R: Phylogenetic Tree Statistics

# Phylogenetic Tree Statistics

## Documentation for package ‘treestats’ version 1.70.8

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

## Help Pages

treestats-package | Collection of phylogenetic tree statistics
area_per_pair | Area per pair index
average_leaf_depth | 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
avg_vert_depth | Average vertex depth metric
b1 | B1 metric
b2 | B2 metric
beta_statistic | Aldous' beta statistic.
blum | Blum index of (im)balance.
branching_times | Branching times of a tree
calc_all_stats | Apply all available tree statistics to a single tree
calc_brts_stats | Apply all tree statistics related to branching times to a single tree.
calc_topology_stats | Calculate all topology based statistics for a single tree
cherries | Cherry index
colless | Colless index of (im)balance.
colless_corr | Corrected Colless index of (im)balance.
colless_quad | Quadratic Colless index of (im)balance.
create_fully_balanced_tree | Create a fully balanced tree
create_fully_unbalanced_tree | Create an unbalanced tree (caterpillar tree)
crown_age | Crown age of a tree.
diameter | Diameter statistic
double_cherries | Double Cherry index
eigen_centrality | Eigen vector centrality
entropy_j | Intensive quadratic entropy statistic J.
ew_colless | Equal weights Colless index of (im)balance.
four_prong | Four prong index
gamma_statistic | Gamma statistic
ILnumber | ILnumber
imbalance_steps | Imbalance steps index
i_stat | Mean I statistic.
j_one | J^1 index.
laplacian_spectrum | Laplacian spectrum statistics, 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 | Stepwise increase the imbalance of a tree
max_betweenness | Maximum betweenness centrality.
max_closeness | Maximum closeness
max_del_width | Maximum difference of widths of a phylogenetic tree
max_depth | Maximum depth metric
max_ladder | Maximum ladder index
max_width | Maximum width of branch depths.
mean_branch_length | Mean branch length of a tree, including extinct branches.
mean_branch_length_ext | Mean length of external branch lengths of a tree, e.g. of branches leading to a tip.
mean_branch_length_int | Mean length of internal branches of a tree, e.g. of branches not leading to a tip.
mean_i | Mean I statistic.
mean_pair_dist | Mean Pairwise distance
minmax_adj | Adjancency Matrix properties
minmax_laplace | Laplacian Matrix properties
mntd | Mean Nearest Taxon distance
mw_over_md | Maximum width of branch depths divided by the maximum depth
nLTT | Normalized LTT statistic
nLTT_base | Reference nLTT statistic
number_of_lineages | Number of tips of a tree, including extinct tips.
phylogenetic_diversity | Phylogenetic diversity at time point t
phylo_to_l | Function to generate an ltable from a phy object.
pigot_rho | Pigot's rho
pitchforks | Number of pitchforks
psv | Phylogenetic Species Variability.
rebase_ltable | a function to modify an ltable, such that the longest path in the phylogeny is a crown lineage.
rogers | Rogers J index of (im)balance.
root_imbalance | Root imbalance
rquartet | Rquartet index.
sackin | Sackin index of (im)balance.
sshape | s shape statistic of (im)balance.
stairs | Stairs index
stairs2 | Stairs2 index
sym_nodes | Symmetry nodes metric
tot_coph | Total cophenetic index.
tot_internal_path | Total internal path length
tot_path_length | Total path length
treeness | Treeness statistic
treestats | Collection of phylogenetic tree statistics
tree_height | Height of a tree.
var_branch_length | Variance of branch lengths of a tree, including extinct branches.
var_branch_length_ext | Variance of external branch lengths of a tree, e.g. of branches leading to a tip.
var_branch_length_int | Variance of internal branch lengths of a tree, e.g. of branches not leading to a tip.
var_leaf_depth | Variance of leaf depth statistic
var_pair_dist | Variance of all pairwise distances.
wiener | Wiener index