Package index • treestats

All functions

ILnumber(): ILnumber

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

imbalance_steps(): Imbalance steps index

j_one(): J^1 index.

l_to_phylo(): Convert an L table to phylo object

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

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.

phylo_to_l(): Function to generate an ltable from a phy object.

phylogenetic_diversity(): Phylogenetic diversity at time point t

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

tree_height(): Height of a tree.

treeness(): Treeness statistic

treestats-package treestats: Collection of phylogenetic tree statistics

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