jaccard.mean: Expected value of the Jaccard distance matrix

In LDM: Testing Hypotheses About the Microbiome using the Linear Decomposition Model

Expected value of the Jaccard distance matrix

Description

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

Usage

jaccard.mean(
  otu.table,
  rarefy.depth = min(rowSums(otu.table)),
  first.order.approx.only = FALSE
)

Arguments

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

Value

a list consisting of

jac.mean.o1	Expected Jaccard distance matrix by the first order approixmation.
jac.mean.o2	Expected Jaccard distance matrix by the second order approixmation.
jac.mean.sq.o1	Expected squared Jaccard distance matrix by the first order approixmation.
jac.mean.sq.o2	Expected squared Jaccard distance matrix by the second order approixmation.

Author(s)

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

Examples

res.jaccard <- jaccard.mean( throat.otu.tab5 )

LDM documentation built on Sept. 8, 2023, 5:58 p.m.