Supporting information to the manuscript: Red fox predation dominates threats to the Southern Squatter Pigeon: Evidence from contemporary and hindcasted distribution models

The zip file contains information support and replicate the results of the manuscript: Red fox predation dominates threats to the Southern Squatter Pigeon: Evidence from contemporary and hindcasted distribution models.Supporting information includes:R scripts to:collate occurrence and pseudo-absence data for squatter pigeon (ALA_occurrence_data_download.R)prepare National Vegetation Information System data into an ordinal framework (NVIS_veg_continuous.R)prepare rasters into a standardised grid (raster_prep_grid_alignment.R)extract raster information to squatter pigeon occurrence and pseudo-absence records (extract_from_raster.R)create an ensemble species distribution model for squatter pigeon (SDM_contemporary_ensemble_w_eval.R)interpret species distribution model results (SDM_results.R)interpret occurrence records (results_calcs.R)interpret historical occurrence records in the context of our projection of historical squatter pigeon habitat (historical_evaluation.R)Data used during the analysis, including:Squatter pigeon occurrence and pseudoabsence data (Data/)Rasters of environmental data and threat distributions (Data/Rasters/)Input into the squatter pigeon species distribution model (Data/data_model_0.01deg_sdm)Output from biomod2 species distribution modelling process (biomod2_output)Figures, including:Figure 1: Contemporary and historical relative likelihood of occurrence of the southern squatter pigeonFigure 2: Variable importance plotFigure 3: Variable response curvesSupplementary Figures 1 and 2: Receiver operating characteristic curves of the contemporary and historical southern squatter pigeon species distribution models.<br>

本压缩包包含支撑并复现论文《赤狐捕食对南方矮脚鸠的威胁占主导地位：来自当代和后报分布模型的证据》的相关资料。配套支撑信息如下：
1. 用于各类分析的R脚本：
- 整理矮脚鸠的出现记录与伪缺席数据（脚本文件：ALA_occurrence_data_download.R）
- 将国家植被信息系统（National Vegetation Information System）数据整理为序数分析框架（脚本文件：NVIS_veg_continuous.R）
- 将栅格数据处理为标准化网格（脚本文件：raster_prep_grid_alignment.R）
- 提取栅格信息至矮脚鸠的出现记录与伪缺席数据条目（脚本文件：extract_from_raster.R）
- 构建矮脚鸠的集成物种分布模型（脚本文件：SDM_contemporary_ensemble_w_eval.R）
- 解读物种分布模型结果（脚本文件：SDM_results.R）
- 解读出现记录（脚本文件：results_calcs.R）
- 结合矮脚鸠历史栖息地预测结果，解读历史出现记录（脚本文件：historical_evaluation.R）
2. 分析过程中使用的数据集：
- 矮脚鸠的出现记录与伪缺席数据（存放于Data/文件夹）
- 环境数据与威胁因子分布栅格（存放于Data/Rasters/文件夹）
- 矮脚鸠物种分布模型的输入数据（文件路径：Data/data_model_0.01deg_sdm）
- biomod2物种分布建模流程的输出结果（存放于biomod2_output文件夹）
3. 相关图表：
- 图1：南方矮脚鸠当代与历史出现相对概率
- 图2：变量重要性图谱
- 图3：变量响应曲线
- 补充图1与补充图2：当代与历史南方矮脚鸠物种分布模型的受试者工作特征（Receiver Operating Characteristic）曲线