Changelog
Source:NEWS.md
Version 1.70.7
- Fixed numerical issue in calculating mean pair distance for very large trees
- Now use armadillo to calculate Eigen values
- added the function ‘sshape’, which was previously called the blum statistic ( the blum function remains available as well). Thanks Sophie Kersting for pointing this out!
- polished the manual
Version 1.70.6
- Added support for unrooted trees
- Added check if tree is unrooted, and aborting if statistic does not support this
- Updated reference table in the README file, showing which statistics are available for unrooted trees, and which statistics (appear) to be affected by root position
- using treebalance functions when treestats functions do not suffice (e.g. for rquartet for polytomous trees)
- updated Wiener test, to include distance matrix based calculation
Version 1.1.3
- Reduced dependencies, Matrix and RSpectra are no longer required (but availability will improve speed!)
- calc_all_stats, calc_topology_stats and calc_brts_stats no longer return a named list, but return a named vector, for ease of rapid calculation across many trees
Version 1.1.2
- Removed dependencies to nodeSub by integrating functions to generate fully balanced and unbalanced into treestats.
- Renamed ‘calc_balance_stats’ to ‘calc_topology_stats’, and included only statistics that take the topology (without the branch lengths) into account.
Version 1.1.1
Added the following statistics:
minimum(>0) eigenvalue of the Adjacency matrix
maximum eigenvalue of the Adjacency matrix
minimum(>0) eigenvalue of the Laplacian matrix
maximum eigenvalue of the Laplacian matrix
double cherries
root imbalance
four prong
Renamed eigenvector to eigen_centrality (in line with the analogous function in igraph)
Version 1.1.0
Add several new statistics:
Colless-corrected
Colless-Quadratic
Total path index
Total internal path index
Average vertex depth
Max Width over Max Depth
Version 1.0.7
- Added checks to each statistic verifying the statistic requires an ultrametric or binary tree - this should avoid some rare instances where memory access violations would pop up when providing a non-binary tree to a statistic assuming a binary input phylogeny. Many thanks to Fien Strijthaegen for pointing this out.
Version 1.0.5
CRAN release: 2024-01-30
- Squashed a bug in imbalance_steps that would incorrectly calculate for smaller trees
- Added bioRxiv link to DESCRIPTION
- Added CITATION file