The analysis of spatial patterns in biodiversity: geographical information systems and species distribution models
In the second week of the course we will concern ourselves with spatial patterns in biodiversity: where do species occur? What are the local conditions there? Can we infer species' preferences for particular areas? In the morning we will have plenary sessions where we will review the theory and current practices, illustrated with several case studies. In the afternoon we will do hands-on work to develop our own case of geospatial biodiversity analysis: we will collect (and clean) our own occurrence data, import it for visualization, prepare it further, then analyze it by species distribution modelling. We will present our findings in a brief report.
2019-12-02, Sylvius 1.5.03 (morning), F101 van Steenis gebouw (afternoon)
- Lecture I: Introduction to the week and to GIS, technical inventory (laptop OS's, Java versions)
- Lecture II: Introduction to GIS (2) and The geographical approach
- Lecture III: GIS+SDM project example: Birds of the Philippines - Merlijn van Weerd (CML)
- Practical: Getting your data into ArcGIS: Plotting species distributions on a map 2 pers.
2019-12-03, Sylvius 1.5.03
- Lecture I: Data sources (e.g. web services, spatial data sets, attribute data, incl. GBIF and BioPortal)
- Lecture II: Digitalization, georeferencing and GPS - Jeroen Creuwels (Naturalis)
- Lecture III: Satellite images and remote sensing - Joris Timmermans (CML)
- Homework: Download occurrence data for your crop species from GBIF
2019-12-04, Sylvius 1.5.03 (morning), F101 van Steenis gebouw (afternoon)
- Lecture I: Basic database management (e.g. records, variables, types, querying, geodatabases)
- Lecture II: Data conversions and transformations (e.g. vector <=> raster, reclassification, (re)projections)
- Cool website for comparing country sizes in reality, thanks Richard Frische
- Lecture III: Data and file versioning (e.g. version management, backup, history, provenance) - Rutger Vos
- Practical: Analysing your data in ArcGIS: Data preparation with use of spatial tools for SDM 2 pers.
2019-12-05, Sylvius 1.5.03
- Lecture I: Methods for spatial data analysis (e.g. overlay, reclassification, spatial join, clip, neighbourhood analysis)
- Lecture II: Automated spatial data analysis (e.g. flowcharts, model builder, python scripting)
- Lecture III: Other tools, for spatial data (e.g. ArcGIS extensions, QGIS, DIVA-GIS, R, MAXENT)
- Guest lecture: Species Distribution Modelling using Deep Learning - Mark Rademaker
2019-12-06, Sylvius 1.5.03
- Lecture I: Export and visualisation (e.g. maps, histograms, tables, WebGIS, etc.)
- Lecture II & III: Species Distribution Models: Principles and Applications - Nuno De Mesquita César de Sá & Rosaleen March (CML)
- Practical: Ecological Niche Modelling - Nuno/Rosaleen/Rutger/Maarten