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College of Liberal Arts and Sciences University of Florida

Software

deBinfer for Bayesian inference

Boersch-Supan, P., Ryan, S.J., Johnson, L.R. 2017. deBInfer: Bayesian inference for dynamical models of biological systems in R. Methods in Ecology and Evolution 8(4): 511-518. [PDF] (R package on CRAN)

​Simple R scripts for life’s little anxieties with GIS data

These scripts are just plocked into a text box webapge. You can copy and paste them into R. If you can’t do that, you probably shouldn’t. 

Turn grids into ASCII to bring into ArcGIS – with the superior option of a tiff to keep the projection

Import a Shapefile, export a KML file (for Google Earth) and never go near ArcGIS

The proj4 for sinusoidal modis is +proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs
This page is a phenomenal resource for the R-ArcGIS transition

Software for Structures in Community Ecology

Software for structures in community ecology
To access software, click on the icon
The following are nice GUIs for implementing some community ecology tests to examine structure in communities generated by competition, facilitation or habitat structuring. 

If the remote hosts are down, please inform Sadie J Ryan (sjryan@ufl.edu).

MPower, Software for Assessing the Reliability of Null Model Tests in Ecology, Ladau and Ryan, 2008

MPower (Ladau and Ryan, 2008, 2010) is a user-friendly program for determining which null model tests in the application EcoSim (Gotelli and Entsminger 2007) are reliable for analyzing your ecological data.
MPower is key for ensuring that you draw accurate inferences from your ecological data.

CoOccur, Software for Implementing Robust Null Model Tests in Ecology, Ladau et al., 2008

CoOccur is a user-friendly program that implements robust null model tests developed in Ladau and Schwager (2008). The tests allow reliable inferences about interspecific interactions for a wide array of presence-absence data sets.

References: Gotelli, N.J. and G.L. Entsminger. 2007. EcoSim: Null models software for ecology. Version 7. Acquired Intelligence Inc. & Kesey-Bear. Jericho, VT 05465. http://garyentsminger.com/ecosim.htm.

Ladau, J. and Ryan, S.J. 2010. MPowering ecologists: community assembly tools for community assembly rules. Oikos 119(7): p. 1064-1069 [PDF]

Ladau, J. and S.J. Schwager. 2008. Robust hypothesis tests for independence in community assembly. J. Mathematical Biology 57(4): 555