Software

The Spatio Temporal Asset Catalog (STAC) family of specifications standardizes the way geospatial metadata is structured to better enable data querying. The United States Geological Survey (USGS) utilizes STAC to better enable the search and discovery of Landsat data by providing STAC metadata for every Landsat data product accessible through the Amazon Web Services (AWS) cloud platform...

geofetch is an R package that provides an interface for interacting with online rasters. By making use of drivers from the Geospatial Data Abstraction Library (GDAL) for accessing online rasters, it facilitates efficient raster operations by only retrieving data that falls in the user-specified area of interest. The package is built so that adding interfaces to new datasets is simple...

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

We provide R Markdown files that are built by Bookdown to create a tutorial (HTML) that contains step-by-step examples on how to use trigonometric and cyclic cubic spline hierarchical models to analyze animal diel activity patterns from time-stamped data.

Separates a subduction zone earthquake catalog into three tectonic regions: upper plate, interface, and lower plate

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...

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.

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...

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...

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.

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...

In this tutorial, we will use London, England, one of the brightest cities on Earth, to show users how to convert provided Level-1 Radiance products to TOA Radiance, Reflectance, and Brightness for the area. The tutorial will also show how to pull and parse the metadata file (MTL file) for a Landsat scene; the MTL file is used to obtain the necessary parameters for calculating Radiance...