Zenodo
Beauchesne, David;
Cazelles, Kevin;
Daigle, Remi;
Gravel, Dominique;
Archambault, Philippe
—
2024-12-20
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].
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