Calculate a range of topological properties for one or more phylogenetic trees.
phyloTop(treeList, funcs = "all", normalise = FALSE)a list or multiPhylo object, or a single tree of class phylo or phylo4. All trees should be binary and rooted; if not they will be coerced into binary rooted trees using multi2di, if possible.
a list of functions. The default is to apply all of the topological functions from the package, but a subset can be specified instead. The functions available are:
stairs (note that this adds two columns to the output, "stairs1" and "stairs2")
option to normalise the results of functions where possible. Default is FALSE
A matrix where rows correspond to trees and columns correspond to topological properties.
## Apply all of the functions to a list of 10 random trees, each with 50 tips:
phyloTop(rmtree(10,50))
#> avgLadder cherries colless.phylo ILnumber maxHeight pitchforks sackin.phylo
#> 1 2.500000 19 185 12 13 3 399
#> 2 2.000000 18 131 14 10 8 337
#> 3 2.600000 16 107 18 10 9 323
#> 4 2.000000 17 103 16 8 10 321
#> 5 2.400000 17 148 16 11 8 346
#> 6 2.000000 18 228 14 12 10 426
#> 7 2.000000 19 124 12 9 8 334
#> 8 5.000000 19 236 12 12 8 426
#> 9 3.666667 16 195 18 11 6 391
#> 10 3.200000 14 125 22 10 8 339
#> stairs1 stairs2
#> 1 0.5102041 0.6802028
#> 2 0.6326531 0.6439597
#> 3 0.6530612 0.6533854
#> 4 0.5510204 0.6927446
#> 5 0.6326531 0.6333167
#> 6 0.5918367 0.6672684
#> 7 0.5102041 0.7188422
#> 8 0.5918367 0.6495456
#> 9 0.6326531 0.6038674
#> 10 0.6530612 0.6170498
## Normalising the results where possible:
phyloTop(rmtree(10,50), normalise=TRUE)
#> avgLadder cherries colless.phylo ILnumber maxHeight pitchforks
#> 1 0.04166667 0.80 0.09778912 0.2083333 0.1836735 0.48
#> 2 0.05952381 0.52 0.13010204 0.5000000 0.2040816 0.48
#> 3 0.05555556 0.60 0.10459184 0.4166667 0.2040816 0.48
#> 4 0.04166667 0.64 0.15816327 0.3750000 0.2653061 0.60
#> 5 0.04166667 0.68 0.19557823 0.3333333 0.2653061 0.30
#> 6 0.05208333 0.68 0.10119048 0.3333333 0.2040816 0.60
#> 7 0.05555556 0.76 0.08673469 0.2500000 0.1836735 0.30
#> 8 0.05833333 0.60 0.13265306 0.4166667 0.2244898 0.48
#> 9 0.04166667 0.80 0.09863946 0.2083333 0.2040816 0.36
#> 10 0.06250000 0.64 0.08673469 0.3750000 0.1632653 0.48
#> sackin.phylo stairs1 stairs2
#> 1 0.2629513 0.4897959 0.7507223
#> 2 0.2880691 0.6734694 0.5765037
#> 3 0.2582418 0.6734694 0.6087621
#> 4 0.2951334 0.6530612 0.6105791
#> 5 0.3343799 0.6122449 0.6057727
#> 6 0.2660911 0.5918367 0.6858025
#> 7 0.2496075 0.5306122 0.7013912
#> 8 0.2825746 0.6326531 0.6252178
#> 9 0.2558870 0.5102041 0.7002742
#> 10 0.2527473 0.5918367 0.6815878