Software

This repository contains analysis codes to reproduce the key findings reported in the manuscript, "Re-Oligotrophication Over 20 years Contributed to Macrophyte Community Shifts and Recovery in the Upper Mississippi River." The supporting data has been released as a USGS data release: Larson, D., Rohweder, J., Jankowski, K.J., and Jones, M., 2026, Macrophyte Communities and Environmental...

This repository contains an individual-based integral projection model with Allee effect. The repository includes a Jupyter Notebook that explains the model and the model outputs in addition to a Python file with code necessary to run the model.

This repository contains a R script to help with the U.S. Fish and Wildlife Service bigheaded carps monitoring program in the Upper Illinois River. The repository includes code to fit an occupancy model to the data and compare different monitoring program designs.

Nestucca Bay National Wildlife Refuge winter goose status and trend analyses.- Nestucca Bay National Wildlife Refuge, located on the central Oregon coast near Pacific City, Oregon, was founded in 1991 to provide coastal habitat to wintering Semidi Island Aleutian Cackling and Dusky Canada geese. To determine the success of the refuge in meeting its mission, the refuge annually conducts...

This repository contains the code used determine the effects of a carbon dioxide mat on zebra mussels. The supporting data has been released as a USGS data release: Meulemans, M.J., Waller, D.L., Wise, J.K., Severson, T.J., Barbour, M.T., and Morris, B.E., 2026, Evaluation of benthic barrier layers/tarps for open water control of invasive mussels in 2024 in Loon Lake, Benzie Co...

The North American Breeding Bird Survey (BBS) (https://www.pwrc.usgs.gov/bbs/) has counted birds annually for over fifty-five years. Survey 'routes' each consist of 50 'stops' (point counts) placed along a route path. Inter-stop distances and stop locations can vary from route to route and from year to year, and precise locations of each stop are not typically recorded. Burner et al....

The code was used to analyze pollinator COI amplicon FASTQ sequence data in the paper titled "Development and validation of an eDNA assay for detection of the endangered Franklin’s bumble bee (Bombus franklini)" (IPDS number IP-175306, [DOI link]). The corresponding data release can be found here (IPDS number, [DOI link]). Although we use this code to analyze a pollinator COI dataset, it...

This repository contains applications of the Metapopulation Integral Projection Model (MetaIPM; https://doi.org/10.5066/P9427H6M), which is a Python package that uses a integral projection model (IPM) to model meta-population dynamics and continuous growth rates of species living in spatially discrete habitat units. In this particular implementation, we use MetaIPM to model invasive...

This script is for analyzing raw eDNA qPCR data. It is designed to efficiently concatenate qPCR data from multiple plates exported as *.csv files. It will assist with completing several QA/QC checks and output documentation of these checks as well as helpful files for further review.

Anurans (frogs and toads) were surveyed using aural call surveys across the upper Midwest, United States from 2003 to 2008, and again in 2024. This code analyzes these data (from the associated data releases) using a multi-species occupancy model with imperfect detection, species traits, and species associations. It tests for relationships between covariates, occupancy, and detection...

Analysis code to evaluate Burbot tolerance to lampricide TFM, which is used in tributaries of the Great Lakes to control larval Sea Lamprey. A lab test of toxicity of this non-target species was conducted. This code examines the length and weight of test animals, visualizes water quality measures taken during the tests, and fits a dose response curve.

This repository contains an example application of the `Meta-IPM` Python package (https://doi.org/10.5066/P9PW673G). The specific application focuses on the upper Mississippi River using existing public data. The code for this project assumes the reader is familiar with Jupyter Notebooks, enough Conda and Python to install the `Meta-IPM` package, and population ecology. The example also...