Reassessment of the global distribution and diversity of modern planktonic Foraminifera (FORCIS) — Analysis code

Description This repository contains R code to reproduce the analyses and figures for the manuscript “Reassessment of the global distribution and diversity of modern planktonic Foraminifera from the FORCIS database.”The scripts quantify global biogeographic patterns of 26 dominant morphospecies since 1970 using the FORCIS database: (i) species distributions from presence-rate histograms and thresholding, (ii) basin-scale diversity (richness, Shannon), (iii) rarity metrics, (iv) vertical habitat metrics (depth of maximum abundance, and abundance-weighted in 0–200 m), and (v) thermal preferences from EN4.2.1 temperatures (0–100 m). Sensitivity analyses address taxonomy/mesh-size harmonization and α-threshold selection. Scripts written by Sonia Chaabane. Code included (scripts) Species_distribution.R — global presence/absence gridding & maps Presence rate histograms_Thresholds_allshellscounted.R — presence-rate by latitude (full assemblage counted) + binomial SE Presence rate histograms_Thresholds.R — α-threshold sweep (0.10–0.30) and selection (α = 0.20) Diversity analyses.R — assemblage matrices, ordinations/clustering, basin stratification Diversity indexes.R — species richness & Shannon vs latitude (global and per basin) Thermal preferences.R — species temperature niches (box/violin/heatmaps) from normalized abundances Depth habitat.R — DMAX & AOD per species/basin; Welch ANOVA + Games–Howell; basin-to-basin DMAX correlation heatmaps Thermal preferences by ocean basin.R — basin-resolved thermal niches with habitat coloring Presence rate histograms_fine fraction.R — fine-fraction sensitivity to sampling strategy Data sources (not redistributed here) FORCIS database: https://doi.org/10.5281/zenodo.7390791 PF abundance mesh-size normalization (to 100 µm): https://doi.org/10.5281/zenodo.10750545 Software & requirements R ≥ 4.2 (tested on 4.3.x) Packages: dplyr, tidyr, readr, openxlsx, ggplot2, viridis, vegan, reshape2, ggExtra, purrr, rstatix, patchwork, gridExtra