MicrobTiSDA: A flexible R package for inferring interspecies interactions and abundance dynamics in microbiome time‐series data

MicrobTiSDA is a user-friendly and flexible R package specifically designed for longitudinal microbiome data analysis. By integrating process-oriented functional modules—including data input, data preprocessing, interspecies interaction inference, natural spline regression modeling, temporal pattern clustering, and random forest classification—MicrobTiSDA enables users to efficiently and systematically infer reliable interspecies interactions and accurately characterize microbial abundance dynamics from time-series data. The package is compatible with diverse experimental designs and provides comprehensive, intuitive visualizations, thereby substantially enhancing both the efficiency of longitudinal microbiome data analysis and the depth of biological interpretation.