enve.tribs {enveomics.R}

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]