DOI: 10.6084/m9.figshare.28713143
title: Data required to run the analyses in 'Bumble bee probability of occurrence responds to interactions between local and landscape land use, climatic niche properties and climate change' Version 2

description: Contained here are all of the data needed to run the analyses in 'Bumblebee occupancy responds to complex interactions between local and landscape land use, climatic niche properties and climate change', as detailed in the analysis code on GitHub (https://github.com/timnewbold/BumblebeesLUClimStudy).<br><br>The R packages used to process the data are as follows (all available on CRAN, unless otherwise specified):<br>terra Version 1.7-71<br>predictsFunctions Version 1.0, available at https://github.com/timnewbold/predicts-demo<br>raster Version 3.6-26<br>rgdal Version 1.6-7brms Version 2.21.0<br>The datasets contained in this repository are:BUMBLEBEE NICHE PROPERTIES<br>Estimates of the realized climatic niches of bumblebees, presented as the temperature (BaselineTEI_Spp) or precipitation niche position (BaselinePEI_Spp) across each species distribution, where a value of 0 represents the coldest or driest conditions and 1 the warmest or wettest conditions within the species realized niche. Also estimates of how these temperature and precipitation position values have changed under recent climate change (DeltaTEI_Spp_Period3 and DeltaPEI_Spp_Period3).<br>The creation of these estimates is described in Soroye et al. (2020), DOI: 10.1126/science.aax8591The files need to be stored in the main 0_data folder in the code repository, i.e.:<br>0_data\BaselineTEI_Spp<br>0_data\BaselinePEI_Spp<br>0_data\DeltaTEI_Spp_Period3<br>0_data\DeltaPEI_Spp_Period3<br>To test consistency in niche property estimates between the version of the CRU data that were used in the main analyses and the Version 4 that was published after the original estimation of niche properties, there is also a folder titled 'ThermalLimits_CRU4', which needs to be saved as a sub-folder in the main '0_data' folder, i.e. 0_data\ThermalLimits_CRU4<br><br>LAND-USE HISTORYData on the year in which landscapes were first substantially converted to human land uses, where substantial use is defined either as 10% (yocPS15002005_1_0.1), 30% (yocPS15002005_1_0.3) or 50% (yocPS15002005_1_0.5) conversion to human land-use types (cropland, pasture or urban areas).<br>For more information on these estimates, see Newbold et al. (2015), DOI: 10.1038/nature14324<br>These files need to be stored in the main data folder in the code repository, i.e.:0_data\yocPS15002005_1_0.1<br>0_data\yocPS15002005_1_0.3<br>0_data\yocPS15002005_1_0.5<br>UN SUB-REGIONS MAP<br>A map of UN sub-regions (UN_subregion), for plotting purposes.The files need to be saved in the main data folder in the code repository:<br>0_data\UN_subregion.*<br>Datasets that are required to run the analysis but omitted here are those for which we do not have permission to republish, but which are nevertheless available in other public repositories. Instructions for obtaining these additional datasets are as follows:COVERAGE OF NATURAL HABITAT<br>Data on the coverage of natural (primary and secondary) habitats can be downloaded here:<br>https://data.csiro.au/collection/csiro:15276v3 (Data Version 3, DOI: 10.4225/08/56DCD9249B224)The files that need to be downloaded are PRI_2005.ZIP and SEC_2005.ZIP. The files in data\PRI_2005 and data\SEC_2005 need to be extracted and saved in in corresponding sub-folders in the analysis code repository, i.e.:<br>0_data\PRI_20050_data\SEC_2005FERTILIZERS<br>Global data on the density of application (kg/ha) of nitrogen, phosphorous and potassium fertilizer on 17 major crops can be downloaded here:<br>http://www.earthstat.org/nutrient-application-major-crops/The downloaded data need to be in a sub-folder 'FertilizerCropSpecific_Geotiff' in the main data folder in the code repository:<br>0_data\FertilizerCropSpecific_Geotiff<br>PESTICIDES<br>Global data on the density of application (kg/ha) of different types of pesticides on different agricultural crops can be downloaded (in GeoTIFF format) here:<br>https://doi.org/10.6084/m9.figshare.7764014.v6The downloaded data need to be in the sub-folder 'PEST-CHEMGRIDS_v1_01_APR/GEOTIFF' in the main data folder in the code repository:<br>0_data\PEST-CHEMGRIDS_v1_01_APR\GEOTIFF<br>PREDICTS DATABASE<br>The PREDICTS database, documenting the structure of ecological assemblages across different land-use types and intensities, can be downloaded from the data portal of the Natural History Museum:<br>http://dx.doi.org/10.5519/j4sh7e0w<br>You should download the RDS-format file, and save as 0_data\database.rds in the main data folder of the code repository:<br>0_data\database.rds<br><br>ELEVATION<br>A Digital Elevation Model at 30 arc-second spatial resolution can be downloaded from WorldClim:<br>https://www.worldclim.org/data/worldclim21.html<br>Filename should be wc2.1_30s_elev.tif, and should be saved in the main data folder in the code repository:<br>0_data\wc2.1_30s_elev.tif<br>PROCESSED MAP AND BIODIVERSITY DATA:<br>To ensure that our analyses remain reproducible, this data repository also contains a copy of the output of the first step of the code (1_PrepareMapData), which contains processed versions of the input environmental data, and the second step of the code (2_PrepareDiversityData), which contains the final processed biodiversity data with all input environmental data appended.