Script compiles each dataset into a standardized format for analysis. Also compiles some species into genera or families based on the lowest common resolution of all datasets or changes to taxonomic classifications over time.

This dataset corresponds to Step "1_raw_data" 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 "1_raw_data" :

Step 1: Raw Data Merge and Presence Tables

Purpose: consolidate drop sample datasets (2006, 2016, 2022, 2023) and produce community matrices and presence summaries for downstream CTI analyses.

Primary script/notebook

dataset_merge_and_process_BCODMO.ipynb: annotated Jupyter notebook that loads raw CSVs, standardizes taxonomic names, and outputs presence/community products.

Inputs (inputs/)

raw_2006_fish.csv, raw_2006_invert.csv, raw_2006_peneid.csv, 2006_site_data.csv (+ parameter descriptions).
raw_2016.csv (+ parameter description).
raw_2022.csv, raw_2023.csv (+ parameter descriptions).
final_aphia_codex_edited.csv (taxonomic lookup across survey years). Additional columns added to "aphia_codex.csv" in the BCO-DMO dataset.
species_presence_2006_2016_2022.csv (coarse presence metadata).

Outputs (outputs/)

pivot_all.csv: community matrix (SampleID x Taxon) with Year column. [BCO-DMO note: this data is listed as 991168_v1_port-fourchon_drop-sampling.csv on the BCO-DMO page, See BCO-DMO Processing section for minor differences between the workflow file and the BCO-DMO hosted file]
presence_summary.csv, presence_pivot.csv: per-taxon site-level presence proportions.
presence_summary2.csv, presence_pivot_merged_sp.csv: presence after taxonomic harmonization for CTI use.

Software

Run order

Open and run dataset_merge_and_process_BCODMO.ipynb.
Confirm outputs in outputs/ before proceeding to GBIF downloads (Step 2).