Lecture 4a: Guest speaker (Larry Crowder) Spatial ecological analysis and OBIS SEAMAP (Spatial Ecological Analysis of Megavertebrate Animal Populations)
Lecture 4b: Species Distribution Modeling with MGET (Best)
Lecture 4c: MGET Applications: Spatially Predictive Modeling & Mapping of Rockfishes (Wedding)
Resources for Final Projects on SDM
create_absences.R - create shapefile of pseudo-absence points from within buffer (specified by inner and outer rings) around shapefile of presence points. Also create map for quick sanity check. Here's the example map of created absence points (red) and buffers (blue) using presence points (green) for bristlecone pine (Pinus longaeva).
Becker JJ, DT Sandwell, WHF Smith, J Braud, B Binder, J Depner, … P Weatherall (2009). Global Bathymetry and Elevation Data at 30 Arc Seconds Resolution: SRTM30_PLUS. Marine Geodesy, 32(4): 355–371.
Hijmans RJ, SE Cameron, JL Parra, PG Jones, A Jarvis. (2005). Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25(15): 1965–1978.
Robinson N, J Regetz, RP Guralnick (2014). EarthEnv-DEM90: A nearly-global, void-free, multi-scale smoothed, 90m digital elevation model from fused ASTER and SRTM data. ISPRS Journal of Photogrammetry and Remote Sensing, 87: 57–67.
Tuanmu MN, W Jetz (2014) A global 1-km consensus land-cover product for biodiversity and ecosystem modelling. Global Ecology and Biogeography, 23(9):1031–1045.
Tyberghein L, H Verbruggen, K Pauly, C Troupin, F Mineur, O De Clerck (2012) Bio-ORACLE: a global environmental dataset for marine species distribution modelling. Global Ecology and Biogeography, 21(2): 272–281.
Elith J, JR Leathwick (2009) Species Distribution Models: Ecological Explanation and Prediction Across Space and Time. Annual Review of Ecology, Evolution, and Systematics, 40(1):677–697.
Pearson RG (2007). Species’ Distribution Modeling for Conservation Educators and Practitioners.
Roberts JJ, BD Best, DC Dunn, EA Treml, PN Halpin (2010) Marine Geospatial Ecology Tools: An integrated framework for ecological geoprocessing with ArcGIS, Python, R, MATLAB, and C++. Environmental Modelling & Software, 25(10):1197–1207.
Young MA, PJ Iampietro, RG Kvitek, CD Garza (2010) Multivariate bathymetry-derived generalized linear model accurately predicts rockfish distribution on Cordell Bank, California, USA. Marine Ecology-Progress Series, 415:247–261.
Zuur AF, EN Ieno, CS Elphick (2010) A protocol for data exploration to avoid common statistical problems. Methods in Ecology and Evolution, 1(1):3–14.