assess_duplicates {fossilbrush}

assess_duplicates

Description

Function to assess and resolve elements with multiple higher classifications in a tgraph object. Assessment is performed based on the topology of the graph they form. Linear paths (i.e. two totally separate paths diverging from the a shared node), rings (divergent paths which only reunite at the highest rank in the tgraph) or more than two divergent paths are treated as distinct. If not any of these cases, the distance between the focal element and the reunion of the divergent paths, along with their subtopologies are assessed and a consensus or preferred path based on the frequency of each path in the tgraph or their completeness returned, or the element judged as having multiple distinct classifications

Usage

assess_duplicates(
  x,
  node,
  mode = c("frequency", "completeness"),
  jump = 3,
  plot = FALSE
)

Arguments

x

A tgraph object

node

character vector of elements with multiple higher classifications in x, or a tvertseq object with those same elements as focal

mode

The rule to be used in selecting between multiple higher classifications. It is possible for the most complete pathway to also be the most frequent

jump

The maximum number of levels between the point of divergence and the point of reunion (if present) for a given path, below which the divergence will be taken as conflicting

plot

A logical speciying if the divergent paths should be plotted

Value

A list with as many items as elements with multiple classifications, each recording the assessment for a given element