Phylogenetic Tree Statistics

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Documentation for package ‘treestats’ version 1.70.4

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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
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.
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