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| areaPerPairI | Calculation of the area per pair index for rooted trees |
| auxE_l_X | Auxiliary functions |
| avgLeafDepI | Calculation of the average leaf depth index for rooted trees |
| B1I | Calculation of the B1 index for rooted trees |
| B2I | Calculation of the B2 index for rooted trees |
| cherryI | Calculation of the cherry index for rooted trees |
| collessI | Calculation of the Colless index for rooted binary trees |
| collesslikeI | Calculation of the Colless-like indices for rooted trees |
| colPlaLab | Calculation of the Colijn-Plazzotta rank for rooted trees |
| colPlaLab_inv | Generation of the rooted binary tree corresponding to a given Colijn-Plazzotta rank |
| cPL_inv | Auxiliary functions |
| ewCollessI | Calculation of the equal weights Colless index for rooted binary trees |
| furnasI | Calculation of the Furnas rank for rooted binary trees |
| furnasI_inv | Calculation of rooted binary tree for tuple (rank, leaf number) |
| get.subtreesize | Auxiliary functions |
| getAllAncestors | Auxiliary functions |
| getAncVec | Auxiliary functions |
| getDescMatrix | Auxiliary functions |
| getfurranks | Auxiliary functions |
| getlca | Auxiliary functions |
| getNodesOfDepth | Auxiliary functions |
| getsubtree | Auxiliary functions |
| IbasedI | Calculation of the I-based indices for rooted trees |
| is_binary | Auxiliary functions |
| is_phylo | Auxiliary functions |
| maxDelW | Calculation of the maximal difference in widths for a rooted tree |
| maxDepth | Calculation of the maximal depth of the tree |
| maxDepthLeaf | Auxiliary functions |
| maxWidth | Calculation of the maximal width of the tree |
| rogersI | Calculation of the Rogers J index for rooted binary trees |
| rQuartetI | Calculation of the rooted quartet index for rooted trees |
| sackinI | Calculation of the Sackin index for rooted trees |
| sShapeI | Calculation of the s-shape statistic for rooted trees |
| stairs1 | Calculation of the stairs1 value for rooted binary trees |
| stairs2 | Calculation of the stairs2 value for rooted binary trees |
| symBucketLexicoSort | Auxiliary functions |
| symNodesI | Calculation of the symmetry nodes index for rooted binary trees |
| totCophI | Calculation of the total cophenetic index for rooted trees |
| treenumber | Auxiliary functions |
| treenumber_inv | Auxiliary functions |
| tree_decomposition | Auxiliary functions |
| tree_merge | Auxiliary functions |
| varLeafDepI | Calculation of the variance of leaf depths index for rooted trees |
| wedEth | Wedderburn Etherington numbers (from OEIS) |
| weighL1dist | Calculation of weighted l1 distance index for rooted binary trees |
| we_eth | Auxiliary functions |