Species and their respective ancestral nodes
get_spp_nodes.RdThis function computes a matrix containing species and their respective ancestral nodes
Arguments
- tree
Phylogenetic tree
- node.prefix
Character indicating the prefix to be used to name nodes, default is the letter "N"
Value
A matrix with species in lines and nodes in columns. 1 indicates that the node corresponds to the ancestor of that species and zero indicates that species does not share the ancestor node
Details
This is an auxiliary function that, by taking a phylogenetic tree, allows to represent in a matrix format
the relationship between present-day species (tips) and their ancestors (nodes). The function provides an
easy way to obtain certain objects that can be used in other functions, like calc_ancestral_state
Examples
data(akodon_newick)
get_spp_nodes(tree = akodon_newick, node.prefix = "N")
#> A_mimus A_lindberghi A_subfuscus A_lutescens A_sylvanus A_boliviensis
#> N31 1 1 1 1 1 1
#> N32 0 1 1 1 1 1
#> N33 0 1 1 1 1 1
#> N34 0 0 1 1 1 1
#> N35 0 0 1 1 1 1
#> N36 0 0 1 1 1 1
#> N37 0 0 1 1 1 1
#> N38 0 0 1 1 0 0
#> N39 0 0 0 0 1 1
#> N40 0 0 0 0 0 1
#> N41 0 0 0 0 0 0
#> N42 0 0 0 0 0 0
#> N43 0 0 0 0 0 0
#> N44 0 0 0 0 0 0
#> N45 0 0 0 0 0 0
#> N46 0 0 0 0 0 0
#> N47 0 0 0 0 0 0
#> N48 0 0 0 0 0 0
#> N49 0 0 0 0 0 0
#> N50 0 0 0 0 0 0
#> N51 0 0 0 0 0 0
#> N52 0 0 0 0 0 0
#> N53 0 0 0 0 0 0
#> N54 0 0 0 0 0 0
#> N55 0 0 0 0 0 0
#> N56 0 0 0 0 0 0
#> N57 0 0 0 0 0 0
#> N58 0 0 0 0 0 0
#> N59 0 0 0 0 0 0
#> A_spegazzinii A_azarae A_fumeus A_kofordi A_juninensis A_cursor A_montensis
#> N31 1 1 1 1 1 1 1
#> N32 1 1 1 1 1 1 1
#> N33 1 1 1 1 1 1 1
#> N34 1 1 1 1 1 1 1
#> N35 1 1 1 1 1 0 0
#> N36 1 1 0 0 0 0 0
#> N37 1 0 0 0 0 0 0
#> N38 0 0 0 0 0 0 0
#> N39 1 0 0 0 0 0 0
#> N40 1 0 0 0 0 0 0
#> N41 0 0 1 1 1 0 0
#> N42 0 0 1 1 0 0 0
#> N43 0 0 0 0 0 1 1
#> N44 0 0 0 0 0 0 1
#> N45 0 0 0 0 0 0 0
#> N46 0 0 0 0 0 0 0
#> N47 0 0 0 0 0 0 0
#> N48 0 0 0 0 0 0 0
#> N49 0 0 0 0 0 0 0
#> N50 0 0 0 0 0 0 0
#> N51 0 0 0 0 0 0 0
#> N52 0 0 0 0 0 0 0
#> N53 0 0 0 0 0 0 0
#> N54 0 0 0 0 0 0 0
#> N55 0 0 0 0 0 0 0
#> N56 0 0 0 0 0 0 0
#> N57 0 0 0 0 0 0 0
#> N58 0 0 0 0 0 0 0
#> N59 0 0 0 0 0 0 0
#> A_reigi A_paranaensis A_mystax A_aerosus A_affinis A_mollis A_orophilus
#> N31 1 1 1 1 1 1 1
#> N32 1 1 1 1 1 1 1
#> N33 1 1 1 0 0 0 0
#> N34 1 1 1 0 0 0 0
#> N35 0 0 0 0 0 0 0
#> N36 0 0 0 0 0 0 0
#> N37 0 0 0 0 0 0 0
#> N38 0 0 0 0 0 0 0
#> N39 0 0 0 0 0 0 0
#> N40 0 0 0 0 0 0 0
#> N41 0 0 0 0 0 0 0
#> N42 0 0 0 0 0 0 0
#> N43 1 1 1 0 0 0 0
#> N44 1 1 1 0 0 0 0
#> N45 1 1 1 0 0 0 0
#> N46 0 1 1 0 0 0 0
#> N47 0 0 0 1 1 1 1
#> N48 0 0 0 1 1 1 1
#> N49 0 0 0 1 1 1 1
#> N50 0 0 0 1 1 1 1
#> N51 0 0 0 1 1 0 0
#> N52 0 0 0 0 0 1 1
#> N53 0 0 0 0 0 1 1
#> N54 0 0 0 0 0 0 0
#> N55 0 0 0 0 0 0 0
#> N56 0 0 0 0 0 0 0
#> N57 0 0 0 0 0 0 0
#> N58 0 0 0 0 0 0 0
#> N59 0 0 0 0 0 0 0
#> A_torques A_budini A_siberiae A_simulator A_varius A_albiventer A_iniscatus
#> N31 1 1 1 1 1 1 1
#> N32 1 1 1 1 1 1 1
#> N33 0 0 0 0 0 0 0
#> N34 0 0 0 0 0 0 0
#> N35 0 0 0 0 0 0 0
#> N36 0 0 0 0 0 0 0
#> N37 0 0 0 0 0 0 0
#> N38 0 0 0 0 0 0 0
#> N39 0 0 0 0 0 0 0
#> N40 0 0 0 0 0 0 0
#> N41 0 0 0 0 0 0 0
#> N42 0 0 0 0 0 0 0
#> N43 0 0 0 0 0 0 0
#> N44 0 0 0 0 0 0 0
#> N45 0 0 0 0 0 0 0
#> N46 0 0 0 0 0 0 0
#> N47 1 1 1 1 1 1 1
#> N48 1 1 1 1 1 1 0
#> N49 1 1 1 1 1 0 0
#> N50 1 0 0 0 0 0 0
#> N51 0 0 0 0 0 0 0
#> N52 1 0 0 0 0 0 0
#> N53 0 0 0 0 0 0 0
#> N54 0 1 1 1 1 0 0
#> N55 0 1 1 0 0 0 0
#> N56 0 0 0 1 1 0 0
#> N57 0 0 0 0 0 0 1
#> N58 0 0 0 0 0 0 0
#> N59 0 0 0 0 0 0 0
#> A_dayi A_toba A_dolores
#> N31 1 1 1
#> N32 1 1 1
#> N33 0 0 0
#> N34 0 0 0
#> N35 0 0 0
#> N36 0 0 0
#> N37 0 0 0
#> N38 0 0 0
#> N39 0 0 0
#> N40 0 0 0
#> N41 0 0 0
#> N42 0 0 0
#> N43 0 0 0
#> N44 0 0 0
#> N45 0 0 0
#> N46 0 0 0
#> N47 1 1 1
#> N48 0 0 0
#> N49 0 0 0
#> N50 0 0 0
#> N51 0 0 0
#> N52 0 0 0
#> N53 0 0 0
#> N54 0 0 0
#> N55 0 0 0
#> N56 0 0 0
#> N57 1 1 1
#> N58 1 1 1
#> N59 0 1 1