Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
Filter Total Items: 962
Code for Fomites could determine severity of SARS-CoV-2 outbreaks in low-density white-tailed deer Odocoileus virginianus populations Code for Fomites could determine severity of SARS-CoV-2 outbreaks in low-density white-tailed deer Odocoileus virginianus populations
This software release contains 1 RMarkdown file (Indirect_SARS_analysis.RMD) and necessary input data and functions that support the analysis presented in referenced manuscript (IP-166277). This RMarkdown file that steps through the estimation of parameters that allow: Compile estimated and derived parameters for both indirect and direct transmission pathways for SARS-CoV-2 in white...
Code for freshwater fish and mussel biodiversity and distribution in the Northeastern United States under climate change and management scenarios Code for freshwater fish and mussel biodiversity and distribution in the Northeastern United States under climate change and management scenarios
This software contains five R Markdown files and two R script files that comprise an analysis to 1. develop freshwater fish and mussel models using survey occurrence data, land use data, stream flow data, and stream temperature data within the Northeast United states, 2. predict the impacts of climate change on vulnerable groups of freshwater fish and mussel species, and 3. asses the...
Code for Idiosyncratic spatial scaling of biodiversity–disease relationships Code for Idiosyncratic spatial scaling of biodiversity–disease relationships
This repository contains data and code supporting the Gilbert et. al manuscript entitled, "Idiosyncratic spatial scaling of biodiversity–disease relationships". The objective of the paper is to evaluate how estimated relationships between Lyme disease risk and host biodiversity change when host biodiversity is quantified at different spatial scales. Data come from the National Ecological
Code for Missouri Stream Conservation and Connectivity Prioritization Tool: Improving and Expanding Existing Conservation Networks Code for Missouri Stream Conservation and Connectivity Prioritization Tool: Improving and Expanding Existing Conservation Networks
The Missouri Stream Conservation and Connectivity Prioritization Tool can be used to identify the number and nature of barriers to fish movement between stream reaches. This data can be used to target stream reaches for protection, conservation, and reestablishing connectivity within and between existing conservation networks. The tool allows users to select a subset of stream reaches...
Code for Population and survival models of greater sage-grouse to investigate effects of precipitation and drought in the Great Basin, USA Code for Population and survival models of greater sage-grouse to investigate effects of precipitation and drought in the Great Basin, USA
This repository includes R code to run nest, brood, and adult hierarchical logistic exposure models, used for analyzing survival responses of Greater sage-grouse (Centrocercus urophasianus) to a suite of environmental covariates, with emphasis on precipitation and/or drought effects. An example population state-space model (the top model according to WAIC; see manuscript results and...
Code for Projected Canadian Forest Fire Danger Rating System (CFFDRS) metrics within Fire Danger Rating Areas in Alaska (1980–2099) (version 1.0.0) Code for Projected Canadian Forest Fire Danger Rating System (CFFDRS) metrics within Fire Danger Rating Areas in Alaska (1980–2099) (version 1.0.0)
Effective future fire planning and decision-making in Alaska requires accessible, interpretable, and locally relevant climate data to anticipate fire danger. To meet this need, we utilized an existing dataset of projected fire danger metrics from the Canadian Forest Fire Danger Rating System (Young et al. 2025). This dataset contains daily projections from 1980 through 2099 for key...
Code for reproductive habitat mismatch influences chytrid infection dynamics in a tropical amphibian community Code for reproductive habitat mismatch influences chytrid infection dynamics in a tropical amphibian community
This repository contains data and code supporting the Gilbert et. al manuscript entitled, "Reproductive habitat mismatch influences chytrid infection dynamics in a tropical amphibian community". The objective of the paper is to identify the influence of life history, rainfall, and habitat on chytrid infection dynamics in a frog community in Brazil’s Atlantic Forest. The code (see...
Code for similar population dynamics before and after a chytridiomycosis outbreak in a tropical riparian amphibian species 2.0 Code for similar population dynamics before and after a chytridiomycosis outbreak in a tropical riparian amphibian species 2.0
This software release contains 4 files with R scripts organized according to the objective (e.g., format the data, model fitting, etc.). The overall objective of the project was to: analyzed ten years of capture-mark-recapture data spanning 2000 − 2014 for a population of Espadarana prosoblepon in El Copé, Panama, encompassing a period before and after a Batrachochytrium dendrobatidis...
Code for similar population dynamics before and after a chytridiomycosis outbreak in a tropical riparian amphibian species. Code for similar population dynamics before and after a chytridiomycosis outbreak in a tropical riparian amphibian species.
This software release contains 4 files with R scripts organized according to the objective (e.g., format the data, model fitting, etc.). The overall objective of the project was to: analyzed ten years of capture-mark-recapture data spanning 2000−2014 for a population of Espadarana prosoblepon in El Copé, Panama, encompassing a period before and after a Batrachochytrium dendrobatidis (Bd)...
Code for the analysis of fish deformity, erosion, lesion, tumor, and parasite anomalies (DELT) in the Chesapeake Bay Watershed, USA Code for the analysis of fish deformity, erosion, lesion, tumor, and parasite anomalies (DELT) in the Chesapeake Bay Watershed, USA
This repository provides the R scripts and stan files to fit hierarchical logistic regression models, using a regularized horseshoe prior on regression coefficients, to examine spatial drivers of DELT occurrence in fishes in the Chesapeake Bay Watershed, USA.
Code for Two-stage approach to automatic detection with machine learning for improved surveillance of the invasive Cuban treefrog Code for Two-stage approach to automatic detection with machine learning for improved surveillance of the invasive Cuban treefrog
This R code release is associated with the paper, Huber, K., H. Waddle, B. Glorioso, and T. Donovan. Two-stage approach to automatic detection with machine learning for improved surveillance of the invasive Cuban treefrog. Ecological Infomatics. In revision. The code begins by downloading the database released on ScienceBase, and accompanying scripts included in this repository to...
Code to create periodic matrix models and simulate population reintroductions for four lizards on Guam Code to create periodic matrix models and simulate population reintroductions for four lizards on Guam
This repository contains code to construct periodic matrix models representing the demography of four lizard species native to or extant on Guam.