ZIdtmFit: Fit the Zero-inflated Dirichlet-tree multinomial (ZIDTM)...

In liudoubletian/phyloMDA: An R package for phylogeny-aware microbiome data analysis

Fit the Zero-inflated Dirichlet-tree multinomial (ZIDTM) distribution.

Description

Fit the Zero-inflated Dirichlet-tree multinomial (ZIDTM) distribution.

Usage

ZIdtmFit(otu.tab, tree)

Arguments

otu.tab	a data frame or matrix containing the count data. Rows of the matrix represent observations and columns are the taxa.
tree	the phylogenetic tree (should be binary here).

Value

Returns a list, containing results of each subtree.

References

Zhou, C., Zhao, H., and Wang, T.: Transformation and differential abundance analysis of microbiome data incorporating phylogeny. Bioinformatics btab543, https://doi.org/10.1093/bioinformatics/btab543 (2021).

Examples

library(phyloseq)
data("combo.phyloseq.obj")
otu.tab <- t(otu_table(combo.phyloseq.obj))
tree <- phy_tree(combo.phyloseq.obj)
fit <- ZIdtmFit(otu.tab, tree)
Extract_logL(fit)

liudoubletian/phyloMDA documentation built on April 28, 2022, 6:51 p.m.