A hierarchical model for eDNA fate and transport dynamics accommodating low concentration samples

Environmental DNA (eDNA) sampling is an increasingly important tool for answering ecological questions and informing aquatic species management . Challenges of using eDNA include determining species source location(s) and accurately and precisely measuring low concentration eDNA samples, especially considering inhibitory compounds and multiple sources of ecological and measurement variability. These challenges must be overcome to optimize our use of modeling frameworks like the eDNA Integrating Transport and Hydrology (eDITH) model. To better understand eDNA fate and transport dynamics, our ability to estimate parameters within the eDITH framework, and our ability to  reliably quantify low concentration samples,  we developed a hierarchical model and used it to evaluate a fate and transport experiment. Our model addresses several low concentration challenges by modeling the number of copies in each PCR replicate as latent variables with a count distribution and conditioning detection an..., , , # A Hierarchical Model for eDNA Fate and Transport Dynamics Accommodating Low Concentration Samples [https://doi.org/10.5061/dryad.8gtht76wc](https://doi.org/10.5061/dryad.8gtht76wc) ## Description of the data and file structure All files used for data analysis and resulting files (posteriors, etc.) are in the \"Data Analysis\" folder on Zenodo. All files used for simulation analyses are in the \"Simulation\" folder on Zenodo, as are all simulation results (posteriors, etc.). **Data Description** The field data are located in greenhollow_techrep 12_4_2.csv on Dryad. Metadata for greenhollow_techrep 12_4_2.csv is in green hollow metadata.csv on Dryad. **Data Analysis** 1\. The data are in greenhollow_techrep 12_4_23.csv. See files to fit models for data processing. 2\. The nimble model files are \"Release NimModel X.R\", where X is one of the four models. 3\. Custom MCMC functions (inhibitor models only) are in \"State Samplers.R\". 4\. Test scripts to run 1 chain for each model are ...环境DNA（Environmental DNA, eDNA）采样现已成为解答生态学问题、指导水生生物管理的重要工具。当前eDNA应用面临的挑战包括确定物种来源位置，以及精准定量低浓度eDNA样本——尤其需要考虑抑制性化合物，以及生态学与测量过程中的多源变异。若要优化eDNA整合输运与水文模型（eDNA Integrating Transport and Hydrology, eDITH）这类建模框架的使用，必须克服上述挑战。为更深入理解eDNA的归趋与输运动力学，提升eDITH框架内的参数估算能力，以及可靠定量低浓度样本的能力，我们开发了一种层级化模型，并将其用于评估一项eDNA归趋与输运实验。该模型将每个聚合酶链式反应（Polymerase Chain Reaction, PCR）重复的拷贝数建模为服从计数分布的隐变量，并对检测结果进行条件建模，以此解决多项低浓度样本相关挑战。 # 适配低浓度样本的eDNA归趋与输运动力学层级化模型 [https://doi.org/10.5061/dryad.8gtht76wc](https://doi.org/10.5061/dryad.8gtht76wc) ## 数据与文件结构说明 所有用于数据分析及生成结果（后验分布等）的文件均存储于Zenodo平台的"数据分析"文件夹中。 所有用于模拟分析的文件，以及所有模拟结果（后验分布等），均存储于Zenodo平台的"模拟"文件夹中。 **数据说明** 野外实测数据存储于Dryad平台的greenhollow_techrep 12_4_2.csv文件中。 greenhollow_techrep 12_4_2.csv的元数据存储于Dryad平台的green hollow metadata.csv文件中。 **数据分析** 1. 所用数据为greenhollow_techrep 12_4_23.csv，相关文件用于数据处理与模型拟合。 2. NIMBLE模型文件命名为"Release NimModel X.R"，其中X代表四种模型之一。 3. 定制化马尔可夫链蒙特卡洛（Markov Chain Monte Carlo, MCMC）函数（仅适用于抑制物模型）存储于"State Samplers.R"文件中。 4. 用于为每种模型运行1条马尔可夫链的测试脚本为……