BEF_Coextinctions_Repo

<h2>Overview</h2><p dir="ltr">This repository contains all data, code, and supplementary materials associated with the manuscript "<i>Co-extinctions and co-compensatory species responses to climate change moderate ecosystem futures</i>". The repository enables full reproduction of all analyses, figures, and results presented in the paper.</p><h2>Repository Structure</h2><h3>�� Data Files</h3><h4>Raw Data</h4><ul><li><code><strong>ChAOS_2018_macrofauna_data.csv</strong></code> - Original macrofaunal survey data from the ChAOS 2018 sampling campaign</li><li><ul><li><b>Columns</b>: <code>ScientificName_accepted</code>, <code>Mi</code> (mobility trait, 1-4 scale), <code>Ri</code> (reworking trait, 1-5 scale), <code>Source</code> (trait classification source), <code>Link</code>, <code>Year</code> (sampling year), <code>Station</code>, <code>Replicate</code>, <code>Abundance</code> (total abundance), <code>Biomass</code> (total biomass in grams)</li><li>Contains species-level abundance and biomass with functional traits</li><li>Used in: <code>CoExt_ChAOS_SupplementaryCode.Rmd</code></li></ul></li></ul><h4>Processed Data</h4><ul><li><code><strong>ChAOS_2018_macrofauna_model_ready.csv</strong></code> - Model-ready macrofaunal dataset with extinction scenarios</li><li><ul><li><b>Columns</b>: <code>ScientificName_accepted</code>, <code>Habitat</code> (Arctic/Boreal region), <code>Station</code> (pre-extinction station), <code>Scenario</code> (extinction scenario, e.g., B17-B16), <code>Mi</code>, <code>Ri</code>, <code>Bi</code> (mean individual body size in grams), <code>Ai</code> (mean abundance at pre-extinction station), <code>Btot</code> (total biomass at pre-extinction station), <code>Atot</code> (total abundance at pre-extinction station), <code>Bind_Habitat</code> (mean body size within habitat), <code>Bind_Scenario</code> (mean body size across scenario stations), <code>B_Vulnerability</code> (vulnerability rank score based on Table S2), <code>Amed</code> (median abundance in post-extinction regional pool)</li><li><b>B_Vulnerability</b>: Ranked vulnerabilities to climate-driven transitions based on percentage biomass differences between pre-extinction (northernmost) and post-extinction (southernmost) stations for regional species pool (n=113). "Inf." indicates taxa absent from pre-extinction but present in post-extinction communities.</li><li>Species-level data structured for co-extinction modeling across climate scenarios</li><li>Used in: <code>CoExt_ChAOS_model.Rmd</code></li></ul></li><li><code><strong>ChAOS_2018_allstations_Competitors[based_off_Biomass].csv</strong></code> - Pairwise species competition coefficients (Table S3b)</li><li><ul><li><b>Columns</b>: Row number, <code>x</code> (species 1), <code>y</code> (species 2), <code>correlation_coefficient</code> (Pearson correlation)</li><li>Contains negative correlations (n = 6) ≥1.5 standard deviations from mean coefficient value</li><li>Represents competitive interactions between species pairs</li><li>Referenced as Table S3(b) and Figure S4 in manuscript</li><li>Used in: <code>CoExt_ChAOS_model.Rmd</code></li></ul></li><li><code><strong>ChAOS_2018_allstations_Co_Occurence[based_off_Biomass].csv</strong></code> - Species co-occurrence correlation matrix (Table S3a)</li><li><ul><li><b>Columns</b>: Row number, <code>x</code> (species 1), <code>y</code> (species 2), <code>correlation_coefficient</code> (Pearson correlation)</li><li>Contains positive correlations (n = 460) representing co-occurrence patterns</li><li>Spatial co-occurrence relationships derived from biomass distributions</li><li>Referenced as Table S3(a) in