A paleoecological trophic network model of the Early Ordovician Lower Fezouata Shale (Morocco) fossil fauna - Data

Description

Supplementary Items for the article "A paleoecological trophic network model of the Early Ordovician Lower Fezouata Shale (Morocco) fossil fauna" by Soucy et al. This dataset contains all data used to conduct the analyses in the aformentioned article. Included are Tables S1.1 to S1.5, which are Excel documents containing various species lists. Also included is the list of trophic interactions used to create the Lower Fezouata Shale trophic network and their certainty level (Table S2).

Steps to reproduce

All species data of the Fezouata Shale fauna was collected from the literature. The way the trophic interactions were established is detailed in the "STAR★Methods" section of the article. The code to conduct the analyses is stored at https://doi.org/10.5281/zenodo.20437943. The network analyses are conducted using the Julia Programming Language (https://julialang.org/ ). The "Supplementary Item 2 - Table S2" document, with the uncertainty levels column removed, needs to be present in the file "raw" within the file "data" in the code provided, as a csv file, and be named "interactions_Fezouata". This will allow the code to be run. To run the code, one can simply run all of the page "main.jl". To run sections separately, run all of "main.jl" with exception of the last "##Load scripts" section. Then run, one at a time and in order, pages : - "01_clean_data.jl" to clean the data. The result will be saved in the folder "clean" within "data". - "02_convert_trophic_species.jl" to aggregate the trophic species. The result will be saved in the folder "clean" within "data". - "03_simulate_networks.jl" to create the simulated trophic networks using the niche model, the cascade model, and the nested-hierarchy model. The results will be saved in the folder "sim" within "data". - "04_compute_measures.jl" to calculate the network properties of the empirical and the simulated networks. Steps are included to calculated the level of Cannibalism and Loops, but neither properties are used in the article. The results will be saved in the folder "results". - "05_make_figures.jl" to create the figures. The results will be saved in the folder "figures". The uncertainty analysis is conducted using the Julia Programming Language and R (https://www.r-project.org/). All code and results and figures produced are in the folder "permutation_analysis". The "Supplementary Item 2 - Table S2" document, with the uncertainty levels column, should be used.

Institutions

• Université de Montréal

  Quebec, Montreal
• Laboratoire de Géologie de Lyon : Terre, Planètes et Environnement

  Auvergne-Rhône-Alpes, Lyon
• Instituto de Geociencias

  Madrid, Madrid
• Universidad Complutense de Madrid

  Madrid, Madrid

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