Ecological Archives E093-015-S2

Nick Ellis, Stephen J. Smith, and C. Roland Pitcher. 2012. Gradient forests: calculating importance gradients on physical predictors. Ecology 93:156–168.

Extended analysis of the Great Barrier Reef data set. This document is provided as part of the documentation of the R package gradientForest.
Ecological Archives E093-015-S2.

Stephen J. Smith
Bedford Institute of Oceanography
Fisheries and Oceans Canada
1 Challenger Drive
Dartmouth NS B2Y 4A2
Canada
Email: stephen.smith@dfo-mpo.gc.ca

Nick Ellis
CSIRO Marine & Atmospheric Research
Ecosciences Precinct
GPO Box 2583
Brisbane QLD 4001
Australia

C. Roland Pitcher
CSIRO Marine & Atmospheric Research
Ecosciences Precinct
GPO Box 2583
Brisbane QLD 4001
Australia

1. 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.

Predictor	Description of environmental predictor
BATHY	Depth from bathymetry
SLOPE	Slope derived from bathymetry
ASPECT	Aspect of slope derived from bathymetry
MUD	Sediment % mud grainsize fraction
SAND	Sediment % sand grainsize fraction
GRAVEL	Sediment % gravel grainsize fraction
CRBNT	Sediment % carbonate composition
BSTRESS	Seabed current stress
NO3_AV	Nitrate bottom water annual average
NO3_SR	Nitrate seasonal range
PO4_AV	Phosphate bottom water annual average
PO4_SR	Phosphate seasonal range
O2_AV	Oxygen bottom water annual average
O2_SR	Oxygen seasonal range
S_AV	Salinity bottom water annual average
S_SR	Salinity seasonal range
T_AV	Temperature bottom water annual average
T_SR	Temperature seasonal range
SI_AV	Silicate bottom water annual average
SI_SR	Silicate seasonal range
CHLA_AV	Chlorophyll annual average
CHLA _SR	Chlorophyll seasonal range
K490_AV	Attenuation coefficient at 490nm annual average
K490_SR	Attenuation coefficient seasonal range
SST_AV	Sea surface temperature annual average
SST_SR	Sea surface temperature seasonal range
BIR_AV	Relative benthic irradiance, annual average
BIR_SR	Benthic irradiance seasonal range

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.