Abstract We present a new R package to provide dendroecologists with tools to infer, quantify, analyze, and visualize growth suppression events in tree rings. dfoliatR is based on the OUTBREAK program and builds on existing resources in the R computing environment and the well-used dplR package. It is designed to aid research in the ecology of insect defoliation events and to reconstruct defoliator outbreak chronologies, but can be applied to other studies where host–non-host comparisons are useful. dfoliatR performs an indexing procedure to remove climatic signals in the host-tree series that are represented in the non-host chronology, or other annually-resolved climate series. It then infers defoliation events in individual trees based on user-specified thresholds. Site-level analyses identify outbreak events that synchronously affect user-defined numbers or proportions of involved host trees. Functions are provided for summary statistics and graphics of tree- and site-level series. We evaluated dfoliatR against OUTBREAK, using eight datasets including 222 host-trees, and found that dfoliatR improves on OUTBREAK with greater user control, identification of defoliation events, computing capacity, and both the statistical summary and graphical outputs. We provide two example data sets and script to enable users to gain familiarity with the package and its capabilities. The source code is available in the Comprehensive R Archive Network (CRAN) and on GitHub.

中文翻译：

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dfoliatR：用于检测和分析树木年轮中昆虫落叶信号的 R 包

摘要 我们提出了一个新的 R 包，为树木生态学家提供工具来推断、量化、分析和可视化树木年轮中的生长抑制事件。dfoliatR 基于 OUTBREAK 程序并建立在 R 计算环境中的现有资源和使用良好的 dplR 包之上。它旨在帮助昆虫落叶事件的生态学研究并重建落叶虫爆发年表，但也可应用于宿主与非宿主比较有用的其他研究。dfoliatR 执行一个索引程序，以删除在非寄主年表或其他每年解析的气候系列中表示的寄主树系列中的气候信号。然后，它根据用户指定的阈值推断个别树木的落叶事件。站点级分析可识别同步影响用户定义数量或相关宿主树比例的爆发事件。提供了用于树级和站点级系列的汇总统计和图形的函数。我们使用 8 个数据集（包括 222 个宿主树）评估了 dfoliatR 与 OUTBREAK，发现 dfoliatR 改进了 OUTBREAK，具有更好的用户控制、落叶事件识别、计算能力以及统计摘要和图形输出。我们提供了两个示例数据集和脚本，使用户能够熟悉该包及其功能。源代码可在综合 R 档案网络 (CRAN) 和 GitHub 上找到。我们使用 8 个数据集（包括 222 个宿主树）评估了 dfoliatR 与 OUTBREAK，发现 dfoliatR 改进了 OUTBREAK，具有更好的用户控制、落叶事件识别、计算能力以及统计摘要和图形输出。我们提供了两个示例数据集和脚本，使用户能够熟悉该包及其功能。源代码可在综合 R 档案网络 (CRAN) 和 GitHub 上找到。我们使用 8 个数据集（包括 222 个宿主树）评估了 dfoliatR 与 OUTBREAK，发现 dfoliatR 改进了 OUTBREAK，具有更好的用户控制、落叶事件识别、计算能力以及统计摘要和图形输出。我们提供了两个示例数据集和脚本，使用户能够熟悉该包及其功能。源代码可在综合 R 档案网络 (CRAN) 和 GitHub 上找到。