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| Formato: | Recurso digital |
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Zenodo
2026
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| Acceso en liña: | https://doi.org/10.5281/zenodo.18547233 |
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Table of Contents:
- <h1> Peneroplis manuscript analysis code</h1> <p>Code and data supporting the manuscript on Peneroplis ecology and habitat suitability (HSI) mapping: <strong>"Predicting the Range Expansion of Larger Benthic Foraminifera under Earth's Changing Climate"</strong>.</p> <p>This repository is prepared for Zenodo deposition and provides reproducible workflows for species distribution modelling (MIAmaxent) and IDW-based habitat suitability mapping.</p> <p>---</p> <h2>Quick start</h2> <p>1. <strong>Set working directory</strong> to the project root (folder containing <em>README.md</em>).<br>2. <strong>Restore R packages</strong>:<br> <code> ```r</code><br><code> renv::restore()</code><br><code> ```</code><br>3. <strong>Run analyses:</strong><br> <code> ```r</code><br><code> source("run_all.R")</code><br><code> ```</code><br> This renders `<em>01_Final_analysis.Rmd` then `02_HSI_kriging.Rmd</em>` and writes outputs under `<em>output/</em>`.</p> <p>---</p> <h2>Requirements</h2> <p>- <strong>R</strong> (>= 4.2)<br>- <strong>RStudio</strong> (optional; recommended for knitting R Markdown)<br>- <strong>System libraries</strong> for spatial packages (sf, terra): GDAL, PROJ, GEOS <br> - macOS: <em>`brew install gdal proj geos</em>` <br> - Linux (Debian/Ubuntu): `<em>sudo apt-get install libgdal-dev libproj-dev libgeos-dev</em>` <br> - Windows: use CRAN binaries; if installation fails, install [OSGeo4W](https://trac.osgeo.org/osgeo4w/)</p> <p>---</p> <h2>Directory structure </h2> <p> </p> <p><code>```</code><br><code>peneroplis-manuscript-code/</code><br><code>├── README.md</code><br><code>├── HOW_TO_RUN.md</code><br><code>├── CITATION.cff</code><br><code>├── LICENSE</code><br><code>├── INPUT_INVENTORY.md</code><br><code>├── run_all.R</code><br><code>├── requirements.R</code><br><code>├── renv.lock</code><br><code>├── peneroplis-manuscript-code.Rproj</code><br><code>│</code><br><code>├── R/</code><br><code>│ └── load_packages.R # Shared package loader; writes output/bibtex/packages.bib</code><br><code>│</code><br><code>├── analysis/</code><br><code>│ ├── 01_Final_analysis.Rmd # MIAmaxent SDM, presence/absence, model selection, regional projections</code><br><code>│ └── 02_HSI_kriging.Rmd # HSI mapping: IDW interpolation for Gulf 2023 and 2100</code><br><code>│</code><br><code>├── scripts/</code><br><code>│ ├── setup/</code><br><code>│ │ └── Relevant_Folders.R</code><br><code>│ ├── data_load/</code><br><code>│ │ ├── Raster_Shape_Files.R</code><br><code>│ │ └── EMEV.R</code><br><code>│ ├── plots/</code><br><code>│ │ ├── Presence_Absence_Plot.R</code><br><code>│ │ ├── Gulf_model.R</code><br><code>│ │ ├── Gulf_model_with_overlay.R</code><br><code>│ │ ├── Global_model.R</code><br><code>│ │ ├── Global_model_with_overlay_points.R</code><br><code>│ │ ├── Central_and_South_America_model_with_overlay_points.R</code><br><code>│ │ ├── East_Asia_and_Australia_model_with_overlay_points.R</code><br><code>│ │ ├── Africa_and_Middle_East_Europe_model_with_overlay_points.R</code><br><code>│ │ └── run_all_plots.R</code><br><code>│ └── stats/</code><br><code>│ └── Stats.R</code><br><code>│</code><br><code>└── input/</code><br><code> ├── env_layers_study/ # EMEV_1.asc .. EMEV_34.asc</code><br><code> ├── env_layers_world/ # EMEV_1.asc .. EMEV_34.asc, MS_bathy_5m.asc</code><br><code> ├── generated_data/ # Gulf_2023_HSI.csv, Gulf_2100_HSI.csv, World_2023_HSI.csv</code><br><code> ├── occurrence/ # Presence/absence CSVs</code><br><code> ├── rasters/ # Gulf_2021.tif</code><br><code> ├── rds/ # Precomputed RDS (EcologyPA_2020_working, EcostudyArea_2020, etc.)</code><br><code> └── shapefiles/ # r2d2 (Gulf), TM_WORLD_BORDERS_SIMPL-0.3, Iranian_Rivers_2</code><br><code>```</code></p> <p> </p>