LDM (version 6.0.1)

jaccard.mean: 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
)

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.

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.

Author

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

Examples

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