Monkeys "over the moon": moonlight as a missing piece in primate sleeping ecology

README Monkeys “over the moon”: moonlight as a missing piece in primate sleeping ecology (Zenodo deposit) This dataset and code accompany the Ecology Letters manuscript. They document how we built used versus available sleeping-site datasets, generated multiple availability designs, and fitted Resource Selection Function (RSF) models to test the influence of moonlight and canopy structure on primate sleeping ecology. The deposit contains both the final dataset used in the main RSF analysis and HTML notebooks that illustrate the complete workflow step by step. Some steps require large external rasters (canopy height, Sentinel-2 NDVI) that are not distributed here, but the main model can be reproduced directly with the provided CSV. Contents of this deposit review_sleep_moon.csvDataset containing the complete details of all articles included in the review. Each entry lists metadata such as citation, species studied, geographic region, and whether moonlight or sleeping behavior variables were reported. This file supports transparency and reproducibility of the literature synthesis. n10_b300_rsf.csvFinal dataset selected for the RSF analysis (10 available points per used point; 300 m buffer). This is the file used to reproduce the main statistical model. covariates.htmlDocuments how the dataset of sleeping sites (used points) and the control points (available points) were created. Describes how available points were generated around each used point, how nightly identifiers were assigned, and how unsuitable areas were masked out. buffers_points.htmlDocuments the generation of all combinations of available-point numbers and buffer sizes (for example: n1_b100, n10_b300, etc.). Each combination is saved as a dataframe with covariates attached (canopy, NDVI, moonlight, weather). The outputs are stored together in an R list. rsf.htmlDocuments the modeling step. It loads the list of datasets, selects the chosen design (n10_b300), fits mixed-effects logistic RSF models, performs diagnostics, and produces figures and tables. This HTML shows the full workflow even though large external raster files are not included. Workflow summary Sleeping-site dataset preparation (covariates.html) Define observed (used) sites and generate matched available points. Apply spatial mask to exclude unsuitable areas. Assign nightly identifiers and bind used/available into one table. Availability design alternatives (buffers_points.html) Iterate across different numbers of available points and buffer sizes. Attach environmental covariates from rasters and weather data. Save all designs into a named list (all_dfs_proc.rds). RSF modeling (rsf.html) Load all designs from the RDS. Select the chosen design (n10_b300). Fit RSF models with lunar × canopy interaction and environmental covariates. Evaluate models, run diagnostics, and produce final figures. Final dataset for reproducibility The CSV file n10_b300_rsf.csv contains exactly the dataset used in the final RSF. With this single file, the main model can be reproduced without needing the heavy raster inputs. External data not included The workflow shown in the HTMLs requires external geospatial datasets that are not part of this deposit due to size and licensing restrictions: ETH Global Canopy Height (10 m) raster, used for canopy metrics. Sentinel-2 imagery, used to calculate NDVI. Mask shapefile to exclude unsuitable areas. Daily weather data (precipitation and temperature). These resources are openly available from their original providers. The included CSV already contains the extracted values needed for the RSF.### README ## 研究主题 “欣喜若狂”的猴子：月光是灵长类睡眠生态学研究中缺失的关键环节 （Zenodo 存档包） 本数据集与配套代码随《Ecology Letters》期刊论文发表，详细记录了研究团队如何构建利用位点与可用位点的睡眠位点数据集、生成多种可用位点设计方案，以及拟合**资源选择函数（Resource Selection Function，RSF）**模型，以检验月光与冠层结构对灵长类睡眠生态学的影响。本存档包包含主RSF分析所用的最终数据集，以及逐步骤展示完整研究流程的HTML交互式文档。部分步骤需调用大型外部栅格数据（冠层高度、Sentinel-2 NDVI），但此类数据未随本存档一同发布，不过用户可直接通过提供的CSV文件复现核心模型。 --- ### 存档包内容 1. **review_sleep_moon.csv**：收录综述纳入的所有文献的完整元数据，每条记录包含文献引用、研究物种、地理区域，以及是否报告了月光或睡眠行为相关变量。该文件保障了文献综合分析的透明度与可复现性。 2. **n10_b300_rsf.csv**：为RSF分析筛选的最终数据集（每个利用位点对应10个可用位点，缓冲区半径300米），是复现核心统计模型的核心文件。 3. **covariates.html**：说明睡眠位点（利用位点）与对照位点（可用位点）的构建流程，涵盖如何在每个利用位点周围生成可用位点、分配夜间标识符，以及通过空间掩膜排除不适宜区域。 4. **buffers_points.html**：说明所有可用位点数量与缓冲区大小组合的生成过程（例如：n1_b100、n10_b300等）。每种组合均以附带环境协变量（冠层、NDVI、月光、天气数据）的数据框形式保存，结果统一存储于R语言列表中。 5. **rsf.html**：详细展示建模流程：加载所有数据集组合、选择预设设计（n10_b300）、拟合混合效应逻辑回归RSF模型、开展模型诊断并生成图表与表格。尽管未包含大型外部栅格文件，该HTML文档仍完整呈现了全部研究流程。 --- ### 研究流程概述 #### 1. 睡眠位点数据集预处理（covariates.html） - 定义观测（利用）位点并生成匹配的可用位点 - 应用空间掩膜排除不适宜区域 - 分配夜间标识符并合并利用位点与可用位点为单一数据表 #### 2. 可用位点设计方案（buffers_points.html） - 遍历不同可用位点数量与缓冲区大小的组合 - 从栅格数据与天气数据中提取环境协变量 - 将所有设计方案保存为命名列表（all_dfs_proc.rds） #### 3. RSF建模（rsf.html） - 从RDS文件中加载所有数据集组合 - 选择预设设计（n10_b300） - 拟合包含月光×冠层交互项与环境协变量的RSF模型 - 评估模型、开展诊断并生成最终图表 --- ### 可复现性核心数据集 CSV文件`n10_b300_rsf.csv`包含了最终RSF分析所用的全部数据。仅需该单个文件，即可复现核心模型，无需依赖体积庞大的栅格输入数据。 --- ### 未包含的外部数据 HTML文档展示的研究流程需调用外部地理空间数据集，因体积与许可限制，本存档未包含此类数据： - ETH全球冠层高度（10米分辨率）栅格数据，用于提取冠层指标 - Sentinel-2影像，用于计算NDVI - 用于排除不适宜区域的掩膜形状文件 - 每日天气数据（降水量与气温） 上述资源均可从其原始提供方公开获取，本存档包含的CSV文件已预先提取了RSF分析所需的全部协变量值。