PaleoTransformation Analysis Model Code

This dataset is a code release containing the scripts for the paleoecological portion of the North Central Climate Adaptation Science Center (NC CASC) project "Risk of ecological transformation across the US West and Pinyon woodlands." The project investigated how climate change over the last 21,000 years, which was characterized by significant warming, influenced vegetation in the Southern and Middle Rockies. The analysis found that rapid vegetation change was initiated across these landscapes once a 2 degree C temperature increase was realized and again recently with reduced rainfall; southwesterly slopes in the Southern Rockies were prone to rapid change, while other landscape features did not have a strong effect. The work also examined vegetation transformations (for example, sagebrush steppe switching to a lodgepole pine forest) and identified between one and four vegetation transformations at each site, for a total of 60 transformations, over half of which occurred rapidly. The scripts reproduce the workflows and analyses that led to these conclusions, including: acquisition of pollen records and geochronologies from the Neotoma Paleoecology Database; Bayesian age-depth modeling (rbacon); cluster analysis of pollen assemblages; rate-of-change analysis (R-Ratepol); extraction of climate covariates (StableClim and Trace21Ka) and landscape covariates (Google Earth Engine); boosted regression tree models; and Bayesian site-level models. The code is maintained in a GitLab repository (https://gitlab.com/crausbay/nc-casc-paleotransformation) and is provided here as a downloadable archive.