Software

Amid climate change and rapidly shifting land uses, effective methods for monitoring wildlife are critical to support scientifically-informed resource management decisions. As such, monitoring is motivated by ecological hypotheses or natural resource management objectives. The practice of using Autonomous Monitoring Units (AMUs) such as trail cameras or audio recorders to monitor...

Hyperpigmented melanistic lesions (HPMLs) are a visual anomaly documented on the skin of smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania and in numerous other geographical locations. Currently, there is a lack of information on environmental and fish characteristics that may influence the prevalence of HPMLs associated with a recently described...

This repository contains all of the scripts to reproduce the analyses, figures, and tables associated with the manuscript Gordon et al. in prep. There is 1 R script that does the following: (1) format the data, (2) explores the data, and (3) goes through the analyses for each objective.

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...

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...

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...

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...