Supplementary code and data for "Foliar stoichiometry of Bornean forest seedlings across a logging–restoration gradient: species turnover and a robust calcium-balance shift"

This deposit contains the analysis code and the processed datasets thatunderlie the article "Foliar stoichiometry of Bornean forest seedlingsacross a logging–restoration gradient: species turnover and a robustcalcium-balance shift" (Goycochea Casas & Ismail, Plant Ecology,submitted). Background. The article is a re-analysis of seedling trait and foliarnutrient data from Danum Valley, Sabah (Malaysian Borneo), comparingunlogged primary forest (UL), naturally regenerating logged forest (NR)and actively restored logged forest (AR). It shows that the multi-elementfoliar stoichiometric differences among management types arepredominantly a species-turnover effect, and that the one signal robustto species composition is a calcium-balance shift (Ca:Mg, with N:Ca). Primary data (not redistributed; openly archived elsewhere): • Burslem et al. (2022) Tropical forest seedling trait data, Danum Valley, Feb 2020. NERC EDS EIDC. https://doi.org/10.5285/e738e8af-554a-4940-bb56-267c7377d74d • Burslem et al. (2022) Tropical forest seedling census data, Danum Valley, 2019–2021. NERC EDS EIDC. https://doi.org/10.5285/c1813d0d-193f-4f23-82c6-333d5d099b42 • Bartholomew et al. (2024) Glob. Change Biol. https://doi.org/10.1111/gcb.17209 Contents of this archive: • scripts/ — 18 numbered Python analysis scripts (01–18) implementing every step from data preparation to the canonical PERMANOVA cross-check and the formatting pass that produces the supplementary tables of the article. • data/processed/ — three processed datasets the scripts consume: traits_stoichiometric.csv (390 individual records with complete foliar nutrients) traits_stoich_deduplicated.csv (128 species–plot–stoichiometric profiles; the analytical dataset) survival_species_treatment.csv (species × management survival) • results/, manuscript/generated/ — empty output folders; populated when the scripts are run. • README.txt — detailed contents, dependencies, mapping of scripts to article outputs (Tables S7–S12 and Figure S1), and reproduction notes. • LICENSE — Creative Commons Attribution 4.0 International (CC-BY 4.0). Reproducibility. All permutation tests use a fixed seed (SEED = 42) and99 999 permutations; the stoichiometric space is standardised once overthe full deduplicated dataset and every subset / scenario is a subset ofthat single space. Reported p-values and pseudo-F statistics aretherefore exactly reproducible. Scripts 11, 13, 14, 16, 17 and 18 rundirectly from this archive against data/processed/; scripts 01–10 and 12rebuild earlier intermediates from the openly archived raw data linkedabove and assume the original project layout. Software. Python 3.11 with pandas, numpy, scipy, scikit-learn,statsmodels, scikit-bio (skbio), matplotlib and seaborn. License. CC-BY 4.0 — you may share and adapt the material withattribution. See the LICENSE file. How to cite. Goycochea Casas, G. & Ismail, Z. H. (2026). Supplementarycode and data for "Foliar stoichiometry of Bornean forest seedlingsacross a logging–restoration gradient: species turnover and a robustcalcium-balance shift". Zenodo. https://doi.org/10.5281/zenodo.XXXXXXX