Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
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occupancyTuts: A package for learning occupancy modeling with RPresence occupancyTuts: A package for learning occupancy modeling with RPresence
Understanding how species are distributed in both space and time is a central question in ecology. Seemingly simple questions such as “How many individuals live in a particular patch?”, “Is a patch occupied by a target species?”, “How many species are there?”, and “what factors shape these pattern?” are questions routinely asked by ecologists. The tutorials in occupancyTuts will...
grsg_lekdb: Compiling and standardizing greater sage-grouse lek databases, version 1.2.0 grsg_lekdb: Compiling and standardizing greater sage-grouse lek databases, version 1.2.0
Greater sage-grouse (Centrocercus urophasianus; hereafter referred to as sage-grouse) are landscape-scale sagebrush obligate species and an important gamebird and iconic species of the West (Hanser & Knick, 2011; Rowland et al., 2006). They occupy the sagebrush biome in western North America, extending east of the Sierra Nevada/Cascade Mountain ranges to the western regions of the Great...
Surface Velocity Tools (SurfVelTools) Surface Velocity Tools (SurfVelTools)
SurfVelTools is a Python application and user interface for computing parameters associated with the Probability Concept method (Fulton and others, in review) parameters using velocity profile data collected in the stationing where the maximum in-channel velocity occurs. SurfVelTools will also compute streamflow (discharge) for a given Probability Concept result given a known cross...
Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels
R code to test for differences in DNA yield from of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed SNP panels. We calculated mean, median and standard deviation with package psych using the describe() function. Additionally, we generated boxplots using package ggplot2 where the quantity for each tissue sample is...
Application of the SEICarP Model to the Illinois River Application of the SEICarP Model to the Illinois River
This repository contains code to run the Spatially Explicit Invasive Carp Population (SEICarP) model in the Illinois Rive. The code uses the `SEICarP` R package. The code for this project assumes the reader is familiar with R, population modeling, and quantitative fisheries methods.
SEIcarP SEIcarP
SEIcarP is an R package (R Core Team 2021) implementing the Spatially Explicit Invasive Carp (SEICarP; sometimes stylize as SEIcarP) population model for the Illinois River. This repository contains the SEIcarP model plus two additional packages required for the main model package to run. These are the SEIcarP Bighead Carp (BH) data (SEIcarPdataBHCP) and the SEIcarP Silver Carp (SV) data...