Systematic review of modeling assumptions and empirical evidence: does parasite transmission increase nonlinearly with host density?

For the paper entitled, “Systematic review of modeling assumptions and empirical evidence: does parasite transmission increase nonlinearly with host density?”, currently in review in Methods in Ecology and Evolution, we systematically reviewed seven representative ecology journals for host–parasite models that contain transmission functions, yielding 262 relevant papers. We analyzed each paper to determine whether each study used a single transmission function – the DD transmission function, the FD transmission function, or a single nonlinear transmission function – or whether the paper qualitatively or quantitatively evaluated multiple transmission functions. We also recorded whether authors worked with host numbers, densities, or frequencies, whether and how area was explicitly included within models, and whether area and/or host density were constants. All of these data are included in a single dataset in this repository. Additionally, we performed an extensive literature review to find experimental or observational studies that compared transmission functions in animal systems. For each of the 42 resulting papers, we determined which transmission functions were evaluated and which function the authors determined to be the most parsimonious description (best fit balanced against number of parameters) of the given host-parasite system. These data are included in a single dataset within this repository. The paper in review also includes a substantial model simulation component, which can be found in a different GitHub repository and as the R package ‘contactr’.

针对题为《系统综述：建模假设与实证证据：寄生虫传播是否随宿主密度非线性增加？》的论文，该论文目前正在《生态与进化的方法》杂志进行审稿，本研究系统性地回顾了七种代表性生态学期刊中包含传播函数的宿主-寄生虫模型，共收集到262篇相关论文。我们对每篇论文进行了分析，以确定研究是否仅使用单一传播函数——DD传播函数、FD传播函数，或单一非线性传播函数——或者论文是否对多个传播函数进行了定性与定量评估。此外，我们还记录了作者是否使用了宿主数量、密度或频率，模型中是否明确包含了面积，以及面积和/或宿主密度是否为常数。所有这些数据均包含在此存储库的单个数据集中。此外，我们还进行了广泛的文献综述，以寻找比较动物系统中传播函数的实验或观察性研究。对于这42篇研究结果，我们确定了哪些传播函数被评估，以及作者认为哪个函数是对给定宿主-寄生虫系统最简约的描述（在参数数量与最佳拟合之间取得平衡）。这些数据也包含在此存储库的单个数据集中。正在审稿的论文还包括大量的模型仿真部分，这些仿真部分可在不同的GitHub存储库以及R包‘contactr’中找到。