Dataset and Replication Code for “Insects Associated with Declining Riparian Black Alder (Alnus glutinosa) Stands: Assemblage Structure, Seasonality, and the Role of Microhabitats in the Valleys of the Utrata and Łutownia Rivers”
Description
This repository contains the primary analytical input, replication code, and selected derived outputs supporting the community-level analyses reported in the associated manuscript on insect assemblages associated with declining riparian black alder stands in the valleys of the Utrata and Łutownia rivers, Poland. The deposit is designed as a compact reproducibility package: it includes the cleaned analytical matrix, the metadata required to interpret that matrix, and machine-readable outputs needed to verify the published diversity, beta-diversity, NMDS, and rarefaction/extrapolation results. Files included: Insects_list.xlsx — Primary input file containing the taxon abundance data arranged by river and distance classes used by the replication workflow. Replication_Code.R — R script that reads the input data, performs the community-level analyses, and generates the reproducible outputs deposited in this repository. clean_species_by_stratum.csv — Cleaned taxon-by-stratum abundance matrix used as the principal analytical dataset for the published results. sample_metadata.csv — Metadata table linking each analytical stratum to river identity and distance from the channel margin. taxon_lookup.csv — Lookup table linking analytical taxon identifiers to the reported taxonomic names used in the study. diversity_bootstrap_CI_long.csv — Full bootstrap output for richness, diversity, evenness, and sample-coverage metrics by stratum. beta_pairwise_long.csv — Complete pairwise Sørensen beta-diversity table, including turnover and nestedness components, for all stratum combinations. nmds_site_scores.csv — Coordinates of the six analytical strata in the exploratory NMDS ordination. nmds_species_scores.csv — Taxon scores from the exploratory NMDS ordination for interpretive use outside the main text. rarefied_richness_to_min_N.csv — Rarefied richness estimates standardised to the smallest observed stratum abundance. iNEXT_AsyEst.csv — Asymptotic richness and diversity estimates generated by iNEXT. iNEXT_iNextEst.csv — Interpolation and extrapolation estimates generated by iNEXT across sample-size and coverage gradients. nmds_diagnostics.txt — Diagnostic summary for the NMDS solution, including stress and dimensionality. README_dataset.txt — Plain-text repository guide containing the title, repository description, and reproduction instructions. The repository does not prioritise technical helper files used only for column detection, automatically regenerated distance matrices, or figure files already shown in the manuscript. These products can be recreated directly from Insects_list.xlsx and Replication_Code.R, so the deposited package remains concise while still fully supporting verification, re-use, and re-analysis.
Files
Steps to reproduce
Place Replication_Code.R and Insects_list.xlsx in the same working directory before running the analysis. Open R and install the packages required by the script, including dplyr, stringr, stringi, readr, readxl, vegan, betapart, ggplot2, and iNEXT. Ensure that the working directory has write permission, because the script creates output folders and exports tables and analytical summaries. Run Replication_Code.R without changing the input filename unless you also modify the path in the script. The script reads Insects_list.xlsx, detects the analytical columns corresponding to the six river–distance strata, cleans and aggregates the taxon data, reconstructs the abundance and presence–absence community matrices, and computes the diversity summaries, bootstrap confidence intervals, beta-diversity decomposition, rarefied richness, iNEXT interpolation/extrapolation outputs, and the exploratory NMDS ordination. The regenerated outputs can then be compared with the deposited csv and txt files included in this repository, which serve as machine-readable reference results. The manuscript tables and figures reporting diversity patterns, rarefaction/extrapolation, beta diversity, and NMDS can be reproduced directly from the regenerated outputs, while purely technical intermediates and duplicate figure files are intentionally not prioritised in the repository because they are already reproducible from the deposited input file and code.
Institutions
- Bialystok University of TechnologyPodlasie, Bialystok