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Data Centric Modeling

This is a repository for the manuscript: Hansen, S. E., M. J. Monfils, R. A. Hackett, R. T. Goebel, and A. K. Monfils. 2024. Data-centric species distribution modeling: Impacts of modeler decisions in a case study of invasive European frog-bit. Applications in Plant Sciences 12: e11573. https://doi.org/10.1002/aps3.11573.

Shield: CC BY 4.0

This work is licensed under a Creative Commons Attribution 4.0 International License.

CC BY 4.0

If you use or adapt this code, please cite the Open Science Framework project: https://osf.io/y6meq/

The scripts on the OSF project and this repository are nearly identical. The one change is that the OSF project uses a series of setwd() commands for accessibility to new R users, while this is structured like a project. Use whatever format you prefer! No matter which one you use, please cite the OSF project.

I am always open to comments and revisions. Get in touch!

Repository structure

  • code

    • SDM1_DataDownload
    • SMD2_ExplanatoryDataImportAndProcessing
    • SDM3_ReponseDataDownloadImportProcessing
    • SDM4_GetBackgroundPoints_FinalProcessingStep
    • SDM5_FitAndEvaluateModels (start here if you just want to run the model code)
    • SDM6_AnalysisAndVisualization (start here if you just want to recreate paper tables and figures)
    • SDM7_DataExplorationForManuscript
    • SDM8_AlternativeQuestion3
    • SDM9_DelineateLargeScale

  • data

    • If you use or adapt the European frog-bit dataset itself, cite the published GBIF version of it, not this one.

  • figures

  • output

    • Many of the raw data files are large and not mine to share, so I'm not including them in the actual output folder. I am including all of the final data used in the models, so you can start with the models in Step 5 without having to run earlier steps.

  • tables