enve.tribs: Enveomics: TRIBS

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

Enveomics: TRIBS

Description

Subsample any objects in "distance space" to reduce the effect of sample-clustering. This function was originally designed to subsample genomes in "phylogenetic distance space", a clear case of strong clustering bias in sampling, by Luis M. Rodriguez-R and Michael R Weigand.

Usage

enve.tribs(
  dist,
  selection = labels(dist),
  replicates = 1000,
  summary.fx = median,
  dist.method = "euclidean",
  subsamples = seq(0, 1, by = 0.01),
  dimensions = ceiling(length(selection) * 0.05),
  metaMDS.opts = list(),
  threads = 2,
  verbosity = 1,
  points,
  pre.tribs
)

Arguments

dist	Distances as a dist object.
selection	Objects to include in the subsample. By default, all objects are selected.
replicates	Number of replications per point.
summary.fx	Function to summarize the distance distributions in a given replicate. By default, the median distance is estimated.
dist.method	Distance method between random points and samples in the transformed space. See dist.
subsamples	Subsampling fractions.
dimensions	Dimensions to use in the NMDS. By default, 5% of the selection length.
metaMDS.opts	Any additional options to pass to metaMDS, as list.
threads	Number of threads to use.
verbosity	Verbosity. Use 0 to run quietly, increase for additional information.
points	Optional. If passed, the MDS step is skipped and this object is used instead. It can be the $points slot of class metaMDS (from vegan). It must be a matrix or matrix-coercible object, with samples as rows and dimensions as columns.
pre.tribs	Optional. If passed, the points are recovered from this object (except if points is also passed. This should be an enve.TRIBS object estimated on the same objects (the selection is unimportant).

Value

Returns an enve.TRIBS object.

Author(s)

Luis M. Rodriguez-R [aut, cre]

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