A Bayesian approach for analysis of ordered categorical responses subject to misclassification

PLoS One. 2018 Dec 13;13(12):e0208433. doi: 10.1371/journal.pone.0208433. eCollection 2018.

Abstract

Ordinal categorical responses are frequently collected in survey studies, human medicine, and animal and plant improvement programs, just to mention a few. Errors in this type of data are neither rare nor easy to detect. These errors tend to bias the inference, reduce the statistical power and ultimately the efficiency of the decision-making process. Contrarily to the binary situation where misclassification occurs between two response classes, noise in ordinal categorical data is more complex due to the increased number of categories, diversity and asymmetry of errors. Although several approaches have been presented for dealing with misclassification in binary data, only limited practical methods have been proposed to analyze noisy categorical responses. A latent variable model implemented within a Bayesian framework was proposed to analyze ordinal categorical data subject to misclassification using simulated and real datasets. The simulated scenario consisted of a discrete response with three categories and a symmetric error rate of 5% between any two classes. The real data consisted of calving ease records of beef cows. Using real and simulated data, ignoring misclassification resulted in substantial bias in the estimation of genetic parameters and reduction of the accuracy of predicted breeding values. Using our proposed approach, a significant reduction in bias and increase in accuracy ranging from 11% to 17% was observed. Furthermore, most of the misclassified observations (in the simulated data) were identified with a substantially higher probability. Similar results were observed for a scenario with asymmetric misclassification. While the extension to traits with more categories between adjacent classes is straightforward, it could be computationally costly. For traits with high heritability, the performance of the methodology would be expected to improve.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Bayes Theorem
  • Bias
  • Body Weight / physiology
  • Breeding / methods
  • Breeding / statistics & numerical data*
  • Cattle* / classification
  • Cattle* / genetics
  • Datasets as Topic / classification
  • Datasets as Topic / statistics & numerical data
  • Female
  • Genetic Association Studies / statistics & numerical data
  • Genetic Association Studies / veterinary
  • Markov Chains
  • Meat / statistics & numerical data
  • Models, Statistical*
  • Parturition / physiology
  • Phenotype
  • Physical Fitness
  • Pregnancy
  • Quantitative Trait, Heritable

Grants and funding

AL was funded by the United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) through the National Needs Grant, grant number 11754154 to RR, https://nifa.usda.gov/. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.