https://github.com/AvianMetaNetwork/AvianMetaNetwork
This repository contains code, workflows, documentation, and support data to build the AvianMetaNetwork (aka "AvianMetaNet").
The database is in preparation for publication as an open access data paper. From 2012-2014, Zarnetske and Zonneveld compiled bird-bird interactions among cavity nesting birds and their interacting bird species, based on species accounts in the Birds of North America (now Birds of the World). This led to an analysis of the influence of biotic interactions on North American cavity nesting bird species distributions (Belmaker and Zarnetske et al. 2015 GEB).
Starting in 2019, a new protocol was established and all prior records were updated and further bird-bird interactions were added in by Zarnetske and MSU SpaCE Lab undergraduates (2019-present), initially focusing on North America.
The published AvianMetaNet, documentation, and this code is available from the Environmental Data Initiative (EDI) repository for download as a zip file: LINK PROVIDED UPON PUBLICATION
The workflow for this repository follows the guidelines set out by the Environmental Data Initiative (EDI). Briefly, this involves aligning with FAIR data practices, and employing a workflow that uses different levels for harmonization and derived data products (see diagram for overview).
For Data entry workflow (L0), see our detailed data entry protocol we make available to all project members.
For data cleaning and harmonizing workflow (L1), as well as summarizing and visualizing the database (L2) see R script workflow
- data Directory containing instructions for interaction data entry, metadata, and species checklists (raw in L0, synthesized in L1). Note that species interaction data files are not directly available in this repository, but available for dowload from the EDI repository (see above) upon publication.
- R Code and support files to build a clean and harmonized database from version-controlled data entry files. See R code documentation for detailed descriptions and instructions for using Code/Workflows and descriptions of the files.
- website: code files to build the website for the database.
- docs: output of website.
Funding is provided by Michigan State University (to P.L. Zarnetske), and by a MSU Ecology Evolution, and Behavior SEED Grant (to P.L. Zarnetske). Original work on a subset of species was funded by the Yale Climate and Energy Institute (to P.L. Zarnetske), Erasmus Mundus Fellowship (to S. Zonneveld).
- Phoebe L. Zarnetske, PI, Spatial and Community Ecology Lab (SpaCE Lab)
- Kelly Kapsar, Post-doctoral Fellow 2025-
- Lucas Mansfield, PhD student 2025-
- Vincent Miele, CNRS France
- Stephane Dray, University of Lyon and CNRS, France
- Emily Parker, staff data manager 2022-2024
- Patrick Bills, staff data scientist 2023-2025 Institute for Cyber-enabled Research (ICER)
- 2025-
- Caroline Roche
- Liz Bauer
- Vivian Smith
- Olive Graves
- Sarah Pecis
- Addison Hoddinott
- Elliot Palmer
- Jamie Soehl
- 2024
- India Hirschowitz
- Giovanni DePasquale
- Caroline Roche
- Ava Fountain
- Ann Joseph
- Maddie Andreatta
- 2023
- India Hirschowitz
- Giovanni DePasquale
- Caroline Roche
- 2022
- India Hirschowitz
- Jordan Zapata
- Elaine Hammond
- 2021-2024
- Emily Parker
- 2018-2020
- Erik Ralston
- Minali Bhatt
MSU Undergraduates led the presentation of a research poster at the 2024 MSU Undergraduate University Research and Arts Forum: DePasquale, G., I. Hirschowitz, C. Roche, E.G. Parker, P. Bills, P.L. Zarnetske. April 2024. The North American AvianMetaNet. Michigan State University Undergraduate Research and Arts Forum (UURAF). East Lansing, MI. Poster Presentation.
In Prep: AvianMetaNetwork: biotic interactions among birds of the continental United States and Canada, Phoebe Zarnetske, Patrick Bills, Kelly Kapsar, Lucas Mansfield, Emily G Parker Caroline Roche, India Hirschowitz, Giovanni DePasquale, Sara Zonneveld
*Cornell Lab of Ornithology: Birds of The World, and especially insights from Brian Sullivan and Pam Rasmussen.
*MSU undergraduates listed above
Belmaker, J., P. Zarnetske, M.-N. Tuanmu, S. Zonneveld, S. Record, A. Strecker, and L. Beaudrot. 2015. Empirical evidence for the scale dependence of biotic interactions. Global Ecology and Biogeography 24:750–761. https://doi.org/10.1111/geb.12311
Birds of the World - Comprehensive life histories for all bird species and families. (Accessed January 13, 2022). http://birdsoftheworld.org/bow/home.
Hurlbert, A. H., A. M. Olsen, M. M. Sawyer, and P. M. Winner. 2021. The Avian Diet Database as a source of quantitative information on bird diets. Scientific Data 8:260. https://www.nature.com/articles/s41597-021-01049-9