Software

Pysochron is a Python-based tool designed to calculate isochron burial ages from in-situ cosmogenic 26Al and 10Be data. It uses orthogonal distance regressions to fit isochron lines to 1000 Monte Carlo simulations of nuclide concentration measurements to account for uncertainty, and allows the user to modify various aspects of the fitting process, including constants relating to the...

This is nimble model code for a hierarchical Bayesian analysis to estimate walrus herd density at multiple sites, where some surveys entailed counting walruses in a sample of grid cells overlain on the surveyed herd on shore; whereas, other surveys were censuses (complete counts.) The model code also predicts herd densities for new surveys taken at existing sites and a new site.

his is an R program for simulating multiple fish populations using species-specific projection matrices, interaction matrices, and bioenergetics submodels with hierarchical stochasticity. This program was designed to model the pallid sturgeon (Scaphirhynchus albus) and associated fish species in the Lower Missouri River (Wildhaber et al. 2024), but it should be sufficiently general to...

This release adds the `data` package, which provides routines to download commonly used datasets from the internet. The release also provides pfdf tutorials as Jupyter Notebooks, improves array broadcasting in the `gartner2014` and `staley2017` modules, and introduces the `RasterMetadata` class (which manages raster metadata without loading data arrays to memory). Documentation: https:/...

DynRat was developed by the USGS to develop dynamic rating models using a method called DYNPOUND, which accommodates compound and compact channel geometry to model hysteresis. The latest release can be downloaded from the releases section in the repository. Additions, bug fixes, changes, and links to releases can be viewed in the [/dynamic-rating/dynrat/-/blob/master/userguide/docs...

This standalone software application provides a means of inferring water depth from passive optical remotely sensed data via a machine learning-based workflow: Hyperspectral Imaging of River Bathymetry using an Ensemble of Regression Trees, or HIRBERT for short. This approach could provide accurate depth estimates in clear-flowing, relatively shallow streams but is less likely to yield...

Examinations of contact rates among white-tailed deer (Odocoileus virginianus; hereafter, deer) are important to applied management objectives given their societal value and disease transmission potential. This R script was used to curate the original GPS collar and capture data from Pennsylvania DMA2 in preparation for contact rates analysis.

This repository contains the code needed to reproduce computations presented in Barnhart and others (under review). This readme contains instructions for reproducing results and a list of the git hashes for each source repository used. Computation for this manuscript was done on the U.S. Geological Survey Denali High Performance Computer (Falgout and others, 2024). Barnhart, K.R., George...

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...

Wildlife conservation and management increasingly considers genetic information to plan, understand, and evaluate implemented population interventions. These actions commonly include conservation translocation and population reductions through removals. Change in genetic variation in response to management actions can be unintuitive due to the influence of multiple interacting drivers of...

The need to assess the effects of variability in climate, biota, geology, and human activities on water availability and flow can be assessed with computer models that simulate the hydrologic cycle at a watershed scale. The Precipitation-Runoff Modeling System (PRMS) is a deterministic, distributed-parameter, physical process-based modeling system developed to evaluate the response of...

The program computes eight metrics reflective of lake and stream connectivity including duration, timing, recurrence, continuance, disconnectedness, dry season, wet season, and seasonality.