| NSF Org: |
AGS Division of Atmospheric and Geospace Sciences |
| Recipient: |
|
| Initial Amendment Date: | March 15, 2021 |
| Latest Amendment Date: | May 21, 2021 |
| Award Number: | 2054516 |
| Award Instrument: | Standard Grant |
| Program Manager: |
David Verardo
AGS Division of Atmospheric and Geospace Sciences GEO Directorate for Geosciences |
| Start Date: | June 1, 2021 |
| End Date: | September 30, 2024 (Estimated) |
| Total Intended Award Amount: | $143,148.00 |
| Total Awarded Amount to Date: | $143,148.00 |
| Funds Obligated to Date: |
|
| History of Investigator: |
|
| Recipient Sponsored Research Office: |
845 N PARK AVE RM 538 TUCSON AZ US 85721 (520)626-6000 |
| Sponsor Congressional District: |
|
| Primary Place of Performance: |
888 N Euclid Ave Tucson AZ US 85719-4824 |
| Primary Place of
Performance Congressional District: |
|
| Unique Entity Identifier (UEI): |
|
| Parent UEI: |
|
| NSF Program(s): | Paleoclimate |
| Primary Program Source: |
|
| Program Reference Code(s): | |
| Program Element Code(s): |
|
| Award Agency Code: | 4900 |
| Fund Agency Code: | 4900 |
| Assistance Listing Number(s): | 47.050 |
ABSTRACT
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.
PROJECT OUTCOMES REPORT
Disclaimer
This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.
Dendrochronology, the science of analyzing tree rings, is a cornerstone of paleoclimatology and environmental science. However, many of its core software tools are outdated, locked in legacy programming languages, and maintained by only a handful of volunteers. The openDendro project aimed to address these challenges by creating an open-source, unified set of analytic tools in R and Python, making dendrochronology accessible, rigorous, and reproducible for modern scientists.
Key accomplishments include:
1. Enhancements to dplR
The widely used R package, dplR, has been improved with advanced features like signal-free detrending, pooled autoregressive modeling, and age-dependent spline curve fitting. These tools are critical for building robust chronologies from tree-ring data. Improved documentation and tutorials now guide users through complex analyses, and the package includes functions to identify and resolve errors in raw datasets from the International Tree Ring Data Bank (ITRDB).
2. Development of dplPy
dplPy, the Python counterpart to dplR, is now available on PyPI and includes tools for data reading, detrending, chronology building, and crossdating. This represents the first comprehensive Python implementation of dendrochronology software. dplPy’s modular design and ongoing enhancements will make it the go-to tool for future dendrochronological research.
3. Interactive Tools and Training
The openDendro website (https://opendendro.org) serves as a central hub for resources, including tutorials, detailed documentation, and online Shiny applications for crossdating and detrending. These tools allow users to explore key functionalities without installing additional software. In January 2024, a two-day openDendro Bootcamp at the Laboratory of Tree-Ring Research trained 30 participants, fostering community engagement and identifying opportunities for further development.
4. AI Integration for Accessibility
To further democratize dendrochronology, an AI agent is being developed to assist new users. Trained on project documentation and tutorials, this agent will answer questions and guide users through analyses, lowering barriers to entry and encouraging adoption of open-source workflows.
5. Improved Collaboration with NOAA ITRDB
Collaborations with NOAA staff have improved data quality in the ITRDB, the primary repository for tree-ring data. Enhancements to dplR have enabled comprehensive evaluations of ITRDB datasets, ensuring they are accessible and error-free.
Broader Impacts
The openDendro project embodies the principles of open science, transparency, and reproducibility. By modernizing dendrochronological tools, this project has empowered researchers to link raw data to large-scale climate reconstructions with unprecedented accuracy. Training workshops, user-friendly tools, and the integration of R and Python environments have broadened participation in dendrochronology, from students to experienced researchers.
The project’s outcomes also include professional development for students and early-career scientists. Participants gained valuable skills in programming, time-series analysis, and software development, leading to professional opportunities in academia and industry.
The openDendro initiative has set a new standard for open-source tools in dendrochronology, ensuring that these essential resources remain accessible and adaptable for future generations.
Last Modified: 01/30/2025
Modified by: Kevin J Anchukaitis
Please report errors in award information by writing to: awardsearch@nsf.gov.
