Capture general branching information for an inputted phylogenetic tree
Source:R/nodes_config.R
nodes_config.RdThis function captures general tree information, including branching, node positions, and depths. It serves as a core function underlying all algorithms for slicing phylogenies.
Value
The function returns a phylogenetic tree in the "phylo" format containing three novel pieces of information (stored within "config", "node_matrix", and "tree_depth").
Details
This function captures node and edge information from an ultrametric phylogenetic tree. The function provides a data frame containing detailed branching information (within the internal "config" object), a node matrix (within "node_matrix"), and the tree age (within "tree_depth").
More specifically, the "config" object returns the following information: NodeBegin: the node at which a given branch begins. NodeEnd: the node at which a given branch ends. NodeLength: the branch length of that nodes interval. YearBegin: the year at which a given node begins. YearEnd: the year at which a given node ends.
See also
Phylogenetic slicing methods: squeeze_tips(),squeeze_root(),squeeze_int().
Author
Matheus Lima de Araujo matheusaraujolima@live.com
Examples
# Generate a random tree
tree <- ape::rcoal(20)
# Capture tree information
tree <- nodes_config(tree)
# Accessing these informations
tree$config # Nodes configurations
#> NodeBegin NodeEnd NodeLength YearBegin YearEnd
#> 35 21 35 2.503496442 0.000000 2.503496
#> 1 35 1 0.060905527 2.503496 2.564402
#> 37 35 37 0.036147256 2.503496 2.539644
#> 2 37 2 0.024758271 2.539644 2.564402
#> 3 37 3 0.024758271 2.539644 2.564402
#> 22 21 22 1.838031229 0.000000 1.838031
#> 23 22 23 0.007406870 1.838031 1.845438
#> 25 23 25 0.296216525 1.845438 2.141655
#> 26 25 26 0.147841978 2.141655 2.289497
#> 4 26 4 0.274905367 2.289497 2.564402
#> 27 26 27 0.073927650 2.289497 2.363424
#> 5 27 5 0.200977717 2.363424 2.564402
#> 31 27 31 0.062010584 2.363424 2.425435
#> 39 31 39 0.137040149 2.425435 2.562475
#> 6 39 6 0.001926984 2.562475 2.564402
#> 7 39 7 0.001926984 2.562475 2.564402
#> 8 31 8 0.138967133 2.425435 2.564402
#> 29 25 29 0.272217236 2.141655 2.413872
#> 30 29 30 0.011234939 2.413872 2.425107
#> 9 30 9 0.139295170 2.425107 2.564402
#> 36 30 36 0.095165857 2.425107 2.520273
#> 10 36 10 0.044129313 2.520273 2.564402
#> 11 36 11 0.044129313 2.520273 2.564402
#> 12 29 12 0.150530109 2.413872 2.564402
#> 34 23 34 0.643689703 1.845438 2.489128
#> 13 34 13 0.075274167 2.489128 2.564402
#> 14 34 14 0.075274167 2.489128 2.564402
#> 24 22 24 0.015138193 1.838031 1.853169
#> 28 24 28 0.537365423 1.853169 2.390535
#> 15 28 15 0.173867124 2.390535 2.564402
#> 32 28 32 0.076823843 2.390535 2.467359
#> 16 32 16 0.097043281 2.467359 2.564402
#> 17 32 17 0.097043281 2.467359 2.564402
#> 33 24 33 0.632292435 1.853169 2.485462
#> 18 33 18 0.078940112 2.485462 2.564402
#> 38 33 38 0.058234518 2.485462 2.543696
#> 19 38 19 0.020705595 2.543696 2.564402
#> 20 38 20 0.020705595 2.543696 2.564402
tree$node_matrix # Node matrix
#> t8 t11 t7 t19 t10 t14 t15 t2 t3 t18 t20 t6 t5 t17 t12 t16 t9 t1 t4 t13
#> 21 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> 35 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> 37 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> 22 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> 23 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0
#> 25 0 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0
#> 26 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
#> 27 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
#> 31 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
#> 39 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
#> 29 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0
#> 30 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0
#> 36 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0
#> 34 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0
#> 24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1
#> 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0
#> 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0
#> 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1
#> 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1
tree$tree_depth # Tree age
#> [1] 2.564402