Generic R workflow for longitudinal, multi-site wastewater metagenomics: microbiome and antimicrobial resistance gene analysis

Generic R workflow (template). Companion code to a manuscript under review (Pathogens, ID pathogens-4535216). ## What this deposit contains `Generic_Analysis_Workflow.R` is a generic template of the statistical steps used in the study. It takes user-supplied tables (formats described in the script header: genus counts, sample metadata, ARG annotation events, per-sample ARG abundance) and covers: - **Alpha diversity**: repeated rarefaction, Kruskal-Wallis tests, mixed models with sampling date as random intercept. - **Beta diversity**: PERMANOVA, date-blocked PERMANOVA, PERMDISP, Aitchison distance, and an exhaustive whole-date permutation test of the season effect. - **Differential abundance**: ALDEx2, date-blocked Friedman test, date-level sensitivity analysis. - **Targeted taxa**: detection at read-count thresholds. - **Antimicrobial resistance genes**: independent loci from overlapping annotations, broad resistance classes, sample-resolved resistome composition, dispersion, and sensitivity to a minimum-support threshold. ## Scope and limitations This is a generic template. It contains no study data or sample identifiers and does not reproduce the published numbers. The broad-class mapping is keyword-based and should be checked manually. ## Requirements R (>= 4.3) with: dplyr, tidyr, tibble, vegan, zCompositions, ALDEx2, lme4, lmerTest, pbkrtest, emmeans. Set the input file names and parameters in the CONFIGURATION block of the script. ## Reproducibility `set.seed(123)` is called immediately before every stochastic step. ALDEx2 results are Monte-Carlo based and can differ slightly between package versions. ## Access No data are included in this record. # Licence © 2026 Fatma Z Guerfali. All rights reserved. This work may be cited (please cite the DOI of this record); it may not be reused, modified or redistributed without prior written permission from the corresponding author.