Software
nQuack
Predicting ploidy level from sequence data.
nQuack is an R package for predicting ploidy level from sequence data using site-based heterozygosity. For efficiency, this package is written in C++ and integrated into R with Rcpp.
Here we build upon Weib et al., 2018 (nQuire). We provided expanded tools and implementations to improve site-based heterozygosity inferences of ploidal level.
Our model improves upon the nQuire framework by extending it to higher ploidal levels (pentaploid and hexaploid), correcting the augmented likelihood calculation, implementing more suitable distribution, and allowing additional 'fixed' models.
We also decrease model selection errors by relying on BIC rather than likelihood ratio tests.
nQuack also provides data preparation guidance and tools to decrease noise in input data.
Check out Gaynor et al. (2024), the github repository, or our pkgdown site to find out more.
nQuack-AI
Data-based approach for predicting ploidy level from sequence data.
nQuack-AI is a data-based approach for predicting ploidy level from sequence data. Coming Soon! We are currently building and testing our model with over 10,000 samples representing 20 taxonomic groups. If you have sequence data with known ploidal level, please reach out!
MCPop
Mixed-cytotype population genetics toolkit.
MCPop, a Mixed-Cytotype Population Genetics Toolkit, is a collection of functions I've used in various population genetics projects focused on mixed-cytotypes. This repository is currently under construction, but listed here to keep my ducks in a row.
AutoPop
R-based autopolyploid population simulations.
AutoPop contains a stochastic stage-structured matrix population dynamics model for diploid, triploid, and autotetraploid perennial plants with overlapping generations and two life-stages (reproductively immature and reproductively mature).
Each time step includes Reproduction, Survival, and Maturation.
Check out Gaynor et al. (2025), the github repository, or our pkgdown site to find out more.
gatoRs
Geographic and taxonomic occurrence record scrubbing.
gatoRs is an R package for Geographic And Taxonomic Occurrence Record Scrubbing. Here we provide users with tools for downloading and processing biodiversity data.
Check out Patten et al. (2025), the CRAN package, the github repository, or our pkgdown site to find out more.
utremi & PaleoGenerate
Ancestral state reconstruction via a histogram approach.
In collaboration with Ryan Folk, we developed utremi and PaleoGenerate. utremi is code needed to perform maximum likelihood based ancestral niche reconstruction according to the histogram method discussed in Folk and Gaynor et al. 2023.
PaleoGenerate is an open-source approach to infer paleoclimatic layers.
ridigbio
An R package to access iDigBio, the Integrated Digitized Biocollections.
I am a contributor to the ridigbio R package. Specifically, I expanded the documentation and created the pkgdown site, as well as the logo.
This package allows API access to iDigBio, the Integrated Digitized Biocollections.
Teaching Material
- Biodiversity Resource Round-up
- Using Digitized Collections-Based Data in Research, Botany 2020, 2021, 2022, 2023, and 2025
- Using R for Digitized Natural History Collections (dNHC) in Research, BCEENET 2021 Virtual Meeting
- Introduction to R with Biodiversity Data, QUBES Educational Resources (Also available as a bookdown site and on GitHub)
- Cleaning Biodiversity Data: A Botanical Example Using Excel or RStudio, QUBES Educational Resources
- Course-based Undergraduate Research Experience: Florida Plants and Climate Change
- API Office Hours with iDigBio API Working Group
- Ecological Niche Modeling Crash Course
- SPNHC-TDWG 2024, DemoCamp: An introduction to Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data
- FlowHullabaloo: A google drive full of material to aid in ploidal estimation via flow cytometry. Please reach out if you want access to this material.