Supplement 2. Extended analysis of the Great Barrier Reef data set. This document is provided as part of the documentation of the R package gradientForest.

File List 1.biodiversity-survey.pdf 2.GZ.phys.site.Rdata 3.GZ.sps.mat.Rdata 4.GZ.phys.grid.Rdata Description1. This is a vignette from the R package gradientForest, which is available at http://gradientforest.r-forge.r-project.org. The vignette demonstrates the use of the gradient forest method for ecological analysis of biodiversity survey data from a region in the far north Great Barrier Reef. The 3 data files used in the vignette are provided as R data files in this supplement. Alternatively, in an R session once the package has been loaded, the data can be made available using the command data(GBRexample). 2. R data file for data frame Phys_site containing 28 environmental predictors at the 197 sample sites. -- TABLE: Please see in attached file. -- 3. R data file for matrix Sp_mat containing log(y + c)-transformed species abundance (where c is the minimum positive abundance y) at the 197 sample sites. 4. R data file for data frame Phys_grid containing the above 28 environmental variables extrapolated onto 8682 locations on a fine-scale 0.01° × 0.01° grid. The variables NORTH and EAST are included so that the predictions can be plotted geographically.