Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
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sciencebasepy: A Python library for programmatic interaction with the USGS ScienceBase platform sciencebasepy: A Python library for programmatic interaction with the USGS ScienceBase platform
This Python module provides functionality for interacting with the USGS ScienceBase platform: https://www.sciencebase.gov/catalog/ ScienceBase is a Trusted Digital Repository (TDR) in the U.S. Geological Survey (USGS). The platform is developed and maintained by the USGS to provide shared, permission-controlled access to scientific data products and bureau resources. Rather than serving...
Special Contributing Area Loading Program Special Contributing Area Loading Program
Special Contributing Area Loading Program (SCALP) is a hydrologic routing program that uses a linear-reservoir-in-series routing method. Inputs to SCALP include a user input file and runoff depth time series. The outputs of SCALP are outflow time series and a user log file. The user input file is a text file, and the runoff depth time series are contained in a Hydrologic Engineering...
Joint Ecosystem Modeling (JEM) NetCDF R Package Joint Ecosystem Modeling (JEM) NetCDF R Package
R-language code library to support netCDF I/O. This package was written to ease the process of reading and writing netcdfs in R for the Joint Ecosystem Modeling (JEM; https://jem.gov/) community. NetCDF files created using this package follow the Comprehensive Everglades Restoration Plan (CERP) data standards to facilitate data sharing among scientists in the Everglades area.
Inferring pathogen presence when sample misclassification and partial observation occur Inferring pathogen presence when sample misclassification and partial observation occur
This software contains four separate R scripts and one Matlab script that comprise an analysis to estimate the posterior probability of pathogen presence when sample misclassification and partial observations occur. We develop a Bayesian hierarchal framework that accommodates false negative, false positive, and uncertain detections and apply this framework to a case study of the fungal...
Code for Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses Code for Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses
Code will be submitted to the Dryad repository upon acceptance of the manuscript. These R code are used for simulations and case studies. Simulations include data for generating age-period survival data. We have provided code for each of the 10 models that were fit using NIMBLE, where each model has four R scripts including: 1) A script to execute and run all the additional R scripts for...
Code for Rapid prototyping for quantifying belief weights of competing hypotheses about emergent diseases Code for Rapid prototyping for quantifying belief weights of competing hypotheses about emergent diseases
Code submitted to Journal of Environmental Management and ScienceBase for running Bayesian hierarchical models on a dataset that was collected using expert elicitation of a panel of 15 experts on the etiology of stony coral tissue loss disease and its impacts on coral reefs. The code is for a rapid prototyping method for quantifying belief weights for competing hypotheses about the...