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

该研究团队的目标是创建openDendro作为一个开源框架，用于R和Python编程语言中的树木年代学基础分析软件工具。 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，为使用树木年轮数据的研究人员提供必要的基线，以采用开放科学实践，并提高树木年轮学的严谨性和透明度。树木年轮学中使用的大部分软件都是传统的编程语言，几十年来一直由少数志愿者维护。 随着计算架构的加速发展，这些代码有可能变得不可操作或不兼容。受到不利影响的技术和工具包括专门的数据输入和输出、去趋势、交叉定年、年表建立、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程序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仍然没有在R中广泛使用（包括无信号标准化），并且几乎没有在Python生态系统中实现。潜在的更广泛的影响包括创建一个现代化的开源软件库，该软件库将立即被古气候学家使用树木年轮数据进行古气候研究。 现代化和增强这一软件还将扩大其覆盖范围和效用，使其超越树木年代学社区，并允许整合到大气和地球科学的相关举措中，包括LinkedEarth和Pangeo。 使这些工具开放源码还将促进进一步的合作开发，扩大集体维护和增强这一软件的责任，并确保这些独特工具的持久性。该项目通过openDendro工具包的编码“训练营”为下一代古环境科学家提供培训机会，并广泛模拟树木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，并被认为值得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予以支持。

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.