Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
Filter Total Items: 931
Code for manuscript: Post hoc statistical analyses cannot standardize occupancy estimates across variable survey protocols Code for manuscript: Post hoc statistical analyses cannot standardize occupancy estimates across variable survey protocols
The purpose of this code is to replicate the analyses associated with the manuscript: Parvin, L.K., V. Jirinec, M. Leu, and J.J. Valente. (in review). Survey protocols drive heterogeneity in occupancy estimates that cannot be standardized using post-hoc analyses. Ecological Solutions and Evidence.__ This manuscript simulates point count sampling of a simulated Wood Thrush (Hylocichla...
Phenological date matching for invasive species mapping: code for an R workflow (version 1.0.0) Phenological date matching for invasive species mapping: code for an R workflow (version 1.0.0)
This code set is an R workflow for phenological date matching to provide an open-source solution for projects with limited funding to allow users to calculate Normalized Difference Vegetation Index (NDVI) from sentinel-2 imagery dates specified by a user supplied date raster (phenology raster) for mapping and forecasting geographic distributions of invasive plant species at large spatial...
Grizzly Bear Simulation Code Examples Grizzly Bear Simulation Code Examples
This software release contains the core code and example data for generating animal movement simulations using step selection functions (SSFs). The approach is based on simulation methods used in a series of grizzly bear studies by Sells et al. (2022–2024). In general, an SSF is fit to animal movement data and associated environmental covariates, and the fitted model is used to simulate...
Phragmites Adaptive Management Framework Model Phragmites Adaptive Management Framework Model
The PAMF Model is the foundation of the Phragmites Adaptive Management Framework. PAMF is an adaptive management and collective learning program that anyone managing Phragmites can join. Participants from around the Great Lakes basin submit Phragmites monitoring and management data to bolster the PAMF predictive model, which uses participant data to continually 'learn' more about which...
SpFut-flexiSDM SpFut-flexiSDM
The purpose of this R software package is to build and fit an integrated species distribution model. Specifically, this package loads species and covariate data, builds a species region, sets up code, parameters, and specification for a NIMBLE model, and processes and plots NIMBLE output. This framework allows the inclusion of any number of count, detection/non-detection, and presence...
Code to analyze data from the Development and validation of an eDNA assay for detection of the endangered Franklin's bumble bee (Bombus franklini) paper Code to analyze data from the Development and validation of an eDNA assay for detection of the endangered Franklin's bumble bee (Bombus franklini) paper
The code was used to analyze pollinator COI amplicon FASTQ sequence data in the paper titled "Development and validation of an eDNA assay for detection of the endangered Franklin’s bumble bee (Bombus franklini)" (IPDS number IP-175306, [DOI link]). The corresponding data release can be found here (IPDS number, [DOI link]). Although we use this code to analyze a pollinator COI dataset, it...