R code accompanying the Reply to Matters Arising "Observed core-to-transition biodiversity gradient may be a statistical artifact"

The code archive contains five R scripts used to reproduce the additional analyses and figures presented in the Reply. The scripts are organized according to the corresponding sections of the Reply. scₛection₁. R supports Section 1 by comparing biodiversity metrics calculated from all species with those calculated from characteristic species, producing Extended Data Table 1. scₛection₂₁. R supports Section 2 by estimating the relative centre-to-boundary position of empirical biodiversity cores, producing Extended Data Table 2. scₛection₃₁. R supports Section 3. 1 by generating synthetic two-dimensional examples showing that different spatial configurations can yield similar one-dimensional trends, producing Figure 1. scₛection₃₂. R supports Section 3. 2 by evaluating whether Zhang and Wang’s randomized null bioregions retain empirical biodiversity structure, producing Extended Data Table 3. Finally, scₛection₃₃. R supports Section 3. 3 by reproducing and extending Zhang and Wang’s one-dimensional simulation across left, central and right bioregions, producing Figure 2 and an alternative supplementary PDF with additional simulation seeds. How to cite: Reply to: “Observed core-to-transition biodiversity gradient may be a statistical artifact”. Nature Ecology and Evolution