Data

This is the data archive for the publication Ungulate Migrations of the Western United States, Volume 3 (Kauffman et al. 2022) and includes the collection of GIS map files that are mapped and described in the report. These map files are meant to provide a common spatial representation of the mapped migrations. This data release provides the means for ungulate migrations to be mapped and...

This software release contains one R script file that allows the user to download data and reproduce all of the figures and analyses associated with DiRenzo et al. In the R script, we provide a guide to understanding and validating complex models using data simulations. In an effort to facilitate the implementation of these methods, we provide a running example throughout DiRenzo et al...

Daily ages of young-of-year Silver Chub were estimated from counts of rings in lapilli otoliths. Lapilli were mounted to glass slides with thermoplastic cement and sanded to the core with 2000 grit sandpaper to expose daily rings. To improve clarity, sanded otoliths were polished with 0.3 μm alumina powder and a polishing cloth prior to viewing. To estimate daily age, counts of rings in...

The U.S. Geological Survey, in cooperation with the Tennessee Department of Transportation, conducted an investigation of acid-rock drainage from road cuts in Tennessee during 2014-2015. The Devonian Chattanooga Shale contains disseminated pyrite and is a primary producer of acid-rock drainage (ARD) in Tennessee. One objective of the overall investigation was to attenuate ARD by...

The software consists of three scripts to be run in the R statistical program: 1) Alligator growth simulation; 2) alligator integrated population model file; and 3) data visualization script. Script #1 produces growth transition probabilities that are used in script #2. The second script uses the outputs from #1 as well as other data files to run an integrated population model. The last...

This is code for an integrated population model developed to understand the effect of horseshoe crab abundance on population demographics of red knot, an Arctic-breeding shorebird. This model was developed as part of the revision to the Atlantic States Marine Fisheries Commission Adaptive Resource Management Plan for horseshoe crabs.

Approximate Dynamic Programming relies on forward simulation of the system, so two population projection models are used, one for crabs and one for red knots. The two models are linked: HSC abundance is a predictor variable in the REKN model. Other useful outputs are produced as well, such as predictions of future harvest.

This software involves R script to fit models of abundance of mosquito vectors (' Script_for_ECS22-0193_9_13_2215.R') to landscape and environmental covariates using INLA and SPDE. The dataset used for this analysis were originally provided by the Pennsylvania Department of Environmental Protection (DEP) with a confidentiality agreement. The majority of the data used in this study...

This software involves files to fit the physiologically-guided abundance (PGA) model ('fish_predictions_pga.R'), a naive model ('fish_predictions_naive.R'), and a PGA model using simulated data ('PGA_sim.R'). Each R file calls as associated .stan file that contains the model code that is executed by stan when running the R code ('fish_prediction.stan', 'fish_prediction_naive.stan', and...

AMMonitor is an open source R package dedicated to collecting, storing, and analyzing AMU information in a way that 1) is cost-effective, 2) can efficiently process and store information, and 3) can take advantage of the vast and growing community of R analytics.

Small, surface-release dams are ubiquitous across the U.S. and have the potential to alter stream flow, impede sediment and nutrient transport, and fragment biotic assemblages. To mitigate these and other ecological impacts and reduce public safety hazards, dam removal has become an increasingly prevalent method of stream restoration. However, few streams have been consistently monitored...

This dataset contains locations acquired from GPS-tagged Brown Pelicans in the South Atlantic Bight. Locations correspond to the movements of pelicans tracked during the autumn migratory period (post-breed to the following spring, with length of deployment varying individually) from 2017-2020. Additional metrics include intrinsic and extrinsic variables both measured and acquired which...