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 in the dataframe (metadata). Tip name variable must correspond to tip names in the tree.
phylogenetic_distance: Matrix of phylogenetic distance
variant_distance: Matrix with secondary distance measure, presumably SNPs. This is OPTIONAL. If not specified, the first entry will be gathered (OPTIONAL)
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 focus on isolates with/without a trait
comparison_feature: Name of variable to compare.

Value

The nearest neighbor of interest.