R Code and Data for Null-Model Randomization and Competition Analysis in Aquatic Macrophyte Communities

Description This repository provides R code and empirical data supporting the analysis of functional trait convergence and divergence in aquatic macrophyte communities within the framework of the Stress–Dominance Hypothesis (SDH). The analytical framework integrates null-model randomization, functional diversity assessment, environmental filtering, and interspecific competition analysis to distinguish the contributions of deterministic and stochastic processes to community assembly. Null-model randomization The R code implements ten alternative randomization models designed to evaluate departures from random patterns of functional diversity: C1–C5: Randomization of community composition and species abundances under different constraints. T1–T4: Randomization of functional traits, including independent trait permutations and permutations constrained by species abundance classes. Range: Randomization based on species-pool constraints. Functional diversity is quantified using Rao's quadratic entropy (Rao's Q). Deviations from null-model expectations are expressed as standardized effect sizes (SES), allowing the identification of functional convergence and divergence. Environmental and competition-related trait components The analytical framework includes the decomposition of species functional traits into environmentally structured, competition-associated, and residual components. RLQ analysis is used to identify joint relationships among environmental conditions, species composition, and functional traits. The environmentally structured component is estimated using weighted regression of species traits on RLQ-derived axes. Interspecific competition is represented through a competition coefficient matrix. Singular value decomposition (SVD) and regularized regression are used to identify components of functional trait variation associated with competitive interactions. Repository contents library_Null.docx — R code implementing null-model randomization, Rao's Q calculations, SES estimation, and related analyses. library_Competition.docx — R code for functional trait decomposition and competition-related analyses. spec.txt — Species composition and abundance matrix for aquatic macrophyte communities. traits_plant.txt — Species functional trait matrix. Purpose and reproducibility The repository is intended to facilitate methodological transparency, reproducibility, and further application of null-model approaches and competition-based trait analysis in community ecology. The supplied code and data provide a basis for reproducing and adapting the analytical procedures used to investigate functional community assembly and the Stress–Dominance Hypothesis.