Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
Filter Total Items: 921
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...
Reservoir Mixed Outflow Temperature Estimator (ReMOTE): Select U.S. Army Corps of Engineers Reservoirs in the Willamette Valley Project, OR Reservoir Mixed Outflow Temperature Estimator (ReMOTE): Select U.S. Army Corps of Engineers Reservoirs in the Willamette Valley Project, OR
This application was developed to estimate the vertical withdrawal zone and overall mixed release water temperature using a user-provided vertical temperature profile and flow rates of selective withdrawal features at eight dams within the Willamette Valley Project that are operated by the U.S. Army Corps of Engineers - Portland District. The application was developed using a macro...
KWICer: Producing an annotated bibliography from a set of PDFs by quantifying keywords KWICer: Producing an annotated bibliography from a set of PDFs by quantifying keywords
This code can be used to rapidly create an annotated bibliography that will help users navigate and synthesize a large body of literature. Users can input a set of PDF or DOCX files that they have identified as relevant to their question as well as lists of relevant search terms. This code will convert the input documents into TXT files, trim the files to exclude extraneous text such as...
SpFut-covariates SpFut-covariates
The purpose of this R software package is to easily download and process climate, anthropological, and environmental covariate data for specified areal units to use primarily in an integrated species distribution model. The package contains wrapper functions for the `geodata` R package and externally downloaded datasets.
SpFut-processGBIF SpFut-processGBIF
The purpose of this R software package is to easily download and clean species data from the Global Biodiversity Information Facility (GBIF). This package relies on functions in the `rgif` package and contains wrappers to download and format data for the purposes of building an integrated species distribution model.