SamAde1203/ecological-memory-hysteresis: Ecological memory hysteresis – analysis code and synthetic data
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2026
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| _version_ | 1866901460787134464 |
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| author | SamAde1203 |
| author_facet | SamAde1203 |
| contents | <h2>Overview</h2> <p>This release contains the complete analysis pipeline, synthetic example data, and figure-generation code for:</p> <p><strong>Adeyemi S.</strong> "Ecological Memory Generates Scale-Dependent Hysteresis in Complex Ecosystems" (PNAS submission).</p> <p>It provides a frozen, citable snapshot of the code and data used to generate all main-text and Supporting Information figures.</p> <h2>Contents</h2> <ul> <li><p><code>code/</code></p> <ul> <li><code>generate_pnas_figures.R</code> – scripts to reproduce all main manuscript figures.</li> <li><code>generate_si_figures.R</code> – scripts to reproduce Supporting Information figures.</li> <li><code>generate_additional_si_figures.R</code> – extra SI visualizations.</li> <li><code>arfima_estimates.R</code> – ARFIMA-based memory parameter estimation for all sites.</li> </ul> </li> <li><p><code>data/</code></p> <ul> <li><code>site_metadata.csv</code> – metadata for 84 ecosystems (72 regime-shifting, 12 stable).</li> <li>Synthetic example time series for:<ul> <li>Coral reefs (<code>data/coral_reefs/</code>)</li> <li>Savannah–forest systems (<code>data/savannah_forest/</code>)</li> <li>Lakes (<code>data/lakes/</code>)</li> <li>Stable LTER reference sites (<code>data/lter_stable/</code>)</li> </ul> </li> </ul> </li> <li><p><code>results/</code></p> <ul> <li><code>arfima_estimates.csv</code> – memory parameter (μ) estimates with SE and 95% CI.</li> <li><code>hysteresis_measures.csv</code> – Irreversibility Index (ℐ) and raw hysteresis (H) per site.</li> </ul> </li> </ul> <h2>Reproducibility</h2> <p>To regenerate all figures:</p> <pre><code># Install required packages (once) # install.packages(c("ggplot2","dplyr","tidyr","fracdiff","fractal", # "patchwork","scales","ggrepel","viridis","cowplot")) # Run from the repository root: source("code/arfima_estimates.R") source("code/generate_pnas_figures.R") source("code/generate_si_figures.R") source("code/generate_additional_si_figures.R") </code></pre> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18635902 |
| institution | Zenodo |
| language | |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | SamAde1203/ecological-memory-hysteresis: Ecological memory hysteresis – analysis code and synthetic data SamAde1203 <h2>Overview</h2> <p>This release contains the complete analysis pipeline, synthetic example data, and figure-generation code for:</p> <p><strong>Adeyemi S.</strong> "Ecological Memory Generates Scale-Dependent Hysteresis in Complex Ecosystems" (PNAS submission).</p> <p>It provides a frozen, citable snapshot of the code and data used to generate all main-text and Supporting Information figures.</p> <h2>Contents</h2> <ul> <li><p><code>code/</code></p> <ul> <li><code>generate_pnas_figures.R</code> – scripts to reproduce all main manuscript figures.</li> <li><code>generate_si_figures.R</code> – scripts to reproduce Supporting Information figures.</li> <li><code>generate_additional_si_figures.R</code> – extra SI visualizations.</li> <li><code>arfima_estimates.R</code> – ARFIMA-based memory parameter estimation for all sites.</li> </ul> </li> <li><p><code>data/</code></p> <ul> <li><code>site_metadata.csv</code> – metadata for 84 ecosystems (72 regime-shifting, 12 stable).</li> <li>Synthetic example time series for:<ul> <li>Coral reefs (<code>data/coral_reefs/</code>)</li> <li>Savannah–forest systems (<code>data/savannah_forest/</code>)</li> <li>Lakes (<code>data/lakes/</code>)</li> <li>Stable LTER reference sites (<code>data/lter_stable/</code>)</li> </ul> </li> </ul> </li> <li><p><code>results/</code></p> <ul> <li><code>arfima_estimates.csv</code> – memory parameter (μ) estimates with SE and 95% CI.</li> <li><code>hysteresis_measures.csv</code> – Irreversibility Index (ℐ) and raw hysteresis (H) per site.</li> </ul> </li> </ul> <h2>Reproducibility</h2> <p>To regenerate all figures:</p> <pre><code># Install required packages (once) # install.packages(c("ggplot2","dplyr","tidyr","fracdiff","fractal", # "patchwork","scales","ggrepel","viridis","cowplot")) # Run from the repository root: source("code/arfima_estimates.R") source("code/generate_pnas_figures.R") source("code/generate_si_figures.R") source("code/generate_additional_si_figures.R") </code></pre> |
| title | SamAde1203/ecological-memory-hysteresis: Ecological memory hysteresis – analysis code and synthetic data |
| url | https://doi.org/10.5281/zenodo.18635902 |