Supplement 1. Commented R and JAGS codes of the models and the complete data set used in this study.
fine_data.csv (MD5: 9ec6458220867aba02650559267a47b2)
coarse_data.csv (MD5: 66ba1aac22c1995ff2cf87afcfd67dce)
grid_shapefiles.zip (MD5: 75f1050618a50cf2f1b4ffbdb8c9ca4d)
R&JAGS_codes_and_descriptions.r (MD5: 1038789e9074783d00e3314b0414c201)
The fine.data.csv file is a comma-separated text file. It contains data for each fine-grain grid cell in the complete set of 6238 cells. Column definitions:
- id_coarse - String that is unique to the coarse-grain grid cell overlapping the focal fine-grain cell. All fine-grain cells that share the same id_coarse lay within the same coarse-grain cell.
- lon-lat025 - Unique string that identifies each fine-grain cell. It can also be used to link the data to the shapefile of the fine-grain grid.
- NPP - Net primary productivity [kg carbon m-2].
- LC - Shannon index of land-cover classes.
- PW - Precipitation in the wettest month [mm/month].
- HFP - Human footprint index [Units provided in Trombulak et al. 2010].
- PS - Precipitation seasonality [Coefficient of Variation].
- T - Mean annual temperature [C°].
- S.coarse - Number of species in the coarse-grain cell that encompasses the focal fine-grain cell.
- S.fine - Number of species in the cell.
- ref.data - Indicator variable that distinguishes the well-sampled 600 cells of the Reference data set (value of 1) from the rest (value of 0).
The coarse.data.csv file is a comma-separated text file. It contains data for each coarse-grain cell in the complete set of 107 coarse-grain cells. Column definitions:
- id_coarse - String that is unique to each coarse-grain grid cell. It can be used to link the data to the shapefile of the coarse-grain grid.
- S.coarse - Number of species in the coarse-grain cell.
- START - Index variable (see below).
- STOP - Index variable. All fine-grain grid cells that lay within the coarse-grain cell have index j where START j STOP. The index j identifies rows in the fine.data.csv table.
The file grid_shapefiles.zip is a .zip archive that contains two Esri shapefiles. The first one is the 0.25° fine-grain grid. The second one is the 2° coarse-grain grid. These shapefiles are not essential for the replication of the analyses, but they can be useful for visualization purposes or for further research. Both shapefiles can be linked to the fine_data.csv and coarse_data.csv by using the lon-lat025 and id_coarse fields respectively.
The file R&JAGS_codes_and_descriptions.r is a text file that contains R and JAGS codes (together with their descriptions) that can be used to run the three models presented in the study.