Identify the phylogenetic nearest neighbor of a tip — nearest_neighbor

This function uses phylogenetics to identify an isolate's nearest neighbor.

Usage

nearest_neighbor_algorithm(
  isolate,
  tip_name_variable,
  phylogenetic_distance,
  variant_distance,
  metadata,
  annotate = NULL,
  variables_of_interest = NULL,
  comparison = NULL,
  comparison_feature = NULL
)

Arguments

isolate: Isolate of interest
tip_name_variable: Name of variable containing tip names. Must be found in the metadata, dataframe. Tip name entries must also correspond to tip names in the tree
phylogenetic_distance: Matrix of phylogenetic distance. Generated by ape::cophenetic.phylo(tree)
variant_distance: (OPTIONAL) Matrix with secondary distance measure, presumably SNPs. If not specified, the first entry will be gathered
metadata: Dataframe with trait and variables of interest
annotate: Boolean (TRUE/FALSE) indicating if annotation is necessary
variables_of_interest: Variables found in the metadata
comparison: Boolean (TRUE/FALSE) indicating whether to restrict analysis to isolates with/without a trait (comparison_feature)
comparison_feature: Name of variable to compare

Value

Dataframe with the nearest neighbor of interest.