Collaborative Research: OpenDendro - Advanced Open-source Tools for Paleoenvironmental Reconstruction

该研究小组的目标是创建OpenDendro，作为R和Python编程语言中用于树状年代学的基本分析软件工具的开源框架。研究目标是在开源环境中创建和管理一套统一的关键工具，为研究人员使用树轮数据采用开放科学做法提供必要的基线，并提高树木年代学的严密性和透明度。树木年代学使用的大多数软件都是传统编程语言，几十年来一直由少数志愿者维护。随着计算体系结构的进步，这些代码面临着无法操作或不兼容的风险。受到不利影响的技术和工具包括专门的数据输入和输出、趋势分析、交叉年代测定、年表编制、光谱建模、描述性统计以及其他常见的数据处理和数据处理任务。研究小组认为，这种情况可以通过将这些遗留项目纳入现代开源和开放科学框架来解决。虽然其中一些工作已经在R包dplR中完成，但更广泛的研究社区最需要的许多工具在R中仍然没有广泛使用(包括无信号标准化)，而且几乎没有一个是在Python生态系统中实现的。潜在的更广泛的影响包括创建一个现代的开源软件库，将立即被古气候学家利用树木年轮数据进行古气候研究使用。对这一软件进行现代化改造和改进，还将把它们的影响范围和用途扩展到树状年代学之外，并使之能够融入包括LinkedEarth和Pangeo在内的大气和地球科学领域的相关倡议。使这些工具开源还将促进进一步的协作开发，扩大对该软件的集体维护和增强的责任，并确保这些独特的工具的持久性。该项目为下一代古环境科学家提供了关于OpenDendro工具包的编码“训练营”的培训机会，并广泛模拟了树状年代学中开放科学概念和实践的应用。该奖项反映了国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The research team aims to create openDendro as an open-source framework of the base analytic software tools used in dendrochronology in both the R and Python programming languages. The research goal is to create and curate a unified set of critical tools in open-source environments that will provide the necessary baseline for researchers using tree-ring data to adopt open-science practices and increase both rigor and transparency in dendrochronology.Much of the software used in dendrochronology are in legacy programming languages and have been maintained by a small number of volunteers for decades. The codes are at risk of becoming inoperable or incompatible as advances in computing architecture accelerate. The techniques and tools adversely impacted include specialized data input and output, detrending, cross-dating, chronology building, spectral modeling, descriptive statistics, and other common data-handling and data-processing tasks. The research team argues that this situation could be addressed by incorporating these legacy programs into a modern open-source and open-science framework. While some of this work has been completed in the R package dplR, many of the tools most needed by the broader research community are still not widely available in R (including signal free standardization) and virtually none are implemented in the Python ecosystem. The potential Broader Impacts include creating a modern open-source software base that will be immediately usable by paleoclimatologists using tree-ring data for paleoclimate research. Modernizing and enhancing this software will also extend both their reach and utility beyond the dendrochronology community and allow integration into related initiatives in the atmospheric and earth sciences including LinkedEarth and Pangeo. Making these tools open source will also facilitate further collaborative development, broaden the responsibility for collective maintenance and enhancement of this software, and ensure the persistence of these unique tools. This project provides training opportunities for the next generation of paleoenvironmental scientists with a coding `bootcamp' on the openDendro toolkit and broadly models the application of open-science concepts and practices within dendrochronology.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.