Nordic Oikos 2018 – GBIF data with R
Scientific reuse of openly published biodiversity information: Programmatic access to and analysis of primary biodiversity information using R. Nordic Oikos 2018, pre-conference R workshop, 18th and 19th February 2018 in Trondheim, Norway.
Session 5: Linking environment layers to GBIF data
Access to and the linking of GBIF data to environmental raster and vector data is a frequently asked question from users of GBIF mediated species occurrence data.
- WorldClim global climate layers (Fick and Hijmans, 2017), (Hijmans et al. 2005).
- Bioclimatic variables (Bioclim) (Nix 1986; Busby 1991; Booth 2014).
- R Spatial: Guide to environmental data.
Learning target: Understanding basic spatial data manipulation and the basic properties of spatial data, including both raster data (gridded spatial data) and vector data (species occurrence point data, polygon data such as country borders, etc). Learning how to extract information from either raster data (eg. environment layers) and vector data for a list of species occurrences point data.
Workshop training materials for session 5
Excercises for session 5
- Select a stydy area and a species (or species group).
- Download species occurrences from GBIF and environment layers from WorldClim using R.
- Extract climate data for the locations of your species occurrences.
- Plot selected environment layers and species occurrences together on a map.
- BONUS: Transform (and re-project) your spatial data (species occurrences and environment layers) to another coordinate reference system (eg. UTM zone 32N WGS84; EPSG:32632 and make a new map (in R).
- EXTRA: Perform a basic species distribution modelling study - sdm guideline here.
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