Online Program Home
My Program

Abstract Details

Activity Number: 465 - SPEED: Statistical Computing: Methods, Implementation, and Application, Part 1
Type: Contributed
Date/Time: Wednesday, July 31, 2019 : 8:30 AM to 10:20 AM
Sponsor: Section for Statistical Programmers and Analysts
Abstract #306990 Presentation 1 Presentation 2
Title: Tidi_MIBI: a Tidy Pipeline for Microbiome Analysis and Visualization in R
Author(s): Charlie Carpenter*
Companies: University of Colorado-Biostatistics
Keywords: Microbiome; R; tidyverse; pipeline; visualization; negative binomial modeling
Abstract:

We have developed an R package called tidi_MIBI to streamline microbiome management and analysis within the “tidy” framework developed by Hadley Whickham. The package provides a single, built in function that formats OTU tables from multiple taxonomic levels, calculates taxa prevalence, relative abundance, and a CLR transformation, and finally merges in clinical data. It also includes functions for basic ecological calculations and plots. A main feature of tidy_MIBI is negative binomial (NB) regression models for taxa relative abundance. With one line of code users can fit NB models to each taxa within a taxonomic rank with options to include random effects. The function returns user-friendly model summaries including the estimate rate ratios, confidence intervals, and FDR corrected p-values. A unique inclusion for tidi_MIBI is the inclusion of stacked bar charts of estimated relative abundance based on NB models, a novel and powerful tool for visualizing the results of dozens of models simultaneously. We demonstrate the usability of tidi_MIBI through application to an existing study on maternal obesity and gestational diabetes and the infant microbiome.


Authors who are presenting talks have a * after their name.

Back to the full JSM 2019 program