Software

These data were collected to test whether presence-absence surveys can aid in the identification of nesting sites for the Marbled Murrelet (Brachyramphus marmoratus), a threatened seabird that nests in older-aged forests along the Pacific Coast. The code presented here utilizes four data tables (csv documents) which are formatted according to tidy data principles. Those files are also available at

This code contains the data processing for research described in xxxx by Wood et al., 2024. U.S. Department of Transportation (USDOT) highway traffic data for each state and month is processed into a single CSV file containing the monthly total of vehicles passing each traffic station camera, the maximum hourly rate for each station and month, and the timestamp when the maximum occurred. A yearly

This software release contains six R scripts that comprise a population viability analysis for the alligator snapping turtle (Macrochelys temminckii). To predict numbers of M. temminckii in the future, we constructed a female-only, stage-structured matrix projection model. We incorporated multiple types of uncertainty into the simulation model, including parametric uncertainty and temporal variati

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. All Lands

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, with the goa

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 semantic s

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 accessible

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 package. Our s