Synchronous permutation test — synchronous_permutation

Permutation test for synchronous detection function

Usage

synchronous_permutation_test(
  comparitor,
  df,
  tr,
  tip_name_variable,
  trait,
  node_states = "joint",
  confidence_threshold = NULL,
  confidence = NULL,
  num_permutations = 1000,
  num_cores = 1
)

Arguments

comparitor: Comparitor, such as a genotype or a different trait/phenotype
df: Dataframe with comparitor, trait, and tip_name_variable
tr: Phylogenetic tree
tip_name_variable: Tip name variable
trait: Trait of interest, such as a trait/phenotype
node_states: Joint or marginal reconstruction
confidence_threshold: Confidence threshold if using marginal reconstruction
confidence: Whether to use high or low confidence transition nodes when node_states are marginal
num_permutations: Number of permutations. Default: 1000
num_cores: Number of cores. Default: 1

Value

Synchronous gain and loss events of two traits with p-value permutation testing results