Software

D-Claw is a software library for the simulation of dense granular flows over spatially variable topography. D-Claw builds on clawpack, is written in Fortran, and has a python wrapper. The code is hosted on code.usgs.gov and mirrored on github. D-Claw is supported on Linux/Unix only.

This repository provides the R scripts and stan files to fit hierarchical logistic regression models, using a regularized horseshoe prior on regression coefficients, to examine spatial drivers of DELT occurrence in fishes in the Chesapeake Bay Watershed, USA.

This repository contains code to construct periodic matrix models representing the demography of four lizard species native to or extant on Guam.

This release allows users to select the CRS of exported files, and to specify alternate configuration files. The release also updates wildcat’s backend for compatibility with pfdf 3+. Documentation: https://ghsc.code-pages.usgs.gov/lhp/wildcat/ Release Notes: https://ghsc.code-pages.usgs.gov/lhp/wildcat/resources/release-notes/1.1.0.html

Rapid heating events, such as heatwaves, are becoming more frequent and intense as a result of climate change. Importantly, such extreme weather events can be more important drivers of extirpation and selection than changes in annual or seasonal averages and they pose a particularly large threat to poikilothermic organisms. In this study, we evaluate the thermal stress response of a...

This repository contains code for training and running the DeepFaune New England (DFNE) model for species classification in trail camera imagery. This model is a re-trained version of the DeepFaune model for classifying European species in trial cameras, fine-tuned to classify taxa from northeastern North America. The DFNE model takes as input cropped images of each animal, which can be...

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...