enve.recplot2.compareIdentities: Enveomics: Recruitment Plot (2) Compare Identities

In enveomics.R: Various Utilities for Microbial Genomics and Metagenomics

Enveomics: Recruitment Plot (2) Compare Identities

Description

Compare the distribution of identities between two enve.RecPlot2 objects.

Usage

enve.recplot2.compareIdentities(
  x,
  y,
  method = "hellinger",
  smooth.par = NULL,
  pseudocounts = 0,
  max.deviation = 0.75
)

Arguments

x	First enve.RecPlot2 object.
y	Second enve.RecPlot2 object.
method	Distance method to use. This should be (an unambiguous abbreviation of) one of: "hellinger" (Hellinger, 1090, doi:10.1515/crll.1909.136.210), "bhattacharyya" (Bhattacharyya, 1943, Bull. Calcutta Math. Soc. 35), "kl" or "kullback-leibler" (Kullback & Leibler, 1951, doi:10.1214/aoms/1177729694), or "euclidean"
smooth.par	Smoothing parameter for cubic spline smoothing. Use 0 for no smoothing. Use NULL to automatically determine this value using leave-one-out cross-validation (see smooth.spline parameter spar).
pseudocounts	Smoothing parameter for Laplace smoothing. Use 0 for no smoothing, or 1 for add-one smoothing.
max.deviation	Maximum mean deviation between identity breaks tolerated (as percent identity). Difference in number of id.breaks is never tolerated.

Value

A numeric indicating the distance between the objects.

Author(s)

Luis M. Rodriguez-R [aut, cre]

enveomics.R documentation built on April 13, 2022, 5:10 p.m.