Biome changes and biome stability during the Quaternary

*** Scripts require data from different sources:

The Olson et al (2001) biome map was taken from Fischer et al (2022): https://datadryad.org/stash/landing/show?id=doi%3A10.5061%2Fdryad.hqbzkh1jm

Bioclimatic variables were taken from Barreto et al. (2023): https://figshare.com/s/d45714f7212de7225fe2

The BIOME6000 biome reconstructions were taken from Harrison et al. (2017): https://researchdata.reading.ac.uk/99/

Diversity data were take from Cai et al. 2023: https://gift.uni-goettingen.de/shiny/predictions/

*** Model resultsThe repository contains different data file produced by the R scripts as well as paleo_models.zip including raw data from the SDM.

*** Scripts should be run in the following order:

1) paleo_modeling_pgen.R - Create SDM for current conditions based on bioclimatic variables and Olson (2021) biome map. Modeling is done with biomod2.

2) all_pgem_models.R - Evalute SDM for bioclimatic conditions of last 2.6 million years from Barreto et al. (2023) to create time series of biome maps. This script only calculates suitability maps per biome and time period by doing an ensemble forcasting of the model developed in paleo_modeling_pgen.R.

3) all_pgem_models_analyses.R - Analyze model results and create a set of figures. This includes biome maps for different time periods, comparisons of biome maps, biome stability maps, an animaption of biome changes. This script requires results from all_pgem_models.R.

4) plot_chrono.R - create chrono-sequence plots of biome coverage using the rioja package, and histograms of biome coverage.

5) benchmarking_b6000.R - Compare model results and Olson biome map to paleo-reconstructions from BIOME6000 (Harrison et al. 2017). This includes a matching between biomes in Olson map and BIOME6000 data and plots.

6) convert_diversity.R - Process Cai et al. (2023) diversity data for further analysis, required for plot_diversity.R.

7) plot_diversity.R - Create plots with relation between diversity and biome stability and maps with overlap between stable areas and centers of species richness.