Unravelling the complexities of temporal biotic homogenisation and heterogenisation

Data and scripts to recreate the analyses within "Unravelling the complexities of temporal biotic homogenisation and heterogenisation".
Data is contained within the "Datafiles" folder. This data consists of:
Bird_list.csv: List of birds present in the study area during the study periodsCentroids_10.csv: Centroids (latitude and longitude) of the centers of each hectad (10 km x 10 km grid).ClimChaprec_30.csv: Change in precipitation between the two study periodsClimChatavg_30.csv: Change in average temperature between the two study periodsconsensus_jetz_3000: Jetz consensus trees (see Jetz et al. 2012 for more information)data_30km.csv: the full dataset (if only the data is needed without running the script to obtain metrics and combine into one datafile)elev_30km: Elevation data for Britain in 30 km x 30vkm gridsFunc: Functional traits for bird species in the study (see Tobias et al. 2022 for more information)graph_2291_1.5: Spatial graph for use within the modellinggrid_10: Shapefile of the 10 km x 10 km hectadsLandChange.csv: Land cover change between 1990 and 2015 (see Rowland et al. 2020 for more information)pa_1990_10.csv: Presence absence data for each hectad in BA1990 (see Gillings et al. 2019 for more information)pa_2010_10.csv: Presence absence data for each hectad in BA2010 (see Gillings et al. 2019 for more information)Shan1990_30.csv: Shannon's diversity for landcover in each 30 km x 30 km grid in 1990.Shan2015_30.csv: Shannon's diversity for landcover in each 30 km x 30 km grid in 2015.ShanCha_30.csv: Change in Shannon's diversity between the two time periods.Specialisation.csv: Habitat specialisation values and quartiles for British birds (see Sullivan et al. 2016 for more information).status_sp.csv: A database of information for each bird species found within the study area.Data was derived from the following sources:
Gillings, S., Balmer, D. E., Caffrey, B. J., Downie, I. S., Gibbons, D. W., Lack, P. C., Reid, J. B., Sharrock, J. T. R., Swann, R. L., & Fuller, R. J. (2019). Breeding and wintering bird distributions in Britain and Ireland from citizen science bird atlases. Global Ecology and Biogeography, 28(7), 866–874. https://doi.org/10.1111/geb.12906Hollis, D., McCarthy, M., Kendon, M., Legg, T., & Simpson, I. (2019). HadUK‐Grid—A new UK dataset of gridded climate observations. Geoscience Data Journal, 6(2), 151-159.Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K., & Mooers, A. O. (2012). The global diversity of birds in space and time. Nature, 491(7424), Article 7424. https://doi.org/10.1038/nature11631Rowland, C., Marston, C., Morton, D., & O'Neil, A. (2020). Land Cover Change 1990-2015 (25m raster, GB).Sullivan, M. J. P., Newson, S. E., & Pearce-Higgins, J. W. (2016). Changing densities of generalist species underlie apparent homogenization of UK bird communities. Ibis, 158(3), 645–655. https://doi.org/10.1111/ibi.12370Tobias, J. A., Sheard, C., Pigot, A. L., Devenish, A. J. M., Yang, J., Sayol, F., Neate-Clegg, M. H. C., Alioravainen, N., Weeks, T. L., Barber, R. A., Walkden, P. A., MacGregor, H. E. A., Jones, S. E. I., Vincent, C., Phillips, A. G., Marples, N. M., Montaño-Centellas, F. A., Leandro-Silva, V., Claramunt, S., … Schleuning, M. (2022). AVONET: Morphological, ecological and geographical data for all birds. Ecology Letters, 25(3), 581–597. https://doi.org/10.1111/ele.13898All scripts and functions are included within the folder for analysing the data to produce the outputs found in the manuscript: Unravelling the complexities of temporal biotic homogenisation and heterogenization: avian assemblage dynamics in Britain. All code is for use within the R coding environment (v4.2.1; R Core Team 2022).
The main.script script loads all necessary data and packages from the script source.script. The script then runs through all the necessary steps to reproduce the results in the manuscript.