Davenport et al. Initial responses of songbird communities to forest reclamation on legacy surface mines

This repository includes data, code for the model, and code to make basic plots for the hierarchical community occupancy model of [Davenport, R.N, C. Barton, J. Cox, J.C. Guzy, L. Sherman, J.L. Larkin and S.J. Price 2025. Initial responses of songbird communities to forest reclamation on legacy surface mines. <i>Ecosphere</i>, <i>in press</i>In June 2022, we conducted repeated point count surveys in high-elevation, red spruce-northern hardwood forests in the Appalachian Mountains of eastern West Virginia, USA . We used a multi-species, hierarchical Bayesian model developed by Zipkin et al. (2009) to estimate species-specific occupancy responses to recently restored (i.e., reforested) surface mines (2-5 yr and 8-11 yr post restoration), naturally regenerating forests on surface mines and unmined mature forests.Data include point count survey data files as a .csv that includes presence-absence data for each species at 32 sites during 3 surveys. The point count survey data also include site covariates: day of year (DOY), time of day (Time), estimated cloud cover (Cloud), estimated wind speed (Wind), and air temperature (Temp ). We also include site covariate file that include site number and treatment type as YFRA (young, forestry reclamation approach), OFRA (older FRA), REGEN (naturally regenerating forests on surface mines and MAT (mature, unmined forests). We provide text files for each multi-species occupancy model, as a single model was developed for each avian guild (i.e., generalist species, mature forest species, and young forest species). Data are brought into Program R, and the model is run using the package R2Winbugs. Each model file includes the annotated model as well as code to generate some basic plots.

本仓库涵盖[Davenport RN、Barton C、Cox J、Guzy JC、Sherman L、Larkin JL与Price SJ于2025年发表于《Ecosphere》（即将刊出）的论文《遗留露天煤矿森林修复后鸣禽群落的初始响应》]所涉及的层次化群落占用模型（hierarchical community occupancy model）所需的数据、模型代码及基础绘图代码。
2022年6月，我们于美国西弗吉尼亚州东部阿巴拉契亚山脉的高海拔红云杉-北部硬木林中开展了重复点计数调查（point count surveys）。我们采用Zipkin等人（2009）开发的多物种层次贝叶斯模型（multi-species hierarchical Bayesian model），估算鸣禽群落对三类生境的物种特异性占有率（species-specific occupancy）响应：近期完成造林修复的露天煤矿（修复后2~5年及8~11年）、露天煤矿自然恢复林，以及未受开采的成熟林。
本数据集包含以逗号分隔值（CSV）格式存储的点计数调查数据文件，其中记录了32个样点在3次调查中各物种的存在-缺失数据。该数据同时包含样点协变量（site covariates）：年中日（Day of Year, DOY）、当日时间（Time）、预估云量（Cloud）、预估风速（Wind）与气温（Temperature, Temp）。我们还提供了样点协变量文件，其中包含样点编号与处理类型：YFRA（年轻林业修复法，Young Forestry Reclamation Approach）、OFRA（老龄林业修复法，Older Forestry Reclamation Approach）、REGEN（露天煤矿自然恢复林）与MAT（未受开采的成熟林，Mature Unmined Forest）。
我们为每个鸟类功能群（avian guild）分别构建了多物种占用模型，每个功能群对应一套模型，涵盖广适性物种、成熟林物种与幼林物种三类，并提供了对应模型的文本文件。数据将导入R语言（Program R）环境，模型通过R2WinBUGS包（R2WinBUGS package）运行。每个模型文件均包含带注释的模型代码，以及用于生成基础绘图的代码。