Function to generate an annotated edge matrix with ancestral and tip states
Usage
get_parent_child_data(
tr,
ancestral_states,
trait_data,
node_states,
confidence_threshold = NULL
)Arguments
- tr
Phylogeny object of class "phylo"
- ancestral_states
Ancestral states inferred by corHMM. Stored in corHMM_obj$states
- trait_data
Named phenotype/trait string. Strings' values correspond to the tip states. Strings' names correspond to the tip names.
- node_states
Perform "joint" or "marginal" reconstruction. Default: joint
- confidence_threshold
The confidence threshold to categorize ancestral state inferences from a marginal reconstruction.We suggest using a value of 0.5 (i.e., winner takes all), but permit modification to elevated values. Required when node_states == "marginal". If the MLE estimate does not fit under or above the threshold, the node's prediction is 'unsure' and labeled as 0.5.