Software

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

For some sites and constituents the three dimensions of the Weighted Regressions on Time, Discharge, and Season (WRTDS) model do not capture all the important aspects of water quality variability. For example, in some locations hysteresis or antecedent flow conditions are important influences on water quality concentration and loads. In other places, daily flow is less predictive than...

This repository contains the code used to analyzed the water quality from a formalin study. We examined how formalin affected the total nitrogen and nitrite nitrogen in water that was passed through a biofilter.

This python package works with Quarto MarkDown files to allow authors to supply dois for references while writing a document. Tools in this utilities package provide the ability to automatically query https://doi.org to return valid BiBTeX entries from dois. Further utilities allow users to supply a list of dois, look up the BiBTeX entries, and update them into a new or existing BiBTeX...

This repository contains a journal template for the Journal of Fish and Wildlife Management. The template uses Quarto, a Markdown-based "open-source scientific and technical publishing system." The template uses an MS Word file as a template to format a manuscript for the Journal of Fish and Wildlife Management. Users will want to edit the qmd file and the bib file if they adapt this...

This repository contains an example application of the Meta-IPM Python package (https://doi.org/10.5066/P9427H6M). The specific application focuses on the Illinois 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 assumes the...

MetaIPM is a Python package (Python Software Foundation 2020) that models meta-population dynamics and continuous growth rates via an integral projection model (IPM) for species living in distinct habitat patches. The package stems from a model that compares invasive carp population control strategies (Erickson et al. 2018). For example, Erickson et al. (2017) used an R predecessor...

This version 1.1.2 release of the Groundwater Nitrate Decision Support Tool (GW-NDST) for Wisconsin supersedes the version 1.1.1 release. This version 1.1.2 release includes updated instructions in the readme file and fixes minor bugs.

This repository contains study materials for python programming for hydrologic applications and a focus on groundwater modeling with flopy. The materials are used in an in-person curriculum at the USGS and provided here for reference for the larger hydrologic community.

Official version 1.1.0 software release of the Groundwater-Nitrate Decision Support Tool (GW-NDST) for Wisconsin. This release (v1.1.0) is matched with and described by Juckem, P.F., Corson-Dosch, N.T., Schachter, L.A., Green, C.T., Ferin, K.M., Booth, E.G., Kucharik, C.J., Austin, B.P., and Kauffman, L.J., 2024, Design and calibration of a Nitrate Decision Support Tool for Groundwater...

This repository contains the data, code for modeling and analysis, and publication markdown documents for a comparison of various methods for fitting multi-state models, including maximum likelihood and Bayesian approaches via R.

A groundwater Nitrate Decision Support Tool (GW-NDST) for wells in Wisconsin was developed to assist resource managers with assessing how legacy and possible future nitrate leaching rates, combined with groundwater lag times and potential denitrification, influence nitrate concentrations in wells (Juckem et al. 2024). The GW-NDST was reviewed and approved by the journal via this official...