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Stream hydrology and a pulse subsidy shape patterns of fish foraging Stream hydrology and a pulse subsidy shape patterns of fish foraging
Pulsed subsidy events create ephemeral fluxes of hyper-abundant resources that can shape annual patterns of consumption and growth for recipient consumers. However, environmental conditions strongly affect local resource availability for much of the year, and can heavily impact consumer foraging and growth patterns prior to pulsed subsidy events. Thus, a consumer’s capacity to exploit...
Comparing datasets by surveillance method using spatial models Comparing datasets by surveillance method using spatial models
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...
Code to Support Hypoxia vulnerability in the salmon watersheds of Southeast Alaska Code to Support Hypoxia vulnerability in the salmon watersheds of Southeast Alaska
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...
Population Viability Model for Western Pond Turtle Population Viability Model for Western Pond Turtle
The code herein uses a triple loop structure to simulate a spatially implicit stage structured matrix model for two species of western pond turtle with parametric uncertainty and temporal stochasticity.
R code for calculating imperilment of freshwater fish with a Bayesian belief network R code for calculating imperilment of freshwater fish with a Bayesian belief network
This R script is reproduces a Bayesian belief network built within the propriety software program, Netica. The R- and Netica-based belief networks were used in Dunn and Schumann et al. (in press), which presents an approach for calculating imperilment of freshwater fishes.
Microsatellite genotypes and metadata for white-tailed deer samples from the Mid-Atlantic region of USA Microsatellite genotypes and metadata for white-tailed deer samples from the Mid-Atlantic region of USA
Dataset containing information for white-tailed deer samples from Ohio, Pennsylvania, Maryland, Virginia and New York, genotyped for 11 microsatellites markers. Marker OvirQ should not be used as it presents alleles inconsistent with reported pattern, with some alleles separated by only 1 base pair and inconsistent between runs. Projected coordinates representing sampling location are in...
Population Viability Model for Spot-tailed earless lizard Population Viability Model for Spot-tailed earless lizard
Code for simulating Spot-tailed earless lizard populations under habitat loss and road mortality threats in central Texas
Predicting fish responses to climate change using a joint species, spatially dependent physiologically guided abundance model Predicting fish responses to climate change using a joint species, spatially dependent physiologically guided abundance model
Predicting the effects of warming temperatures on the abundance and distribution of organisms under future climate scenarios often requires extrapolating species-environment correlations to thermal conditions not currently experienced by a species or to temperatures that exceed the range of observed data. For poikilotherms, incorporating species’ thermal physiology to inform...
Population genetic structure of white-tailed deer using microsatellites i the Mid-Atalntic region Population genetic structure of white-tailed deer using microsatellites i the Mid-Atalntic region
Results of 11 microsatellites for white-tailed deer collected in Maryland, New York, Ohio, Pennsylvania, and Virginia from 2014 to 2022 for genetic analysis. In this project we assessed genetic structure using different analyses, and evaluated the performance of assignment tests to correctly match deer to origin (defined as genetic cluster, state or physiographic province). This...
Chronic Wasting Disease Surveillance Optimization Software Version 2 Chronic Wasting Disease Surveillance Optimization Software Version 2
The Chronic Wasting Disease Surveillance Optimization Software Version 2 computes sampling recommendations to detect chronic wasting disease (CWD) in white-tailed deer (Odocoileus virginianus). Driven by a combinatorial optimization algorithm, the software maximizes the return-on-investment to the wildlife agency while keeping the overall surveillance program within budget. The software...
Optimal harvest of a theoretical population under system change Optimal harvest of a theoretical population under system change
This code solves optimal harvest policies under different scenarios of system change, represented as changes in demographic parameters over time. This document contains code to solve policies using backwards iteration stochastic dynamic programming, project populations forward to simulate the policies, and generate figures.
Code for: Small enzootic survival costs mask the potential for long-term population size suppression Code for: Small enzootic survival costs mask the potential for long-term population size suppression
This repository contains all of the scripts to reproduce the analyses, figures, and tables associated with the manuscript Glorioso et al. in review. The scripts are organized into folders, and the folders are numbered in the order in which they should be executed. Briefly, there are six folders that do the following: (1) format the data, (2) fit the model, (3) run the population...