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

Lead PI: Dr. Edward R. Cook

Unit Affiliation: Biology and Paleo Environment, Lamont-Doherty Earth Observatory (LDEO)

June 2021 - May 2023
Project Type: Research

DESCRIPTION: 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.