This dataset corresponds to Step 3 of the study's processing workflow 'Fourchon Nekton Turnover Workflow' (doi: 10.5281/zenodo.18165331). See "Description" and "BCO-DMO Processing" sections for context about the relationship between the workflow files and the data as published at BCO-DMO.

Workflow README for Step "3_CTI_calculations" :
Step 3: CTI Calculations

Abstract

This step links cleaned GBIF occurrences to climatology to quantify species- and community-scale thermal affinities. Occurrence points are spatially thinned to reduce sampling bias, paired with WorldClim SST (bio6; Hijmans, et al., 2005) to derive per-taxon species thermal indices and latitudinal envelopes, then joined to multi-year community matrices to compute CTI metrics (means and confidence bounds) for each sample.

Purpose: extract sea surface temperature (SST) for GBIF occurrences, thin spatially dense records, compute species thermal indices (STI), and derive community temperature indices (CTI).

Primary script

CTI_calculation_BCODMO.R: annotated script performing SST extraction (WorldClim WC_bio6 via sdmpredictors/terra), 50 km spatial thinning, STI summaries, and CTI computation from community matrices.

Inputs

../2_gbif_workflow/gbif_downloads/clean_csvs/*.csv: cleaned GBIF occurrences.
../1_raw_data/outputs/pivot_all.csv: community matrix with Year column.
../1_raw_data/outputs/presence_pivot_merged_sp.csv: used for taxon alignment.

Outputs (outputs/)

species_latitudes.csv: min/mean/max latitudes by taxon after thinning.
STI_results_by_taxon.csv: STI mean/quantiles and northern latitude metrics.
pivot_clean.csv: community matrix augmented with CTI metrics (mean_sti, mean_sti_2.5, mean_sti_range).

Software

R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default
LAPACK version 3.12.1

locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] ggrepel_0.9.6           sf_1.0-21               CoordinateCleaner_3.0.1
[4] sdmpredictors_0.2.15    sp_2.2-0                terra_1.8-60
[7] lubridate_1.9.4         forcats_1.0.1           stringr_1.5.2
[10] dplyr_1.1.4             purrr_1.1.0             readr_2.1.5
[13] tidyr_1.3.1             tibble_3.3.0            ggplot2_4.0.0
[16] tidyverse_2.0.0         rgbif_3.8.3

loaded via a namespace (and not attached):
[1] generics_0.1.4      class_7.3-23        xml2_1.4.0
[4] KernSmooth_2.23-26  stringi_1.8.7       lattice_0.22-7
[7] hms_1.1.4           magrittr_2.0.3      grid_4.5.1
[10] timechange_0.3.0    RColorBrewer_1.1-3  rnaturalearth_1.1.0
[13] plyr_1.8.9          jsonlite_2.0.0      whisker_0.4.1
[16] e1071_1.7-16        DBI_1.2.3           httr_1.4.7
[19] scales_1.4.0        oai_0.4.0           codetools_0.2-20
[22] lazyeval_0.2.2      cli_3.6.5           rlang_1.1.6
[25] units_0.8-7         withr_3.0.2         tools_4.5.1
[28] raster_3.6-32       tzdb_0.5.0          geosphere_1.5-20
[31] vctrs_0.6.5         R6_2.6.1            proxy_0.4-27
[34] classInt_0.4-11     lifecycle_1.0.4     pkgconfig_2.0.3
[37] pillar_1.11.1       gtable_0.3.6        data.table_1.17.8
[40] glue_1.8.0          Rcpp_1.1.0          tidyselect_1.2.1
[43] farver_2.1.2        compiler_4.5.1      S7_0.2.0
>

Run order

Confirm GBIF cleaned CSVs (Step 2) and pivot_all.csv (Step 1) exist.
Run CTI_calculation_BCODMO.R; check outputs in outputs/.