# Phylogenetic Tree Statistics

## Documentation for package ‘treestats’ version 1.0.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

treestats-package | Collection of phylogenetic tree statistics
area_per_pair | Fast function using C++ to calculate the area per pair index
average_leaf_depth | Calculate the average leaf depth statistic. The average leaf depth statistic is a normalized version of the Sackin index, normalized by the number of tips.
avg_ladder | Average ladder index
b1 | Fast function using C++ to calculate the B1 metric
b2 | Fast function using C++ to calculate the B2 metric
beta_statistic | Fast function using C++ to calculate the Aldous beta statistic.
blum | Fast function using C++ to calculate the Blum index of (im)balance.
branching_times | Calculates branching times of a tree, using C++
calc_all_stats | function to apply all available tree statistics to a single tree
calc_balance_stats | function to apply all balance statistics to a single tree
calc_brts_stats | function to apply all tree statistics related to branching times to a single tree.
cherries | Cherry index
colless | Fast function using C++ to calculate the Colless index of (im)balance.
crown_age | Calculates the crown age of a tree using C++.
diameter | Fast function using C++ to calculate the diameter
eigen_vector | Fast function using C++ to calculate eigen vector centrality
entropy_j | Fast function using C++ to calculate the intensive quadratic entropy statistic J.
ew_colless | Fast function using C++ to calculate the equal weights Colless index of (im)balance.
gamma_statistic | Calculate the gamma statistic, using a fast implementation in C++.
ILnumber | Calculate ILnumber
imbalance_steps | imbalance steps index
j_one | function to calculate the J^1 index.
laplacian_spectrum | function to calculate the laplacian spectrum, from RPANDA
list_statistics | Provides a list of all available statistics in the package
ltable_to_newick | Convert an L table to newick string
l_to_phylo | Convert an L table to phylo object
make_unbalanced_tree | this function increasingly increases the imbalance of a tree
max_betweenness | Fast function using C++ to calculate maximum betweenness centrality.
max_closeness | Fast function using C++ to calculate maximum closeness
max_del_width | Fast function using C++ to calculate the maximum difference of widths of a phylogenetic tree
max_depth | Fast function using C++ to calculate maximum depth metric
max_ladder | maximum ladder index
max_width | Fast function using C++ to calculate the maximum width of branch depth.
mean_branch_length | Calculates the mean branch length of a tree, including extinct branches.
mean_branch_length_ext | Calculates the mean of external branch lengths of a tree, e.g. of branches leading to a tip.
mean_branch_length_int | Calculates the variation of internal branch lengths of a tree, e.g. of branches not leading to a tip.
mean_i | Fast function using C++ to calculate the mean I value.
mean_pair_dist | Mean Pairwise distance
mntd | Mean Nearest Taxon distance
nLTT | Calculate the nLTT, using C++.
nLTT_base | Calculates the nLTT statistic using a reference 'empty' tree with only two lineages.
number_of_lineages | Calculate the number of tips of a tree, including extinct tips.
phylogenetic_diversity | Calculates phylogenetic diversity at time point t
phylo_to_l | Function to generate an ltable from a phy object.
pigot_rho | calculate Pigot's rho
pitchforks | Calculate pitchforks, from the phyloTop package, a pitchfork is a clade with three tips.
prep_lapl_spec | function to create laplacian matrix
psv | Fast function using C++ to calculate Phylogenetic Species Variability.
rebase_ltable | a function to modify an ltable, such that the longest path in the phylogeny is a crown lineage.
rogers | Fast function using C++ to calculate the Rogers J index of (im)balance.
rquartet | Fast function using C++ to calculate the rquartet index.
sackin | Fast function using C++ to calculate the sackin index of (im)balance.
stairs | Calculates the staircase-ness measure, from the phyloTop package. The staircase-ness reflects the number of subtrees that are imbalanced, e.g. subtrees where the left child has more extant tips than the right child, or vice versa.
stairs2 | Calculates the stairs2 measure, from the phyloTop package. The stairs2 reflects the imbalance at each node, where it represents the average across measure at each node, the measure being min(l, r) / max(l, r), where l and r reflect the number of tips connected at the left (l) and right (r) daughter.
sym_nodes | Fast function using C++ to calculate the symmetry nodes metric
tot_coph | Fast function using C++ to calculate the total cophenetic index.
treestats | Collection of phylogenetic tree statistics
tree_height | Calculates the height of a tree using C++.
var_branch_length | Calculates the variance of branch lengths of a tree, including extinct branches.
var_branch_length_ext | Calculates the variance of external branch lengths of a tree, e.g. of branches leading to a tip.
var_branch_length_int | Calculates the variance of internal branch lengths of a tree, e.g. of branches not leading to a tip.
var_leaf_depth | Fast function using C++ to calculate the variance of leaf depth statistic
var_pair_dist | Fast function using C++ to calculate the variance of all pairwise distances.
wiener | Fast function using C++ to calculate the Wiener index