Software and code

LAGOSNE R PACKAGE

LAGOSNE: Interface to the lake multi-scaled geospatial and temporal database. The LAGOS package provides an R interface to download LAGOS-NE data from the EDI data repository, store the data locally, and perform a variety of filtering and subsetting operations for easier access to the many data tables that make up LAGOS-NE. This package is specific to the version of LAGOS-NE that is used.

SpectralClustering4Regions

R code for a novel method to create ecoregions from geospatial data.

Citation for the R code:   Cheruvelil, K.S. 2016. R code-Creating multi-themed ecological regions for macroscale ecology: testing a flexible, repeatable, and accessible clustering method. https://github.com/cont-limno/SpectralClustering4Regions

Citation for the article that describes this novel method for delineating ecological regions:      Yuan, S., P.-N. Tan, K.S. Cheruvelil, S.M. Collins, and P.A. Soranno. 2015. Constrained spectral clustering for regionalization: Exploring the trade-off between spatial contiguity and landscape homogeneity. Proceedings of the 2015 IEEE International Conference on Data Science and Advanced Analytics.  19-21 October 2015. Pg 1-10. doi:10.1109/DSAA.2015.7344878 PDF

Citation for the article in which the method is applied to an ecological research question:  Cheruvelil, K.S., S. Yuan, K.E. Webster, P.-N. Tan, J.-F. Lapierre, S.M. Collins, C.E. Fergus, C.E. Scott, E.N. Henry, P.A. Soranno, C.T. Filstrup, T. Wagner. 2017. Creating multi-themed ecological regions for macrosystems ecology: Testing a flexible, repeatable, and accessible clustering method. Ecology and Evolution 7: 3046–3058. doi: 10.1002/ece3.2884 Open access

LAGOS GIS Toolbox for ArcGIS 10.1

Python code to run in the ArcGIS environment to calculate the geospatial metrics used to create the LAGOS-GEO module.

Documentation for the toolbox: Nicole J. Smith, Patricia A. Soranno, and Scott Stopyak. 2014. Additional file 8: LAGOS GIS Toolbox Documentation. in Soranno et al. 2015. Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science and data reuse GigaScience 4:28.

Citation for the article that provides additional detail for the data used in the GIS toolbox: Soranno, P.A., E.G. Bissell, K.S. Cheruvelil, S.T. Christel, S.M. Collins, C.E. Fergus, C.T. Filstrup, J.F. Lapierre, N.R. Lottig, S.K. Oliver, C.E. Scott, N.J. Smith, S. Stopyak, S. Yuan, M.T. Bremigan, J.A. Downing, C. Gries, E.N. Henry, N.K. Skaff, E.H. Stanley, C.A. Stow, P.-N. Tan, T. Wagner, K.E. Webster. 2015. Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science and data reuse. GigaScience 4:28 doi:10.1186/s13742-015-0067-4. Open access

 

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