LDM (version 6.0.1)

unifrac.mean: Expected value of the unweighted UniFrac distance matrix

Description

This function computes the expected value of the unweighted UniFrac distance matrix over rarefaction replicates.

Usage

unifrac.mean(
  otu.table,
  tree,
  rarefy.depth = min(rowSums(otu.table)),
  first.order.approx.only = FALSE,
  verbose = TRUE
)

Value

a list consisting of

unifrac.mean.o1

Expected unweighted UniFrac distance matrix by the first order approixmation.

unifrac.mean.o2

Expected unweighted UniFrac distance matrix by the second order approixmation.

unifrac.mean.sq.o1

Expected squared unweighted UniFrac distance matrix by the first order approixmation.

unifrac.mean.sq.o2

Expected squared unweighted UniFrac distance matrix by the second order approixmation.

Arguments

otu.table

the n.obs by n.otu matrix of read counts.

tree

the phylogeneic tree.

rarefy.depth

rarefaction depth. The default is the minimum library size observed in the OTU table.

first.order.approx.only

a logical value indicating whether to calculate the expected value using the first order approixmation by the delta method. The default is FALSE, using the second order approixmation.

verbose

a logical value indicating whether to generate verbose output. Default is TRUE.

Author

Yi-Juan Hu <[e-mail]>, Glen A. Satten <[e-mail]>

Examples

data(throat.otu.tab5)
data(throat.tree)
res.unifrac <- unifrac.mean( throat.otu.tab5[1:20,], throat.tree)