Meso‑structural domains, not aggregated networks, reveal the action of structural selection

This repository contains all data, code, and figure outputs required to fully reproduce the analyses presented in the manuscript "Meso‑structural domains, not aggregated networks, reveal the action of structural selection". The dataset includes the raw trophic network, cleaned edge lists, meso‑structural metrics, structural‑selection outputs, figure‑level CSVs, summary tables, and the complete analysis pipeline used to generate all results. The project is organized into the following components: Manuscript files Miranda-Pérez and Mendoza-Reyes Manuscript.pdf (main text). Miranda-Pérez and Mendoza-Reyes Supplementary Material.pdf (figure and tables). /data/ Raw and processed datasets used throughout the pipeline: FW_008.csv — raw adjacency matrix of the food web. fw_cleaned_edges.csv — cleaned directed edge list (from, to, weight). metrics_global_local.csv — global and local meso‑structural metrics per species. metrics_with_domains.csv — same as above, plus k‑means meso‑structural domains. df_full.csv — full meso‑structural dataset including domains and (when available) structural‑selection outputs. df_slopes.csv — per‑egonet structural‑selection slopes and p‑values. FW_008.csv — Raw adjacency matrix of the Caribbean marine food web Source: Bascompte, J., Melián, C. J., & Sala, E. (2005). Interaction strength combinations and the overfishing of a marine food web. Proceedings of the National Academy of Sciences USA, 102: 5443–5447. Original URL: http://www.pnas.org/content/102/15/5443 Description: 249 species/groups (rows = prey, columns = predators) 3313 trophic interactions Connectance = 0.107 Single connected component Cell values represent the relative frequency of prey items in predator diets Cannibalism documented in 11 species/groups Redistribution: This dataset is publicly available from the original source and is included here solely for reproducibility, following standard scientific practice. /data_figures/ One CSV per figure panel, containing the exact data used to generate each plot. These files ensure full reproducibility of Figures 1–4 and Supplementary Figure S1. /tables/ Summary tables corresponding to Tables 1–4 in the manuscript and supplement: table1_global_metrics.csv table2_mesostructural_correlations.csv table3_mesostructural_domains.csv table4_structural_selection.csv /code/ All scripts required to reproduce the full analysis pipeline: run_all.R — master pipeline. 00_clean_data.R — cleaning of the raw adjacency matrix. 01_fig1.R — code for Figure 1. 02_mesostructural_mosaic.R — code for Figure 2. 03_fig3.R — code for Figure 3. 04_fig4.R — code for Figure 4. 05_supp_figure.R — code for Supplementary Figure S1. 06_tables.R — code for summary tables. R/ — utility functions used by the pipeline. /figures_main/ PDF versions of Figures 1–4. /figures_supp/ PDF version of Supplementary Figure S1. All analyses were performed in R using a fully scripted and reproducible workflow. This Zenodo deposit provides complete transparency and ensures long‑term accessibility of all materials associated with the study.本仓库包含完整复现论文《中结构域（meso-structural domains）而非聚合网络（aggregated networks）可揭示结构选择（structural selection）的作用》中所呈现分析所需的全部数据、代码及图形输出。本数据集包含原始营养网络（raw trophic network）、经清洗的边列表（cleaned edge lists）、中结构度量值（meso-structural metrics）、结构选择分析结果、用于生成图形的CSV文件、汇总表格，以及用于生成所有结果的完整分析流程（analysis pipeline）。 本项目按以下模块组织： ## 论文文件 1. Miranda-Pérez与Mendoza-Reyes所著论文主文本（Miranda-Pérez and Mendoza-Reyes Manuscript.pdf）。 2. Miranda-Pérez与Mendoza-Reyes所著补充材料（Miranda-Pérez and Mendoza-Reyes Supplementary Material.pdf，包含所有图形与表格）。 ## /data/ 目录 包含全流程使用的原始与经处理数据集： 1. FW_008.csv — 食物网（food web）的原始邻接矩阵（adjacency matrix）。 2. fw_cleaned_edges.csv — 经清洗的有向边列表（directed edge list，包含起点、终点与权重）。 3. metrics_global_local.csv — 每个物种的全局与局部中结构度量值。 4. metrics_with_domains.csv — 与上述文件内容一致，额外包含k-means聚类得到的中结构域。 5. df_full.csv — 完整的中结构数据集，包含结构域及（如有）结构选择分析结果。 6. df_slopes.csv — 每个自我中心网络（egonet）的结构选择斜率与p值。 ### FW_008.csv 说明 FW_008.csv为加勒比海海洋食物网（Caribbean marine food web）的原始邻接矩阵。 来源：Bascompte, J., Melián, C. J., & Sala, E. (2005). 交互强度组合与海洋食物网过度捕捞. 美国国家科学院院刊（Proceedings of the National Academy of Sciences USA）, 102: 5443–5447. 原始链接：http://www.pnas.org/content/102/15/5443 描述： - 共249个物种类群（行代表猎物，列代表捕食者） - 共3313条营养交互作用 - 连接度（connectance）为0.107 - 单一连通分量（connected component） - 单元格数值表示猎物在捕食者食谱中的相对出现频率 - 11个物种类群存在同类相食（cannibalism）现象 ### 重发布说明 本数据集可从原始来源公开获取，此处仅为满足可复现性要求而收录，符合标准科学出版惯例。 ## /data_figures/ 目录 每个图形面板对应一个CSV文件，包含生成每幅绘图所需的精确数据，可完全复现图1至图4及补充图S1。 ## /tables/ 目录 包含论文及补充材料中表格1至表格4对应的汇总表格： - table1_global_metrics.csv - table2_mesostructural_correlations.csv - table3_mesostructural_domains.csv - table4_structural_selection.csv ## /code/ 目录 包含复现完整分析流程所需的全部脚本： - run_all.R — 主流程脚本。 - 00_clean_data.R — 原始邻接矩阵清洗脚本。 - 01_fig1.R — 图1的生成代码。 - 02_mesostructural_mosaic.R — 图2的生成代码。 - 03_fig3.R — 图3的生成代码。 - 04_fig4.R — 图4的生成代码。 - 05_supp_figure.R — 补充图S1的生成代码。 - 06_tables.R — 汇总表格生成代码。 - R/ — 流程所用的工具函数目录。 ## /figures_main/ 目录 图1至图4的PDF版本。 ## /figures_supp/ 目录 补充图S1的PDF版本。 所有分析均基于R语言完成，采用完全脚本化且可复现的工作流。本Zenodo存档可确保研究相关所有材料的完全透明性与长期可访问性。