Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
Filter Total Items: 932
FishScale FishScale
FishScale estimates fish lengths, numeric abundance, and biomass density in underwater still images. This software package is further described in a journal article by Esselman et al. (in revision; Methods in Ecology and Evolution) entitled "A transferable approach for quantifying benthic fish sizes and densities in annotated underwater images". FishScale uses binary masks obtained from...
Wood Thrush Movement and Occupancy Wood Thrush Movement and Occupancy
This code contains multiple scripts that (1) analyze Wood Thrush movement data, (2) simulate Wood Thrush movements in an individual-based model, and (3) analyze the results from these simulations.
Identifying Pareto-efficient eradication strategies for invasive populations Identifying Pareto-efficient eradication strategies for invasive populations
Invasive species are a major cause of biodiversity loss and are notoriously expensive and challenging to manage. We developed a decision-analytic framework for evaluating invasive species removal strategies, given objectives of maximizing eradication probability and minimizing costs. The framework uses an existing estimation model for spatially referenced removal data – one of the most...
multistater: A MULTI-STATistical approach to fitting MULTI-STATE models with R multistater: A MULTI-STATistical approach to fitting MULTI-STATE models with R
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...
Baydiff: Bayesian diffusion chronometry for volcanic systems Baydiff: Bayesian diffusion chronometry for volcanic systems
Diffusion chronometry is a powerful tool for estimating the time scales of magmatic processes. This MATLAB software can be used to estimate diffusion time scales using the forsterite content of olivine crystals. Estimates are obtained probabilistically, using a Bayesian framework, and account for uncertainties in data as well as any independent (prior) information.
North American Breeding Bird Survey (BBS) stop-level uncertainty code North American Breeding Bird Survey (BBS) stop-level uncertainty code
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...