Projects
Selected work in conservation science and spatial modeling. All of it is open source — repositories are linked from each write-up.
GAMMa
A web application that allows users to view the extent of their own collection against the data available on GBIF.
- R
- Shiny
- leaflet
- sf
- terra
- GBIF
Botanic Gardens and Gene Banks play an essential role in preserving species diversity by maintaining living collections. Each organization approaches their collections with a set of known priorities and limitations that directly shape what species the organization can protect. Yet the act of effectively conserving a species in ex situ collections goes well beyond the capacity of any single organization. The GAMMa application is intended to enable individuals to evaluate how their collection of a species fits within the larger metacollection of observations and living records maintained by other organizations. This tool provides a quantitative conservation gap analysis assessment that can be used to provide guidance on where additional collection excursions may be most valuable in improving the coverage of a species' living collection.
What GAMMa does
GAMMa compares a species' accession records against wild occurrence records for the same taxon, then scores how much of the wild range the current ex situ collection actually covers. This is possible by pulling records directly from GBIF inside the tool or uploading your own accession data as a spreadsheet. The tool enables individuals to clean the records interactively on a map and table, run a conservation gap analysis, and generate a report to share with others.
The results of the conservation gap analysis are presented through three scores, each bounded 0–100, and averaged into a Final Conservation Score:
- Sampling — number of living accessions relative to reference records.
- Geographic — the proportion of the estimated wild range falling inside buffers around living accession records.
- Ecological — the share of the terrestrial ecoregions the species occupies that are within the buffered area of a living collection record.
Scores and map outputs are intended to support decision making regarding future collection priorities. Additionally, they can be used to compare the conservation status of different species.
The metacollection — the combined holdings of several institutions — is currently only represented by records publicly available on GBIF.
Uploaded data is never stored. Analyses run in a single isolated session, and once closed all data and analysis conducted on the GAMMa application is lost. We provide opportunities to download your edited data as well as the end report to help ensure work within the application can be saved. These files are saved to your computer, not the device on which the application is hosted.
How it was built
An R and Shiny application, modularized by analysis stage, with leaflet for the interactive mapping, sf and terra for the spatial work, rgbif for occurrence retrieval against the GBIF Backbone Taxonomy, and R Markdown for report generation. The gap analysis itself extends the methodology of the GapAnalysis R package — the same lineage as the crop wild relatives work — reworked so that a collections manager, not a programmer, is the intended operator.
Outcome
GAMMa is in public beta. The project has been in development since 2024, and multiple workshops with botanically interested individuals have resulted in a wide suite of feedback that has changed the vision and direction of the tool over time.
The work was initiated in 2023 by the Atlanta Botanical Garden, The Morton Arboretum, and the Montgomery Botanical Center, with a core team drawn from those institutions plus Zest Data Group, the New York Botanical Garden, and BGCI-US. It is supported by the Institute of Museum and Library Services (award MG-252894-OMS-23), BGCI-US, and the United States Botanic Garden.
GapAnalysis R
An R package that scores how well a species is conserved, ex situ and in situ, from occurrence records and a distribution model.
- R
- terra
- sf
- CRAN
The problem
Conservation gap analysis asks a simple question: how much of a species' diversity is already safeguarded, in genebanks and botanic gardens (ex situ) and in protected areas (in situ), and where are the gaps? The method had been applied to hundreds of crop wild relatives, but the code lived in project scripts. Every new study re-implemented it, and results were hard to compare or reproduce.
What GapAnalysis does
The package turns that method into a documented, tested R library. Given occurrence records, a modeled distribution, an ecoregion layer, and a protected-area layer, it computes three scores for each conservation strategy:
- Sampling representativeness — how many occurrences are backed by a conserved accession.
- Geographic representativeness — how much of the modeled range falls within buffers around conserved samples, or inside protected areas.
- Ecological representativeness — how many of the ecoregions the species occupies are represented in collections or protected areas.
The three combine into a final conservation score, ex situ and in situ, and a combined score with a priority category. Maps of the gaps come out alongside the numbers, so a score points at places to collect or protect.
Why it matters
The package is the shared foundation for the work that followed: the crop wild relatives assessment applied it across taxa, and GAMMa wraps the same scoring in a web application for collections managers. Publishing the method as a package means a result from any of those studies can be re-run, and the method can be applied by anyone with occurrence data.
Publication
Carver, D., Sosa, C.C., Khoury, C.K., Achicanoy, H.A., Diaz, M.V., Sotelo, S., Castañeda-Álvarez, N.P., & Ramírez-Villegas, J. (2021). GapAnalysis: an R package to calculate conservation indicators using spatial information. Ecography, 44(7), 1000–1009. doi:10.1111/ecog.05430
Crop wild relatives of the United States
Species distribution modeling and conservation gap analysis for all of the United States crop wild relatives.
- R
- terra
- sf
- targets
The problem
Wild relatives of crops carry genetic diversity that breeders depend on, but their conservation status is poorly documented. The 2020 PNAS assessment established a national baseline; new species needed the same treatment without re-inventing the pipeline.
What was built
A modernized modeling workflow covering occurrence data cleaning, species distribution modeling, and ex situ / in situ gap analysis, structured so that adding a taxon is a configuration change rather than a code change.
Outcome
Reusable methods applied to additional species groups, with a companion repository (cwrSDM) adapting the Aichi Target 13 codebase for ongoing work. The wild grapevine assessment was published in Plants, People, Planet, and the same methodology now underpins GAMMa, a web application bringing gap analysis to botanic garden collections.
Publication
Carver, D., Khoury, C.K., Frances, A., McCarry, N., Diaz-Garcia, L., Galarneau, E., Gora, S., Haidet, M., Heinitz, C., Knapp, W., Meyer, A., Miller, A., Mims, R., Sapkota, S., Spurrier, C., & Wen, J. (2026). Conservation gap analysis for wild grapevines (Vitis L.) of the Americas. Plants, People, Planet. doi:10.1002/ppp3.70246