Analysis of downstream transitions of comparitor traits

Downstream gain and loss of a comparitor trait on stretches of a different trait of interest

Usage

downstream_transitions(
  comparitor_parent_child_df,
  trait_parent_child_df,
  tr,
  node_states = "joint",
  confidence = NULL
)

Arguments

comparitor_parent_child_df

Parent child dataset for a comparitor trait, such as a genotype or a different trait/phenotype

trait_parent_child_df

Parent child dataset for a trait of interest, such as a trait/phenotype

tr

Phylogenetic tree

node_states

Joint or marginal reconstruction

confidence

Whether to use high or low confidence transition nodes when node_states are marginal

Value

Summary stats for downstream gain and loss of a trait