Testing Hypotheses About the Microbiome using the Linear Decomposition Model

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Documentation for package ‘LDM’ version 6.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

adjust.data.by.covariates	Adjusting data (distance matrix and OTU table) by covariates
avgdist.squared	Averaging the squared distance matrices each calculated from a rarefied OTU table
jaccard.mean	Expected value of the Jaccard distance matrix
ldm	Testing hypotheses about the microbiome using a linear decomposition model (LDM)
permanovaFL	PERMANOVA test of association based on the Freedman-Lane permutation scheme
sim.meta	Metadata of the simulated microbiome samples
sim.otu.tab	OTU count table of the simulated microbiome samples
sim.otu.tab5	Filtered OTU count table of the simulated microbiome samples
throat.meta	Metadata of the throat microbiome samples
throat.otu.tab	OTU count table from 16S sequencing of the throat microbiome samples
throat.otu.tab5	Filtered OTU count table from 16S sequencing of the throat microbiome samples
throat.tree	UPGMA tree of the OTUs from 16S sequencing of the throat microbiome samples
unifrac.mean	Expected value of the unweighted UniFrac distance matrix