Software

Oxygen depletion events (hypoxia) in coastal aquatic ecosystems occur more frequently, yet their causes and consequences remain poorly understood. We identified key drivers of hypoxia in Southeast Alaska watersheds for long-term hypoxia monitoring. This software release contains one R script that can be used to calculate hypoxia risk from environmental variables. This R code will re...

This software compares statistical methods to model habitat risk of CWD in white-tailed deer in Pennsylvania using Bayesian hierarchical models in R-INLA and compares these results with model output from WinBugs. The software also uses R-INLA with the Stochastic Partial Differential Approach (SPDE) to compare different surveillance methods to model CWD in relation to habitat features and...

The Bi-State conservation planning tool provides a science-based approach for prioritizing pinyon (Pinus spp.) and juniper (Juniperus osteosperma, J. occidentalis), hereafter, 'conifer', removal to improve habitat for greater sage-grouse (Centrocercus urophasianus) in the Bi-State Distinct Population Segment (DPS, U.S. Fish and Wildlife Service 2010). Conifer negatively affects sage...

This repository contains code for the analysis from a study that examined mortality and qPCR detection in 4 groups of fish: an uninfected control group, an infected control group, and two treatment groups. The main goals were to determine if their were differences in mortality and qPCR detection of the parasite among the differing groups. Mortality was addressed using a Generalized...

A software release of CoSMoS-COAST: The Coastal, One-line, Assimilated, Simulation Tool of the Coastal Storm Modeling System. The software (coded in Matlab) encapsulates a long-term shoreline change model that combines longshore and cross-shore transport and assimilates historical shoreline observations.

DataRetrieval.jl is a Julia alternative to the R dataRetrieval package for obtaining USGS water data directly from web services.

DGMETA (Dissolved Gas Modeling and Environmental Tracer Analysis) is a Microsoft Excel-based computer program that is used for modeling air-water equilibrium conditions from measurements of dissolved gases and for computing concentrations of environmental tracers that rely on air-water equilibrium model results. DGMETA can solve for the temperature, salinity, excess air, fractionation of...

Digger is a python package that provides a number of pre- and post-processing tools for working with the D-Claw model.

Code for implementation of the Dynamic Surface Water Extent algorithm in Google Earth Engine. Multiple scripts allow the creation of single-scene or composited Dynamic Surface Water Extent (DSWE) images from Landsat and MODIS data. All code is written for use in the JavaScript API.

An R-package for the analysis of long-term changes in water quality and streamflow, including the water-quality method Weighted Regressions on Time, Discharge, and Season (WRTDS).

R code to test for differences in DNA yield from of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed SNP panels. We calculated mean, median and standard deviation with package psych using the describe() function. Additionally, we generated boxplots using package ggplot2 where the quantity for each tissue sample is...

This repository contains an example application of the `Meta-IPM` Python package (https://doi.org/10.5066/P9PW673G). The specific application focuses on the Illinois River using existing public data.