Code and data to reproduce "Linking geographic distribution and niche through estimation of niche density"

Code to reproduce the analyses from:
Dallas,T, and C Ten Caten. 2025. Linking geographic distribution and niche through estimation of niche density. Journal of Animal Ecology. Code is written in R and the file is in R markdown (.Rmd). The Rdata file included (env.RData) contains the environmental data layers used, but code to recreate these layers is also included in the analysis.Rmd (keep in mind that it will take some time and processing power). redlist_simple_summary.csv is the information from the IUCN redlist used in Appendix S1 of the manuscript.
sessionInfo() for the R workspace is below for transparency and hopefully reproducibility (we recognize that some code will require modification in the future, as some spatial packages used here are being replaced by others).

```{r}
sessionInfo()
```

R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3; LAPACK version 3.10.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/New_York
tzcode source: system (glibc)

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] RColorBrewer_1.1-3 ggplot2_3.5.1 ape_5.8
[4] alphahull_2.5 rnaturalearthdata_0.1.0 countrycode_1.5.0
[7] CoordinateCleaner_2.0-20 terra_1.7-39 raster_3.6-23
[10] sp_2.1-4 geosphere_1.5-20 geometry_0.4.7
[13] dbplyr_2.5.0 gbifdb_0.1.2 dplyr_1.1.4
[16] plyr_1.8.9

loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 farver_2.1.2 arrow_12.0.1
[4] R.utils_2.12.3 sgeostat_1.0-27 lazyeval_0.2.2
[7] spatstat.geom_3.2-9 digest_0.6.37 lifecycle_1.0.4
[10] sf_1.0-13 spatstat.data_3.0-4 magrittr_2.0.3
[13] compiler_4.4.2 rlang_1.1.4 tools_4.4.2
[16] utf8_1.2.4 data.table_1.16.2 labeling_0.4.3
[19] bit_4.5.0 interp_1.1-4 classInt_0.4-9
[22] xml2_1.3.6 abind_1.4-5 KernSmooth_2.23-24
[25] withr_3.0.2 purrr_1.0.2 R.oo_1.26.0
[28] grid_4.4.2 polyclip_1.10-6 fansi_1.0.6
[31] e1071_1.7-16 colorspace_2.1-1 scales_1.3.0
[34] spatstat.utils_3.0-4 cli_3.6.3 crayon_1.5.3
[37] generics_0.1.3 rgbif_3.7.7 httr_1.4.7
[40] magic_1.6-1 DBI_1.2.3 proxy_0.4-27
[43] stringr_1.5.1 parallel_4.4.2 rnaturalearth_0.3.3
[46] assertthat_0.2.1 vctrs_0.6.5 Matrix_1.7-1
[49] jsonlite_1.8.9 bit64_4.5.2 hexbin_1.28.4
[52] units_0.8-2 splancs_2.01-44 rgdal_1.6-7
[55] glue_1.8.0 spatstat.random_3.2-3 codetools_0.2-19
[58] stringi_1.8.4 gtable_0.3.6 deldir_1.0-9
[61] munsell_0.5.1 tibble_3.2.1 pillar_1.9.0
[64] R6_2.5.1 oai_0.4.0 lattice_0.22-5
[67] R.methodsS3_1.8.2 class_7.3-22 Rcpp_1.0.13-1
[70] nlme_3.1-165 whisker_0.4.1 rgeos_0.6-3
[73] pkgconfig_2.0.3