Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
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Example application of MetaIPM to the upper Mississippi River Example application of MetaIPM to the upper Mississippi River
This repository contains an example application of the `Meta-IPM` Python package (https://doi.org/10.5066/P9PW673G). The specific application focuses on the upper Mississippi River using existing public data. The code for this project assumes the reader is familiar with Jupyter Notebooks, enough Conda and Python to install the `Meta-IPM` package, and population ecology. The example also...
Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park
This repository contains code to fit open population models to capture-mark-recapture data for Sierra Nevada yellow-legged frogs (Rana sierrae). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., Rose, J.P., and Fellers, G.M. 2025. Climate-induced extirpation of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite...
ModelMuse: A Graphical User Interface for Groundwater Models ModelMuse: A Graphical User Interface for Groundwater Models
ModelMuse is a graphical user interface (GUI) for the U.S. Geological Survey (USGS) models MODFLOW 6, MODFLOW–2005, MODFLOW-LGR, MODFLOW-LGR2, MODFLOW-NWT, MODFLOW-CFP, MODFLOW-OWHM versions 1 and 2, MODPATH, ZONEBUDGET, PHAST, SUTRA 2.2, SUTRA 3.0, SUTRA 4.0, MT3D-USGS, and WellFootprint and the non-USGS programs MT3DMS and PEST.
R scripts to run model of bird density and habitat associations R scripts to run model of bird density and habitat associations
The script (habitat_density_model.r) in this code repository filters data, sets up model input, and runs an N-mixture model with two components of detection (availability and perceptibility) to estimate bird density from point-count data. This analysis was developed to evaluate covariates of population density for three species of boreal birds: Lesser Yellowlegs, Olive-sided Flycatcher...
Prioritizing catchments for native freshwater mussel conservation in the Northeastern United States Prioritizing catchments for native freshwater mussel conservation in the Northeastern United States
This software contains two separate R Markdown files that comprise an analysis to: 1.) Build and test MaxEnt models predicting the distribution of twelve species of native freshwater mussels in the Six North-Eastern most U.S. states. We generate models with beta multipliers 1-15 and identify optimal models using the dismo package, maxent.jar, and ENMeval. 2.) Using the species...
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...