setUpData: Set-up data for latent Dirichlet allocation

In PratheepaJ/diffTop: Differential topic analysis using latent Dirichlet allocation

Description

Set-up data for latent Dirichlet allocation

Usage

setUpData(ps, K, alpha = 0.9, gamma = 0.5)

Arguments

ps	phyloseq class.
K	Integer. Number of topics.
alpha	Non-negative numeric. Hyper-parameter alpha is less than one to generate sparse mixtures that are different from each other and avoid generating unrealistic topics.
gamma	Non-negative numeric. Hyper-parameter gamma is less than one to generate sparse mixtures of ASVs in each topic.

Value

List. List of object with number of topics, number of ASVs, number of specimens, count table, hyper parameters for topic and ASVs distribution.

PratheepaJ/diffTop documentation built on Dec. 18, 2021, 7:48 a.m.