Software

This repository contains a R package with 2-level and 3-level occupancy models. The package also contains a set of tutorials designed to help users understand how to use and code occupancy models in Stan. The models include a statistical hierarchy that allows for multi-species modeling and estimating correlations among species. The models may also be used as a more general "random-effect" type occ

This repository contains code to run an occupancy model for eDNA data from a gradient along the Illinois River collected in 2015.

The multistater package can fit several types of multi-state models, including discrete-state discrete-time Hidden Markov Models using both maximum-likelihood and Bayesian approaches (HMMs) and discrete-state continuous-time state-space models (SSMs). The package was created to specify HMM and SSM designs that can be fit in both the frequentist and Bayesian paradigms within a single package. Our s

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 locations using d

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 the quick fl

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 file. Final

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 template for

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 user is fam

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 version of this

This version 1.1.1 release of the Groundwater Nitrate Decision Support Tool (GW-NDST) for Wisconsin supersedes the version 1.1.0 release. This version 1.1.1 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.