Using treestats
The treestats package provides an easy to use interface to calculate summary statistics on phylogenetic trees. To obtain a list of all supported summary statistics use:
## [1] "area_per_pair" "average_leaf_depth" "avg_ladder"
## [4] "avg_vert_depth" "b1" "b2"
## [7] "beta" "blum" "cherries"
## [10] "colless" "colless_corr" "colless_quad"
## [13] "crown_age" "diameter" "double_cherries"
## [16] "eigen_centrality" "eigen_centralityW" "ew_colless"
## [19] "four_prong" "gamma" "i_stat"
## [22] "il_number" "imbalance_steps" "j_one"
## [25] "j_stat" "laplace_spectrum_a" "laplace_spectrum_e"
## [28] "laplace_spectrum_g" "laplace_spectrum_p" "max_adj"
## [31] "max_betweenness" "max_closeness" "max_closenessW"
## [34] "max_del_width" "max_depth" "max_ladder"
## [37] "max_laplace" "max_width" "mean_branch_length"
## [40] "mean_branch_length_ext" "mean_branch_length_int" "min_adj"
## [43] "min_laplace" "mntd" "mpd"
## [46] "mw_over_md" "nltt_base" "number_of_lineages"
## [49] "phylogenetic_div" "pigot_rho" "pitchforks"
## [52] "psv" "rogers" "root_imbalance"
## [55] "rquartet" "sackin" "stairs"
## [58] "stairs2" "symmetry_nodes" "tot_coph"
## [61] "tot_internal_path" "tot_path" "tree_height"
## [64] "treeness" "var_branch_length" "var_branch_length_ext"
## [67] "var_branch_length_int" "var_depth" "vpd"
## [70] "wiener"If your favourite summary statistic is missing, please let the maintainer know, treestats is a dynamic package always under development, and the maintainers are always looking for new statistics!
Given a phylogenetic tree, you can now use of the available functions to calculate your summary statistic of choice. Let’s take for instance the Colless statistic (and we generate a dummy tree):
## [1] 257Looking at the documentation of the colless statistic
(?colless), we find that the function also includes options
to normalize for size: either ‘pda’ or ‘yule’:
treestats::colless(phy, normalization = "yule")## [1] -0.9192387Multiple statistics
The treestats package supports calculating many statistics in one go.
For this, several functions have been set up aptly. Firstly, the
function calc_all_stats will calculate all statistics:
all_stats <- calc_all_stats(phy)## Loading required namespace: RSpectraSimilarly, we can also blanket apply all topology associated summary statistics:
balance_stats <- calc_topology_stats(phy)
unlist(balance_stats)## area_per_pair average_leaf_depth avg_ladder avg_vert_depth
## 1.255859e+01 7.630000e+00 2.250000e+00 6.673367e+00
## b1 b2 beta blum
## 5.339845e+01 5.719727e+00 1.193623e+00 1.101485e+02
## cherries colless colless_corr colless_quad
## 3.200000e+01 2.570000e+02 5.297877e-02 4.235000e+03
## diameter double_cherries eigen_centrality ew_colless
## 2.000000e+01 5.000000e+00 2.833317e-01 4.607934e-01
## four_prong i_stat il_number imbalance_steps
## 1.100000e+01 4.712378e-01 3.600000e+01 8.700000e+01
## j_one max_betweenness max_closeness max_del_width
## 8.707544e-01 1.251500e+04 NA 1.400000e+01
## max_depth max_ladder max_width mw_over_md
## 1.200000e+01 3.000000e+00 4.600000e+01 3.833333e+00
## pitchforks rogers root_imbalance rquartet
## 1.700000e+01 5.900000e+01 7.500000e-01 3.961488e+06
## sackin stairs stairs2 symmetry_nodes
## 7.630000e+02 5.959596e-01 6.650377e-01 5.900000e+01
## tot_coph tot_internal_path tot_path_length var_depth
## 6.686000e+03 5.650000e+02 1.328000e+03 3.245556e+00