This is the code and data repository for the manuscript "Mismatches in functional conservation priorities across scales and locations worldwide" by Griffin et al.

This is the code and data repository for the manuscript “Mismatches in functional conservation priorities across scales and locations worldwide” by Griffin et al.The code is annotated and follows a chronological order. All figures and output are created from code.
01_presabs_matrix.RThis code takes the geographic distributions from the marine megafauna species data from the IUCN database and the AquaMaps database and converts it into a presence-absence matrix.
Output
- IUCN/megafauna_IUCN_presabs_0.5res.txt
- presabs_05_res.rds
02_functional_space.RThis code uses the presence-absence matrix and the focal traits of the species to calculate a 5 dimensional functional space.
Output
- distance_trait_matrix.rds
03_calculate_metrics.RThis code uses the presence-absence matrix and the functional space to calculate functional metrics on a global, provincial, and local level.
Output
- global_metrics.rds
- local_metrics_1_res.rds
- local_metrics_5_res.rds
- realm_metrics.rds
04_correlation_analysis.RThis code calculates correlations of functional metrics on a global, provincial, and local level.
Output
- fig_1.png
05_rank_comparison.RThis code calculates how much rankings of functional metrics agree over spatial scales.
Output
- fig_2.png
06_blue_whale_example.RThis code takes an example species (the blue whale) to showcase the variation in functional metrics over its range.
Output
- fig_3.png
07_hotspot_analysis.RThis code visualises the spatial extent of each functional metric on a global and local level, and calculates hotspots and their overlap.
Output
- fig_4.png
- fig_5.png
08_supplementary_table.RThis code creates the supplementary table showing where species reach the maximum functional uniqueness across their range.
Output
- data/supplementary_table.docx
functions.RThese are the functions used throughout provided by Pimiento, C. et al. Functional diversity of sharks and rays is highly vulnerable and supported by unique species and locations worldwide. Nature Communications 14, 7691 (2023). https://doi.org/10.1038/s41467-023-43212-3
Session InfoR version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default LAPACK version 3.12.1
locale:
[1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 [4] LC_NUMERIC=C LC_TIME=German_Germany.utf8
time zone: Europe/Berlin
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] officer_0.7.1 flextable_0.9.10 patchwork_1.3.1 funrar_1.5.0 raster_3.6-32
[6] sp_2.2-0 ade4_1.7-23 letsR_5.0 terra_1.8-60 sf_1.0-21
[11] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.1.0
[16] readr_2.1.5 tidyr_1.3.1 tibble_3.3.0 ggplot2_3.5.2 tidyverse_2.0.0 [21] here_1.0.1
loaded via a namespace (and not attached):
[1] gtable_0.3.6 xfun_0.52 lattice_0.22-7 tzdb_0.5.0
[5] vctrs_0.6.5 tools_4.5.1 generics_0.1.4 proxy_0.4-27
[9] pkgconfig_2.0.3 Matrix_1.7-3 KernSmooth_2.23-26 data.table_1.17.8
[13] RColorBrewer_1.1-3 uuid_1.2-1 lifecycle_1.0.4 compiler_4.5.1
[17] farver_2.1.2 textshaping_1.0.1 codetools_0.2-20 fontquiver_0.2.1
[21] fontLiberation_0.1.0 htmltools_0.5.8.1 class_7.3-23 pillar_1.11.0
[25] MASS_7.3-65 openssl_2.3.3 rsconnect_1.5.1 classInt_0.4-11
[29] fontBitstreamVera_0.1.1 zip_2.3.3 tidyselect_1.2.1 digest_0.6.37
[33] stringi_1.8.7 rprojroot_2.1.1 fastmap_1.2.0 grid_4.5.1
[37] cli_3.6.5 magrittr_2.0.3 e1071_1.7-16 withr_3.0.2
[41] gdtools_0.4.4 scales_1.4.0 timechange_0.3.0 rmarkdown_2.29
[45] ragg_1.4.0 askpass_1.2.1 hms_1.1.3 evaluate_1.0.4
[49] knitr_1.50 rlang_1.1.6 Rcpp_1.1.0 glue_1.8.0
[53] geosphere_1.5-20 DBI_1.2.3 xml2_1.3.8 rstudioapi_0.17.1
[57] R6_2.6.1 systemfonts_1.3.1 units_0.8-7