Phylogenetic Tree Statistics

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Documentation for package ‘treestats’ version 1.0.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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 variation of branch lengths of a tree, including extinct branches.
var_branch_length_ext	Calculates the variation of external branch lengths of a tree, e.g. of branches leading to a tip.
var_branch_length_int	Calculates the variation 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 variation of all pairwise distances.
wiener	Fast function using C++ to calculate the Wiener index