manuscript</li><li>Used in: <code>CoExt_ChAOS_model.Rmd</code></li></ul></li></ul><h3>�� Code Files</h3><h4>Main Analysis Scripts</h4><ul><li><code><strong>CoExt_ChAOS_model.Rmd</strong></code> - Primary co-extinction and compensation model</li><li><ul><li><b>Purpose</b>: Implements species extinction and compensation dynamics across Barents Sea climate gradient</li><li><b>Study System</b>: Macrobenthic communities from 2018 ChAOS expedition (RRS James Clark Ross)</li><li><b>Scenarios</b>: Six climate transition levels (B17→B16, B16→B15, B15→Xs, Xs→B14, B14→B13, B17→B13)</li><li><b>Model Framework</b>: Species sensitivity based on biomass differences between adjacent stations; co-occurrence relationships determine secondary extinctions and compensatory responses</li><li><b>Function</b>: Runs the model and generates Model Output Files needed for manuscript figures</li><li><b>Output Variables</b>:</li><li><ul><li><code>Simulation</code>: Simulation number</li><li><code>Nsp</code>: Total species remaining in community</li><li><code>CompRep</code>: Number of compensating species per extinction</li><li><code>Nsp_active</code>: Number of species present (active) in community</li><li><code>ExtSp</code>: Species going extinct at next step</li><li><code>CoExtSp</code>: Species undergoing co-extinction at next step</li><li><code>CompSp</code>: Species compensating at next step</li><li><code>AbnComp</code>: Abundance increase in compensating species</li><li><code>BioComp</code>: Biomass increase in compensating species</li><li><code>BioLost</code>: Biomass lost per extinction (if compensation incomplete)</li><li><code>TotBio</code>: Total community biomass remaining</li></ul></li><li><b>Key Features</b>: Only present species can go extinct; all non-extinct species can compensate; extinction is permanent</li><li>Dependencies: See <code>sessionInfo()</code> output in script</li></ul></li><li><code><strong>CoExt_ChAOS_SupplementaryCode.Rmd</strong></code> - Data processing and supplementary analyses</li><li><ul><li><b>Purpose</b>: Data wrangling, quality control, and supplementary code chunks S1-S8</li><li><b>Study System</b>: Same Barents Sea macrobenthic dataset from 2018 ChAOS expedition</li><li><b>Content</b>: Initial data processing pipeline and supplementary analyses referenced in main manuscript</li><li><b>Prerequisites</b>: Should be run before main model script</li><li>Generates supplementary figures and tables</li></ul></li></ul><h3>�� Model Output Files</h3><h4>Full Model (Co-extinction + Co-compensation)</h4><ul><li><code><strong>Full_Model_Coext_Cocomp_Output_[1-6].csv</strong></code> - Main model results (500 simulations per scenario)</li><li><ul><li><b>Columns</b>: <code>Simulation</code>, <code>Nsp</code>, <code>CompRep</code>, <code>Nsp_active</code>, <code>ExtSp</code>, <code>CoExtSp</code>, <code>CompSp</code>, <code>AbnComp</code>, <code>BioComp</code>, <code>BioLost</code>, <code>TotBio</code> (see main script documentation for variable definitions)</li><li>Used in: Main manuscript figures</li></ul></li><li><code><strong>Full_Model_Coext_Cocomp_Output_[1-6].rds</strong></code> - Species-level contributions dataframe ⚠️ <b>Large files</b></li><li><ul><li><b>Columns</b>: <code>Simulation</code>, <code>Nsp</code>, <code>Nsp_active</code>, <code>species</code> (ScientificName_accepted), <code>species_AiSim</code>, <code>species_Bind</code>, <code>species_Mi</code>, <code>species_Ri</code>, <code>species_BPi</code>, <code>BPc</code></li><li>Contains full community state at each simulation iteration for detailed analysis</li><li>Memory intensive: Complete species-by-simulation