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] "gamma" "sackin" "colless"
## [4] "beta" "blum" "crown_age"
## [7] "tree_height" "pigot_rho" "number_of_lineages"
## [10] "nltt_base" "phylogenetic_div" "avg_ladder"
## [13] "max_ladder" "cherries" "il_number"
## [16] "pitchforks" "stairs" "laplace_spectrum_a"
## [19] "laplace_spectrum_p" "laplace_spectrum_e" "laplace_spectrum_g"
## [22] "imbalance_steps" "j_one" "b1"
## [25] "b2" "area_per_pair" "average_leaf_depth"
## [28] "i_stat" "ew_colless" "max_del_width"
## [31] "max_depth" "max_width" "rogers"
## [34] "stairs2" "tot_coph" "var_depth"
## [37] "symmetry_nodes" "mpd" "psv"
## [40] "vpd" "mntd" "j_stat"
## [43] "rquartet" "wiener" "max_betweenness"
## [46] "max_closeness" "diameter" "eigenvector"
## [49] "mean_branch_length" "var_branch_length" "mean_branch_length_int"
## [52] "mean_branch_length_ext" "var_branch_length_int" "var_branch_length_ext"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] 238Looking at the documentation of the colless statistic
(?colless), we find that the function also includes options
to normalize for size: either ‘pda’ or ‘yule’:
## [1] -1.109239The 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:
This generates a named list, which can be very useful to find your
focal statistics, but often a conversion into a vector may be more
interesting (we use unlist and omit as.vector to retain the
names):
## gamma sackin colless
## -4.152725e-01 7.540000e+02 2.380000e+02
## beta blum crown_age
## 1.081738e+00 1.098696e+02 5.332899e+00
## tree_height pigot_rho number_of_lineages
## 5.332899e+00 8.397294e-02 1.000000e+02
## nltt_base phylogenetic_div avg_ladder
## 7.790139e-01 1.178496e+02 2.166667e+00
## max_ladder cherries il_number
## 3.000000e+00 3.500000e+01 3.000000e+01
## pitchforks stairs laplace_spectrum_a
## 1.600000e+01 6.060606e-01 -8.071243e-01
## laplace_spectrum_p laplace_spectrum_e laplace_spectrum_g
## 4.218895e+00 7.573827e+00 1.000000e+00
## imbalance_steps j_one b1
## 8.700000e+01 8.811480e-01 5.435123e+01
## b2 area_per_pair average_leaf_depth
## 5.855957e+00 1.276687e+01 7.540000e+00
## i_stat ew_colless max_del_width
## 4.599563e-01 4.373691e-01 1.000000e+01
## max_depth max_width rogers
## 1.200000e+01 3.800000e+01 6.000000e+01
## stairs2 tot_coph var_depth
## 6.651382e-01 5.725000e+03 2.917576e+00
## symmetry_nodes mpd psv
## 6.000000e+01 8.422200e+00 4.211100e+00
## vpd mntd j_stat
## 7.645229e+00 1.302264e+00 8.422200e-02
## rquartet wiener max_betweenness
## 4.917915e+06 1.442562e+05 1.154700e+04
## max_closeness diameter eigenvector
## 1.086454e-03 2.200000e+01 6.761475e-01
## mean_branch_length var_branch_length mean_branch_length_int
## 5.952001e-01 3.689483e-01 5.381270e-01
## mean_branch_length_ext var_branch_length_int var_branch_length_ext
## 6.511318e-01 3.545903e-01 3.803586e-01Similarly, we can also blanket apply all balance associated summary statistics:
## sackin colless beta blum
## 7.540000e+02 2.380000e+02 1.081738e+00 1.098696e+02
## avg_ladder max_ladder cherries il_number
## 2.166667e+00 3.000000e+00 3.500000e+01 3.000000e+01
## pitchforks stairs b1 b2
## 1.600000e+01 6.060606e-01 5.435123e+01 5.855957e+00
## area_per_pair average_leaf_depth i_stat ew_colless
## 1.276687e+01 7.540000e+00 4.599563e-01 4.373691e-01
## max_del_width max_depth max_width rogers
## 1.000000e+01 1.200000e+01 3.800000e+01 6.000000e+01
## stairs2 tot_coph var_depth symmetry_nodes
## 6.651382e-01 5.725000e+03 2.917576e+00 6.000000e+01
## rquartet imbalance_steps j_one diameter
## 4.917915e+06 8.700000e+01 8.811480e-01 2.200000e+01