Dirichlet factor analysis model with fixed effects and its application in microbiome data analysis.
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R/MCMC.R: main functions for MCMC simulations.
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R/simulation_studies.R: script used to perform all simulation studies in the manuscript.
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R/diabimmune_analysis.R: script used to analyze the Diabimmune dataset based on the mixed effects model.
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R/sim_compare.R: example script used to compare the performance of DirFactor and MIMIX.
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R/utilities.R: useful helper functions.
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R/Added_simulations/: source scripts for the added simulation analyses in the most recent submission.
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data/diabimmune_genus.txt: OTU table collapsed to genus level for Diabimmune project. Shotgun sequencing results.
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data/DIABIMMUNE_metadata_full.RData: RData object for all relevant metadadata.
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data/genus_tree.tre: Newick format phylogenetic tree of microbial genera published in Segata et. al. (2013).