Recalculated woody crown hydraulic network properties and reduced principal component analyses of Caatinga and Cerrado trees

Woody Crown Hydraulic Network (WCHN): mathematical revisions, corrected datasets, and reproducible computational resources This repository provides an integrated historical, mathematical, empirical, and computational resource for the Woody Crown Hydraulic Network (WCHN) framework. It brings together the foundational development of the model, revised property definitions and their algebraic consequences, corrected crown-network records, ecological reanalyses, editable network drawings, and software for reconstructing and analyzing existing or newly constructed WCHNs. The deposit is an independent scientific resource, not tied to a particular journal or manuscript. HISTORICAL FOUNDATION Four publications document the model's development: (1) Souza et al. (2011), the original network analysis of Cerrado crowns (https://doi.org/10.1007/s11258-010-9797-7); (2) Prado et al. (2020), formalization of decomposition, topology, and four initial properties (https://doi.org/10.1016/j.jtbi.2020.110318); (3) Prado and Trovão (2023), expansion to eight properties and Caatinga–Cerrado comparisons (https://doi.org/10.1016/j.ecolmodel.2023.110345); and (4) Prado (2024), stochastic node-addition networks and size-matched comparisons (https://doi.org/10.1007/s40626-024-00340-5). These references allow users to trace the original definitions and later revisions. MATHEMATICAL AND EMPIRICAL CONTENT The author-prepared document “Algebraic relationships and mathematical properties of the Woody Crown Hydraulic Network” explains the revised symmetry (SYM), complexity (COM), and vulnerability (VUL) definitions, algebraic dependencies, network-size effects, and reproducibility checks. In particular, revised VUL is exactly equal to normalized mean node depth in a rooted tree. The observed near-reciprocity between navigability (NAV) and VUL is a strong empirical association, not a second exact identity or independent hydraulic measurement. The deposit retains the original Cerrado and Caatinga source spreadsheets, recalculated property tables, comparisons, reduced principal component analyses (PCAs), and size-adjusted exploratory analyses. The previously deposited PCA outputs are preserved numerically; their interpretations should account for the revised mathematical meaning of VUL. The updated PCA technical note documents the analytical methods and limitations. CORRECTED CERRADO NETWORKS AND TOOLKIT A new workbook records corrections to 20 previously sampled Cerrado WCHNs (not additional independent observations). Six networks were reconstructed manually, including S. polyphyllum 1 as the manual feasibility pilot; fourteen were reconstructed semi-automatically, beginning with S. camporum 1 as the first test of the connector generator, followed by thirteen additional networks. In the semi-automatic workflow, the researcher marked the nodes, deterministic software proposed editable connectors and highlighted ambiguous nodes in red, and the researcher visually checked and corrected the complete graph against the original drawing beneath it. The WCHN toolkit v1.0.3 contains code, documentation, editable PowerPoint networks, intermediate files, tests, and a separate semi-automatic validation exercise using Miconia albicans 5, a network originally reconstructed manually. That exercise led to a verified terminal-connector decomposition correction without changing the network topology or any of its eight WCHN properties. The accompanying Practical Guide v1.0.3 provides step-by-step instructions for reconstructing, inspecting, validating, and analyzing WCHNs, including optional AI assistance under mandatory researcher supervision. REPRODUCIBILITY AND LIMITATIONS The accompanying README.md provides the complete file inventory, foundational references, directions for reusing the toolkit and statistical scripts, links among materials, and version history. These resources enable checking corrected topologies and calculations and exploring newly created WCHNs, with mandatory human inspection where graphical connections are ambiguous. They do not establish that topological vulnerability equals embolism vulnerability, nor do they experimentally validate the proposed links to hydraulic safety or attainable height. The mathematical document is provided for transparency and reproducibility; its inclusion does not imply peer review, journal acceptance, or publication of an associated manuscript. Earlier versions of this Zenodo record retain their historical files and READMEs. Related stochastic network experiments and code are available separately at https://doi.org/10.5281/zenodo.21839645 . For citation and reproducibility, use the version-specific DOI assigned by Zenodo to the files actually consulted; older record versions preserve their historical documentation.