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$config # Nodes configurations
#> NodeBegin NodeEnd NodeLength YearBegin YearEnd
#> 1 21 1 0.887949971 0.0000000 0.8879500
#> 22 21 22 0.116482812 0.0000000 0.1164828
#> 24 22 24 0.538438888 0.1164828 0.6549217
#> 27 24 27 0.098054404 0.6549217 0.7529761
#> 38 27 38 0.122722991 0.7529761 0.8756991
#> 2 38 2 0.012250875 0.8756991 0.8879500
#> 3 38 3 0.012250875 0.8756991 0.8879500
#> 4 27 4 0.134973866 0.7529761 0.8879500
#> 32 24 32 0.194947587 0.6549217 0.8498693
#> 5 32 5 0.038080683 0.8498693 0.8879500
#> 6 32 6 0.038080683 0.8498693 0.8879500
#> 23 22 23 0.368522309 0.1164828 0.4850051
#> 26 23 26 0.244753006 0.4850051 0.7297581
#> 7 26 7 0.158191844 0.7297581 0.8879500
#> 28 26 28 0.024654628 0.7297581 0.7544128
#> 33 28 33 0.102416707 0.7544128 0.8568295
#> 8 33 8 0.031120508 0.8568295 0.8879500
#> 9 33 9 0.031120508 0.8568295 0.8879500
#> 10 28 10 0.133537215 0.7544128 0.8879500
#> 25 23 25 0.221290601 0.4850051 0.7062957
#> 29 25 29 0.050021042 0.7062957 0.7563168
#> 31 29 31 0.087857646 0.7563168 0.8441744
#> 11 31 11 0.043775560 0.8441744 0.8879500
#> 34 31 34 0.015288546 0.8441744 0.8594630
#> 12 34 12 0.028487014 0.8594630 0.8879500
#> 13 34 13 0.028487014 0.8594630 0.8879500
#> 30 29 30 0.065628883 0.7563168 0.8219456
#> 14 30 14 0.066004323 0.8219456 0.8879500
#> 35 30 35 0.037932635 0.8219456 0.8598783
#> 15 35 15 0.028071688 0.8598783 0.8879500
#> 36 35 36 0.001048102 0.8598783 0.8609264
#> 16 36 16 0.027023586 0.8609264 0.8879500
#> 37 36 37 0.010240320 0.8609264 0.8711667
#> 17 37 17 0.016783266 0.8711667 0.8879500
#> 39 37 39 0.007903300 0.8711667 0.8790700
#> 18 39 18 0.008879966 0.8790700 0.8879500
#> 19 39 19 0.008879966 0.8790700 0.8879500
#> 20 25 20 0.181654248 0.7062957 0.8879500
tree$node_matrix # Node matrix
#> NULL
tree$tree_depth # Tree age
#> [1] 0.88795