measure based on the probability that a point chosen randomly in A will be on a branch leading to the same set of tips as a point randomly chosen in B |
| Node.dist |
Kaphi |
Williams & Clifford (1971), Number of nodes traversed in mainimal path from one tip to another in trees A and B |