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

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.

本数据集包含复现《熊蜂占据率响应局地与景观土地利用、气候生态位属性及气候变化间复杂交互作用》一文分析所需的全部数据，具体细节详见GitHub上的分析代码库（https://github.com/timnewbold/BumblebeesLUClimStudy）。

用于处理本数据集的R语言包如下（除非另有说明，所有包均可在R语言综合存档网络（Comprehensive R Archive Network，CRAN）获取）：
terra 版本1.7-71
predictsFunctions 版本1.0，获取地址为https://github.com/timnewbold/predicts-demo
raster 版本3.6-26
rgdal 版本1.6-7
brms 版本2.21.0

本代码仓库包含的数据集如下：
### 熊蜂生态位属性数据集
包含熊蜂实际气候生态位（realized climatic niche）的估算结果，以各物种分布范围内的温度生态位位置（BaselineTEI_Spp）或降水生态位位置（BaselinePEI_Spp）呈现，其中取值0代表该物种实际气候生态位内最冷或最干旱的条件，取值1代表最暖或最湿润的条件；同时还包含近期气候变化下上述温度、降水生态位位置的变化量估算结果（DeltaTEI_Spp_Period3与DeltaPEI_Spp_Period3）。该估算方法详见Soroye等人（2020），DOI: 10.1126/science.aax8591。
上述文件需存储至代码仓库的主0_data文件夹中，对应路径为：
0_data\BaselineTEI_Spp
0_data\BaselinePEI_Spp
0_data\DeltaTEI_Spp_Period3
0_data\DeltaPEI_Spp_Period3

为检验主分析所用气候研究单元（Climatic Research Unit，CRU）数据版本与原始生态位属性估算完成后发布的CRU Version 4版本间的生态位属性估算一致性，本数据集还包含名为“ThermalLimits_CRU4”的文件夹，需将其保存至主0_data文件夹的子目录中，对应路径为0_data\ThermalLimits_CRU4。

### 土地利用历史数据集
包含景观首次大规模转化为人类土地利用类型的年份数据，其中“大规模转化”定义为土地利用类型（耕地、牧场或城市用地）的占比达到10%（yocPS15002005_1_0.1）、30%（yocPS15002005_1_0.3）或50%（yocPS15002005_1_0.5）。有关该数据集的更多信息详见Newbold等人（2015），DOI: 10.1038/nature14324。
上述文件需存储至代码仓库的主0_data文件夹中，对应路径为：
0_data\yocPS15002005_1_0.1
0_data\yocPS15002005_1_0.3
0_data\yocPS15002005_1_0.5

### 联合国次区域地图数据集
包含用于绘图的联合国次区域（UN_subregion）矢量地图。该文件需存储至代码仓库的主0_data文件夹中，对应路径为0_data\UN_subregion.*

以下为分析所需但本数据集未包含的数据集：因无再发布权限，无法随本数据集一同提供，但可通过其他公开仓库获取，获取方式如下：
#### 自然生境覆盖度数据集
自然（原生与次生）生境的覆盖度数据可从以下链接下载：https://data.csiro.au/collection/csiro:15276v3（数据版本3，DOI: 10.4225/08/56DCD9249B224）。需下载的文件为PRI_2005.ZIP与SEC_2005.ZIP，将其中的数据解压后分别保存至代码仓库的对应子目录：
0_data\PRI_2005
0_data\SEC_2005

#### 化肥使用数据集
全球17种主要农作物的氮、磷、钾化肥施用密度（kg/ha）数据可从以下链接下载：http://www.earthstat.org/nutrient-application-major-crops/。下载得到的数据需保存至代码仓库主0_data文件夹下的子文件夹“FertilizerCropSpecific_Geotiff”中，对应路径为0_data\FertilizerCropSpecific_Geotiff

#### 农药使用数据集
不同农作物上各类农药施用密度（kg/ha）的全球数据（GeoTIFF格式）可从以下链接下载：https://doi.org/10.6084/m9.figshare.7764014.v6。下载得到的数据需保存至代码仓库主0_data文件夹下的子目录“PEST-CHEMGRIDS_v1_01_APR/GEOTIFF”中，对应路径为0_data\PEST-CHEMGRIDS_v1_01_APR\GEOTIFF

#### PREDICTS数据库
记录不同土地利用类型与强度下生态群落结构的PREDICTS数据库可从自然历史博物馆的数据门户下载：http://dx.doi.org/10.5519/j4sh7e0w。需下载R数据序列化（R Data Serialization，RDS）格式文件，并保存至代码仓库主0_data文件夹中，对应路径为0_data\database.rds

#### 高程数据集
空间分辨率为30弧秒的数字高程模型（Digital Elevation Model）可从WorldClim下载：https://www.worldclim.org/data/worldclim21.html。文件名为wc2.1_30s_elev.tif，需保存至代码仓库的主0_data文件夹中，对应路径为0_data\wc2.1_30s_elev.tif

#### 处理后的地图与生物多样性数据
为确保分析可复现，本数据集仓库还包含代码第一步（1_PrepareMapData）的输出结果，其中包含经过预处理的输入环境数据；以及代码第二步（2_PrepareDiversityData）的输出结果，其中包含附加了所有输入环境数据的最终处理后生物多样性数据。