DOI: 10.5281/zenodo.14537123
title: Interactions amplify cumulative effects in marine food webs - Data Input

description: README for Input Data Archive

Overview

This README describes the input datasets prepared for the analyses for the manuscript titled "Interactions amplify cumulative effects in marine food webs", presenting a cumulative effects assessment on food webs in the Estuary and Gulf of St. Lawrence. The code to replicate the analyses is available on GitHub: https://github.com/Ecosystem-Assessments/nceastl and the input data is described here. The data has been processed and formatted into tabular format (i.e., CSV files) and geospatial raster files (i.e., GeoTIFFs). Below is a detailed description of the datasets included in the archive.

Included Data

1. Species List   - Description: A comprehensive list of species used in the assessment, with species names formatted to remove extra characters or spaces for consistency.   - File:     - `SpeciesList.csv`: Tabular format of species list.   - **Column description**:     - `species`: Full scientific name of the species, including genus and species.     - `Count`: Total count or frequency of the species in the dataset.     - `sp`: Simplified representation of the species name (genus and species separated by a space).     - `sp.`: Simplified representation of the species name (genus and species separated by a period).     - `species`.: Fully concatenated scientific name with genus and species joined by a period.

2. Simulated Trophic Sensitivities   - Description: Sensitivities of species to various trophic drivers, adapted from a study by Beauchesne et al. (2021; Ecology Letters, 10.1111/ele.13841).   - File:     - `TrophicSensitivity.csv`: Tabular format of trophic sensitivities.   - Column description:     - `pathID`: Identifier for the specific pathway of effect analyzed.     - `SpeciesID`: Unique identifier for the species involved in the motif.     - `motifID`: Identifier for the motif within the trophic network.     - `Species`: Label or shorthand representation of the species in the pathway.     - `pi`: Indicator of the species' presence in position "i" within the pathway (Boolean: True/False).     - `pj`: Indicator of the species' presence in position "j" within the pathway (Boolean: True/False).     - `pk`: Indicator of the species' presence in position "k" within the pathway (Boolean: True/False).     - `sensitivity_original`: Original sensitivity value for the species within the trophic pathway.     - `sensitivity_scaled`: Scaled sensitivity value, normalized for comparison across pathways.     - `sensitivity_1`: Sensitivity value adjusted for a specific analysis or scenario.

3. Biotic Data   - Description: Species presence data transformed into logical matrices and geospatial rasters. Assumes phytoplankton and zooplankton are ubiquitous in the study area.   - Files:     - `txNames.csv`: String of names of taxa included in the biotic dataset.     - `bt.csv`: Logical matrix of species presence with one row per raster cell and one column per species.      - `idBiotic.csv`: Logical string identifying cells with biotic data.     - `r.tif`: Empty raster file for reference.     - `biotic/`: Folder containing GeoTIFF files for each species.

4. Metaweb   - Description: Interaction matrix representing trophic links between species. Includes only species present in the biotic dataset.   - File:     - `metaweb.csv`: Interaction matrix in tabular format, with species names as column and row names.

5. Species-Specific Sensitivities   - Description: Sensitivities of species to different drivers, with added records for phytoplankton and zooplankton (assumed insensitive to all drivers).   - File:     - `species_sensitivity.csv`: Tabular format of species sensitivities to all environmental drivers considered, with driver names as columns and taxa names as row names. 

6. Drivers Data   - Description: Environmental drivers affecting species, aligned with vulnerability assessments. Data is provided in matrix and raster formats.   - Files:     - `dr.csv`: Matrix of drivers intensity with one row per raster cell and one column per driver.     - `drivers/`: Folder containing GeoTIFF files for each driver.

Contact

For questions or clarifications about the dataset, please contact [David Beauchesne] at [david.beauchesne@insileco.io].