Package: treestats 1.70.5

treestats: Phylogenetic Tree Statistics

Collection of phylogenetic tree statistics, collected throughout the literature. All functions have been written to maximize computation speed. The package includes umbrella functions to calculate all statistics, all balance associated statistics, or all branching time related statistics. Furthermore, the 'treestats' package supports summary statistic calculations on Ltables, provides speed-improved coding of branching times, Ltable conversion and includes algorithms to create intermediately balanced trees. Full description can be found in Janzen (2024) <doi:10.1016/j.ympev.2024.108168>.

Authors:Thijs Janzen [cre, aut]

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treestats.pdf |treestats.html✨
treestats/json (API)
NEWS

# Install 'treestats' in R:
install.packages('treestats', repos = c('https://thijsjanzen.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/thijsjanzen/treestats/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

5.67 score 14 stars 1 packages 16 scripts 269 downloads 76 exports 6 dependencies

Last updated 3 months agofrom:be16d5c489. Checks:ERROR: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 09 2024
R-4.5-win-x86_64WARNINGNov 09 2024
R-4.5-linux-x86_64WARNINGNov 09 2024
R-4.4-win-x86_64WARNINGNov 09 2024
R-4.4-mac-x86_64WARNINGNov 09 2024
R-4.4-mac-aarch64WARNINGNov 09 2024
R-4.3-win-x86_64WARNINGNov 09 2024
R-4.3-mac-x86_64WARNINGNov 09 2024
R-4.3-mac-aarch64WARNINGNov 09 2024

Exports:area_per_pairaverage_leaf_depthavg_ladderavg_vert_depthb1b2beta_statisticblumbranching_timescalc_all_statscalc_brts_statscalc_topology_statscherriescollesscolless_corrcolless_quadcreate_fully_balanced_treecreate_fully_unbalanced_treecrown_agediameterdouble_cherrieseigen_centralityentropy_jew_collessfour_pronggamma_statisticILnumberimbalance_stepsj_onel_to_phylolaplacian_spectrumlist_statisticsltable_to_newickmake_unbalanced_treemax_betweennessmax_closenessmax_del_widthmax_depthmax_laddermax_widthmean_branch_lengthmean_branch_length_extmean_branch_length_intmean_imean_pair_distminmax_adjminmax_laplacemntdmw_over_mdnLTTnLTT_basenumber_of_lineagesphylo_to_lphylogenetic_diversitypigot_rhopitchforkspsvrebase_ltablerogersroot_imbalancerquartetsackinstairsstairs2sym_nodestot_cophtot_internal_pathtot_path_lengthtree_heighttreenessvar_branch_lengthvar_branch_length_extvar_branch_length_intvar_leaf_depthvar_pair_distwiener

Dependencies:apedigestlatticenlmenloptrRcpp

Readme and manuals

Help Manual

Help pageTopics
Collection of phylogenetic tree statisticstreestats-package treestats
Area per pair indexarea_per_pair
Average leaf depth statistic. The average leaf depth statistic is a normalized version of the Sackin index, normalized by the number of tips.average_leaf_depth
Average ladder indexavg_ladder
Average vertex depth metricavg_vert_depth
B1 metricb1
B2 metricb2
Aldous' beta statistic.beta_statistic
Blum index of (im)balance.blum
Branching times of a treebranching_times
Apply all available tree statistics to a single treecalc_all_stats
Apply all tree statistics related to branching times to a single tree.calc_brts_stats
Calculate all topology based statistics for a single treecalc_topology_stats
Cherry indexcherries
Colless index of (im)balance.colless
Corrected Colless index of (im)balance.colless_corr
Quadratic Colless index of (im)balance.colless_quad
Create a fully balanced treecreate_fully_balanced_tree
Create an unbalanced tree (caterpillar tree)create_fully_unbalanced_tree
Crown age of a tree.crown_age
Diameter statisticdiameter
Double Cherry indexdouble_cherries
Eigen vector centralityeigen_centrality
Intensive quadratic entropy statistic J.entropy_j
Equal weights Colless index of (im)balance.ew_colless
Four prong indexfour_prong
Gamma statisticgamma_statistic
ILnumberILnumber
Imbalance steps indeximbalance_steps
J^1 index.j_one
Convert an L table to phylo objectl_to_phylo
Laplacian spectrum statistics, from RPANDAlaplacian_spectrum
Provides a list of all available statistics in the packagelist_statistics
Convert an L table to newick stringltable_to_newick
Stepwise increase the imbalance of a treemake_unbalanced_tree
Maximum betweenness centrality.max_betweenness
Maximum closenessmax_closeness
Maximum difference of widths of a phylogenetic treemax_del_width
Maximum depth metricmax_depth
Maximum ladder indexmax_ladder
Maximum width of branch depths.max_width
Mean branch length of a tree, including extinct branches.mean_branch_length
Mean length of external branch lengths of a tree, e.g. of branches leading to a tip.mean_branch_length_ext
Mean length of internal branches of a tree, e.g. of branches not leading to a tip.mean_branch_length_int
Mean I statistic.mean_i
Mean Pairwise distancemean_pair_dist
Adjancency Matrix propertiesminmax_adj
Laplacian Matrix propertiesminmax_laplace
Mean Nearest Taxon distancemntd
Maximum width of branch depths divided by the maximum depthmw_over_md
Normalized LTT statisticnLTT
Reference nLTT statisticnLTT_base
Number of tips of a tree, including extinct tips.number_of_lineages
Function to generate an ltable from a phy object.phylo_to_l
Phylogenetic diversity at time point tphylogenetic_diversity
Pigot's rhopigot_rho
Number of pitchforkspitchforks
Phylogenetic Species Variability.psv
a function to modify an ltable, such that the longest path in the phylogeny is a crown lineage.rebase_ltable
Rogers J index of (im)balance.rogers
Root imbalanceroot_imbalance
Rquartet index.rquartet
Sackin index of (im)balance.sackin
Stairs indexstairs
Stairs2 indexstairs2
Symmetry nodes metricsym_nodes
Total cophenetic index.tot_coph
Total internal path lengthtot_internal_path
Total path lengthtot_path_length
Height of a tree.tree_height
Treeness statistictreeness
Variance of branch lengths of a tree, including extinct branches.var_branch_length
Variance of external branch lengths of a tree, e.g. of branches leading to a tip.var_branch_length_ext
Variance of internal branch lengths of a tree, e.g. of branches not leading to a tip.var_branch_length_int
Variance of leaf depth statisticvar_leaf_depth
Variance of all pairwise distances.var_pair_dist
Wiener indexwiener