This repository will contain files used to conduct complete and structured statial randomizations from a study conducted by JW Dittel, myself, and SB Vadner Wall.
There are 4 files in total, 2 pertaining to the simulations and 2 for creating figures
SpatialRadomizations.R runs a complete randomization and PHatFigures.R plots the complete randomization data. Similarly, SpatialRadomizations_GRF.R runs a structured randomization (GRF refers to the Gaussian Random Fields used from the package RandomFields) and PHatFigures_GRF.R plots the structured randomization data.
The plots for the complete randomization only include the p-hat value. I didn't clean them up because they were completely uninformative (yes, spatial points are not completely random---we know that!). The structured randomizations, however, include the observed test stastic (Spearman's rho, in our case), the p-hat value, and color under the density plot that corresponds to how extreme our observations is, given our data (red is more extreme; blue is less extreme). Each of the complete and structured randomization correlated the 4 major groups: 1. abiotic v. animal variables, 2. abiotic v. plant variables, 3. abiotic v. difference variables, and 4. animal v. plant variables. Each of these 4 groups have subgroups, and these compose the panels in the graphs.
The directory tree, for the time being, should look like:
Each of the .R files allows users to speficy the directory (e.g., wd, fig.wd, save.wd) as one of the first commands that correspond to the directory above.
More detials and a bit of reorganization will come, but the .R files are here for the time being.