Data and code from "Mismatch in reindeer resilience to past and future warming signals ongoing declines"
Creators: name: Canteri, Elisabetta
name: Brown, Stuart
name: Post, Eric
name: Schmidt, Niels Martin
name: Nogués-Bravo, David
name: Fordham, Damien
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 310306
subject: Palaeoecology
classificationCode: 310307
subject: Population ecology

description: "Data S1" is the dataset with the fossil record and the modern occurrences of Rangifer used to reproduce the results in the paper. The first excel sheet includes the fossil record, the second excel sheet includes the GBIF occurrences used for estimating the climatic niche, the third excel sheet contains the GBIF occurrences of Rangifer accessed in 2022, to calculate probability of occupancy. All three sheets are also provided in the "Data" folder inside "ReindeerCode.zip" as separate files ("Reindeer_fossil.csv", "Reindeer_GBIF.csv" and "RT_GBIF_2022.csv")."Data S2" is a NEXUS file that contains the mitochondrial ancient DNA sequences used to estimate the trend in effective population size that was used as target for pattern oriented modelling and model validation."ReindeerCode" is a .zip file that contains:Code in steps to reproduce the results in the manuscript.A folder with data that can be used in the first scripts.The script files are all written in R and allow one to follow each step to replicate the results in the manuscript. The scripts will be used to create intermediate files (not provided) which will be used in following steps. Please note that following all the steps can take several months to run on a High-Performance Computing Server.Description of the data and file structureThe "ReindeerCode.zip" folder contains a "Data" folder that includes:Historical climate data (CRU_corrected.csv) used to pair reindeer occurrences to climatePaleoclimate (rt_paleoclimate.csv and the rasters in the "Paleoclimate" folder) used to pair the fossils to the paleoclimateTable with fossil records (Reindeer_fossils.csv)Table with GBIF occurrences (Reindeer_GBIF.csv)A study region raster that shows the geographic extent of the region used in the manuscript (study_region_mask.tiff)"Paleopop" folder with inside all the data needed to run simulations and analyze the output.rt_tracer.txt (output of Bayesian Skyline Plot analysis using aDNA sequences of reindeer)ince_inv_prj.RDS (glacial ice)OuterCells_Polygons.RDS (modification of the temporal land-sea mask)prj_ext.RDS (extent of CRS projection of the study region)reindeer_region_prj.RDS (paleoregion used in simulations)rt_humans_mean_prj.RDS (Humans mean Ne - from CISGEM)rt_humans_sd_prj.RDS (Humans SD Ne - from CISGEM)GreenlandPolygon (folder with polygon of Greenland used in the simulations)HS_PRJ (folder with examples of habitat suitability projections. 5 files are provided to show how the simulations work)Regions (folder)RegionsPoly.csv (region subdivision in .csv format)RT_Subreg (shapefile and metadata of the subregions)There is an additional "FutureSims" folder, which contains the file "reindeer_region_future.RDS", which is used in the simulations of forecast reindeer abundances.CodeThe code is provided in the "Scripts" folder, which contains all the code that is needed to obtain the results in the manuscripts. Each file name starts with "Step" and the step number, starting at Step1 and ending at Step19. To be able to obtain the same results, some steps will need to be repeated. It is clearly written in the files when this happens, before continuing to the next steps. Some scripts include sourcing functions from external files, which are provided in the "Functions" folder.Step1_PairClimateObservations.RStep2_AddRandomPoints.RStep3_NicheCut.RStep4_NicheStatistics.RStep5_SelectNiches.RStep6_ENMs.RStep7_RescaleENMs.RStep8_Simulations.RmdStep9_ValidationTargets.RStep10_SummaryMetrics.RStep11_POMValidation.RStep12_PosteriorPredictiveChecks.RStep13_InformedPriors.RStep14_Results.RStep15_ExtirpationMap.RStep16_LandUse.RStep17_FutureSimulations.RStep18_FutureResults,RStep19_ProbabilityOfOccupancy.RStep20_ExtinctionRisk.RFig1.RFig2.RFig3.RFig4.RMovie_1.RMovie_2.R<br>