Code and data supporting the manuscript on Peneroplis ecology and habitat suitability (HSI) mapping

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