downstream_permutation_test: Permutation test for downstream analysis

Permutation test for analysis of downstream gain and loss of a comparitor trait on stretches of a different trait of interest

Usage

downstream_permutation_test(
  comparitor,
  df,
  tr,
  tip_name_variable,
  trait,
  node_states = "joint",
  confidence_threshold = NULL,
  confidence = NULL,
  num_permutations = 1000,
  num_cores = 6
)

Arguments

comparitor: Comparitor trait, such as a genotype or a different trait/phenotype
df: Dataframe with trait and comparitor and tip_name_variable
tr: Phylogenetic tree
tip_name_variable: Tip name variable
trait: Trait of interest. Their stretches of trait presence will be characterized and evaluated
node_states: Joint or marginal reconstruction
confidence_threshold: Set value for confidence threshold of MLE calls if marginal
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 = 6

Value

Summary stats for downstream gain and loss of a trait