Bayesian compositional models for ordinal response

Ordinal response is commonly found in medicine, biology, and other fields. In many situations, the predictors for this ordinal response are compositional, which means that the sum of predictors for each sample is fixed. Examples of compositional data include the relative abundance of species in micr...

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Bibliographic Details
Published in:Statistical methods in medical research 2024-06, Vol.33 (6), p.1043-1054
Main Authors: Zhang, Li, Zhang, Xinyan, Leach, Justin M, Rahman, AKM F, Yi, Nengjun
Format: Article
Language:English
Subjects:
Algorithms
Bayes Theorem
Bayesian analysis
Biology
Computer Simulation
Humans
Inflammatory Bowel Diseases
Logistic Models
Microbiota
Models, Statistical
Monte Carlo Method
Monte Carlo simulation
Nutrition
Parameter estimation
Regression models
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Summary:Ordinal response is commonly found in medicine, biology, and other fields. In many situations, the predictors for this ordinal response are compositional, which means that the sum of predictors for each sample is fixed. Examples of compositional data include the relative abundance of species in microbiome data and the relative frequency of nutrition concentrations. Moreover, the predictors that are strongly correlated tend to have similar influence on the response outcome. Conventional cumulative logistic regression models for ordinal responses ignore the fixed-sum constraint on predictors and their associated interrelationships, and thus are not appropriate for analyzing compositional predictors.To solve this problem, we proposed Bayesian Compositional Models for Ordinal Response to analyze the relationship between compositional data and an ordinal response with a structured regularized horseshoe prior for the compositional coefficients and a soft sum-to-zero restriction on coefficients through the prior distribution. The method was implemented with R package rstan using efficient Hamiltonian Monte Carlo algorithm. We performed simulations to compare the proposed approach and existing methods for ordinal responses. Results revealed that our proposed method outperformed the existing methods in terms of parameter estimation and prediction. We also applied the proposed method to a microbiome study HMP2Data, to find microorganisms linked to ordinal inflammatory bowel disease levels. To make this work reproducible, the code and data used in this paper are available at https://github.com/Li-Zhang28/BCO.
ISSN:0962-2802
1477-0334
DOI:10.1177/09622802241247730