Designate clade membership for each tip for downstream analyses summarizing rates for each clade

Usage

clade_membership(tree, ancestral_nodes, other_nodes_label = "other_nodes")

Arguments

tree: Tree object (file path to a Nexus file) used to extract node numbers and tip labels.
ancestral_nodes: A named list specifying the MRCA node number for each clade. The names are the clade labels. To specify non-monophyletic groups, use a character string in the format "inclusive_node - exclusive_node".
other_nodes_label: A label to assign to tips not included in any clade defined by ancestral_nodes.

Value

A data frame with columns: node (node number), ancestral_node (source MRCA node), and clade (clade label). Each row represents the clade assignment of a node in the tree.

Examples

if (FALSE) { # \dontrun{
ancestral_nodes <- list(
  Non_lepidosauria = 242,
  Other_Lepidosauria = 237,
  Gekkota = 222,
  Scincoidea = 210,
  Teiioidea = 192,
  Lacertidae = 209,
  Amphisbaenia = 205,
  Anguiformes = 150,
  Acrodonta = 145,
  Pleurodonta = 133,
  Caenophidia = 170,
  Early_Serpentes = "164 - 170"  # non-monophyletic group
)

Nodes_Clade_Table <- clade_membership(
  tree = "tree.nex",
  ancestral_nodes = ancestral_nodes,
  other_nodes_label = "deep_Squamata_nodes"
)
} # }