Updated calculation of how to crown age was calculated to avoid
edge-case miscalculations, and to speed up calculation as well.
Version 1.71.11
Added inverse sum of branch lengths statistic.
Version 1.70.11
Replaced ::Rf_error with Rcpp::stop()
Added vignette on the effect of tree size
Added vignette visualizing correlations between statistics
Version 1.70.10
Added matrix-free calculations for eigenvalue related calculations,
for the eigenvector and the adjacency matrix related summary statistics.
These are no longer restricted by tree size (although for very large
trees, calculations might still take considerable time, scaling is much
better now).
Added matrix-free calculations for the min_max laplacian
function
Note that the RSpectra related statistics are NOT matrix free
possible: these require all distances between all tips and all nodes,
which can not be done matrix-free (so these are restricted to trees <
~20k nodes, and relatively slow).
Version 1.70.9
Added function to calculate statistics for large trees, which skips
several distance matrix based statistics that can cause extreme memory
usage
Version 1.70.8
Removed all references and vignettes making use of the package
abcrf, as this is longer available on CRAN.
Improved compliance to noSuggests CRAN policy.
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 1.70.5
Updated references.
Version 1.70.4
Removed C++20 dependency
Version 1.70.3
Version numbering has improved to include the number of statistics
available.
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 1.0.6
Added treeness statistic
Version 1.0.5
Squashed a bug in imbalance_steps that would incorrectly calculate
for smaller trees
Added bioRxiv link to DESCRIPTION
Added CITATION file
Version 1.0.4
Corrected wording of variation in branch length statistics to
correctly reflect variance, instead of variation