matrices</li></ul></li></ul><h4>Reduced Model (Co-extinction only)</h4><ul><li><code><strong>Reduced_Model_Coext_No_Comp_Output_[1-6].csv</strong></code> - Model results without compensation mechanisms</li><li><ul><li>Same column structure as Full Model outputs</li><li>Used for: Isolating co-extinction effects and model comparisons</li><li>Used in: Main manuscript figures</li></ul></li><li><code><strong>Reduced_Model_Coext_No_Comp_Output_[1-6].rds</strong></code> - Species contributions without compensation ⚠️ <b>Large files</b></li></ul><h4>Simple Model (No interactions)</h4><ul><li><code><strong>Simple_Model_No_Coext_No_Comp_Output_[1-6].csv</strong></code> - Baseline model without species interactions</li><li><ul><li>Same column structure as other model outputs</li><li>Used for: Baseline comparisons in main manuscript figures</li></ul></li><li><code><strong>Simple_Model_No_Coext_No_Comp_Output_[1-6].rds</strong></code> - Species contributions without interactions ⚠️ <b>Large files</b></li></ul><h2>Usage Instructions</h2><h3>System Requirements</h3><ul><li><b>R version</b>: 4.4.2 (2024-10-31) or higher</li><li><b>Required packages</b>:</li><li><ul><li><b>Main model</b>: <code>tidyverse</code>, <code>rio</code>, <code>patchwork</code>, <code>data.table</code>, <code>formatR</code></li><li><b>Supplementary code</b>: <code>tidyverse</code>, <code>Hmisc</code>, <code>qgraph</code>, <code>rio</code>, <code>patchwork</code>, <code>MetBrewer</code>, <code>ggpmisc</code>, <code>mgcv</code></li></ul></li><li><b>Recommended RAM</b>: ≥ 16GB (for .rds contribution files)</li><li><b>Runtime estimates</b>: 5-20 minutes per scenario (500 simulations)</li><li><ul><li>Full Model: ~20 minutes per scenario</li><li>Reduced Model: ~10-15 minutes per scenario</li><li>Simple Model: ~5-10 minutes per scenario</li><li>Total runtime for all models: ~3-6 hours</li></ul></li></ul><h3>Workflow</h3><ol><li><b>Data Preparation</b>: Run <code>CoExt_ChAOS_SupplementaryCode.Rmd</code> first</li><li><ul><li>Processes raw data and generates derived datasets</li><li>Creates supplementary materials</li></ul></li><li><b>Main Analysis</b>: Run <code>CoExt_ChAOS_model.Rmd</code></li><li><ul><li>Requires processed data from step 1</li><li>Generates main manuscript results</li></ul></li><li><b>Model Outputs</b>: Pre-computed model results are provided for reference</li><li><ul><li>Can be used to reproduce figures without re-running computationally intensive models</li><li>Full model re-runs will overwrite these files</li></ul></li></ol><h3>Reproducibility Notes</h3><ul><li>All model outputs provided are used directly in main manuscript figures</li><li><b>Package management</b>: Automated installation of missing packages included in scripts</li><li><b>Computational considerations</b>: .rds contribution files are memory-intensive; consider available RAM before loading</li><li>Session information available in script outputs</li></ul><h2>Citation</h2><p dir="ltr">If using this code or data, please cite:</p><pre><pre>@article{Williams2025,<br> author = "Tom Williams",<br> title = "{BEF_Coextinctions_Repo}",<br> year = "2025",<br> month = "9",<br> url = "https://figshare.com/articles/dataset/BEF_Coextinctions_Repo/28062653",<br> doi = "10.6084/m9.figshare.28062653.v1"<br>}<br></pre></pre><h2>Contact</h2><p dir="ltr">For questions regarding data or code, see contact info on associated paper.</p><h2>License</h2><p dir="ltr">This work is licensed under <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International (CC BY 4.0)</a></p><h2>Acknowledgments</h2><p dir="ltr">See main manuscript for complete acknowledgments of funding sources and collaborators.</p>