Software
I have developed or co-developed a number of software packages for ecology in the statistical programming language R. I work both privately and collaboratively on Github (username ndimhypervol), so please convey any comments on software as Github issues and I’ll be sure to respond.
Lead developer:
The Wallace ecological modeling application 2.0 (R package
wallace) features an interactive graphical user interface and walks users through a complete species distribution modeling analysis, including data collection, data processing, study extent selection, model complexity tuning, and model predictions. An early version was a finalist for the GBIF Ebbe Nielsen Challenge for innovative applications of open-access biodiversity data.ENMeval 2.0.0, a complete redesign of the original package, featuring new object-oriented structure for adding other algorithms (and native BIOCLIM implementation), customizable algorithmic settings and performance metrics, extensive metadata, a null-model approach to quantify significance and effect sizes, and features to increase the breadth of analyses and visualizations.
Co-developer:
ENMeval <0.3.1 (R package
ENMeval) is the first software in R to provide automated model complexity tuning for species distribution models (here, Maxent) and tools to partition data for cross validation in a variety of ways, including spatial options.Range Model Metadata Standards (R package
rangeModelMetadata), or RMMS, offers a hierarchical metadata framework for species distribution models and tools to autogenerate metadata objects from data and models in R.occCite (R package
occCite) is a collection of tools for downloading and taxonomically verifying species occurrence data, gathering metadata on both database aggregators and primary providers, and generating citations on this metadata for publications.maskRangeR (R package
maskRangeR) is a collection of tools for processing potential range predictions made with species distribution models to estimate species’ current ranges, and includes both expert-driven and data-driven methods
References
Kass, J. M., Pinilla-Buitrago, G. E., Paz, A., Johnson, B. A., Grisales-Betancur, V., Meenan, S. I., Attali, D., Broennimann, O., Galante, P. J., Maitner, B. S., Owens, H. L., Varela, S., Aiello‐Lammens, M. E., Merow, C., Blair, M. E., & Anderson, R. P. (2023). wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions. Ecography, e06547. https://doi.org/10.1111/ecog.06547</li>
Kass, J. M., Muscarella, R., Galante, P. J., Bohl, C., Pinilla-Buitrago, G. E., Boria, R. A., Soley‐Guardia, M., & Anderson, R. P. (2021). ENMeval 2.0: redesigned for customizable and reproducible modeling of species’ niches and distributions. Methods in Ecology and Evolution, 12: 1602 – 1608. https://doi.org/10.1111/2041-210X.13628</li>
Kass, J. M., Vilela, B., Aiello‐Lammens, M. E., Muscarella, R., Merow, C., & Anderson, R. P. (2018). Wallace: A flexible platform for reproducible modeling of species niches and distributions built for community expansion. Methods in Ecology and Evolution, 9(4), 1151-1156. https://doi.org/10.1111/2041-210X.12945
Muscarella, R., Galante, P. J., Soley‐Guardia, M., Boria, R. A., Kass, J. M., Uriarte, M., & Anderson, R. P. (2014). ENM eval: An R package for conducting spatially independent evaluations and estimating optimal model complexity for Maxent ecological niche models. Methods in Ecology and Evolution, 5(11), 1198-1205. https://doi.org/10.1111/2041-210X.12261
Merow, C., Maitner, B. S., Owens, H. L., Kass, J. M., Enquist, B. J., Jetz, W., & Guralnick, R. (2019). Species’ range model metadata standards: RMMS. Global Ecology and Biogeography, 28(12), 1912-1924. https://doi.org/10.1111/geb.12993
Owens, H. L., Merow, C., Maitner, B., Kass, J. M., Barve, V., & Guralnick, R. P. (2020). occCite: Tools for Querying and Managing Large Biodiversity Occurrence Datasets. R package version 0.2.0. https://github.com/hannahlowens/occCite
Merow, C., Galante, P. J., Babich Morrow, C., Kass, J. M., Moore, A., Grisales-Betancur, V., Gerstner, B., Velasquez, J., Anderson, R. P., & Blair, M. E. (2020). maskRangeR: Improving spatial and temporal accuracy of species distribution models. R package version 1.0. https://github.com/cmerow/maskRangeR