Software

Birds were surveyed using time-to-detection count methods across Uganda from 1985 to 2011. This code analyzes these data (from the associated data release) to test for relationships between tree cover, time (year), and species richness and occupancy.

This software release contains a generalized workflow to setup particle tracking analyses to assess groundwater travel times at the Navy-Northrop-Grumman site, in Nassau County, New York. This approach uses the posterior "texture model" inset model described by Fienen and others (2024) and made available in Corson-Dosch and others (2023) that simulates groundwater flow in the sole-source...

This repository contains R and JAGS code for fitting nonstationary demographic state-space models (NDSSM) to count-valued abundance data. Models use reduced dynamics but explicitly characterize growth rate distributions, including changepoints and/or volatility clustering for the timing and impacts of environmental stressors. Species fecundity is used to truncate growth rate...

The toxEval R-package includes a set of functions to analyze, visualize, and organize measured concentration data as it relates to https://www.epa.gov/comptox-tools/toxicity-forecasting-toxcast or other user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological...

This repository is a code release to create and analyze simulated datasets to represent a tag-return study for the purposes of estimating annual removal rates of an invasive fish. The simulated scenarios cover ranges of parameters such as the number of fish tagged per year, magnitude of annual harvest rate, length of simulated study, probability of tag retention, probability of tag...

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...

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...

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...