Software

1: Estimating relative abundance is critical for informing conservation and management efforts and for making inferences about the effects of environmental change on populations. Freshwater fisheries span large geographic regions, occupy diverse habitats, and consist of varying species assemblages. Monitoring schemes used to sample these diverse populations often result in populations...

Software release for a topobathymetric DEM fusion approach. The operation, theory, and processes used in this software release can be used to fuse two topobathymetric digital elevation models (DEMs), creating seamless transitions around the two datasets' seamlines. This software heavily utilizes the arcpy python module, installation of ArcGIS Pro and a valid spatial analyst license is...

A Data Orchestration Manager (ADOM) is a user interface designed to enforce data management goals by entwining and extending the open-source file management tool rclone. The rclone tool provides data movement and management functionality in and between supported end-user-defined endpoints, also known as remotes. ADOM takes rclone a step further by wrapping rclone functionality into USGS...

The goal of algaeClassify is to facilitate the analysis of taxonomic and functional trait data for phytoplankton.

This product contains code to analyze a dataset that was collected to compare a LAMP assay and a qPCR assay for Grass Carp in a pond study. This repository contains the RMarkdown and R files used to analyze the data. It was created to allow for reproducible results. The code assumes the user is experience with R, especially the Tidyverse, and Stan.

Code release for a statistical framework that provides a solution to overcome institutionally siloed monitoring activities in order to inform species conservation across large landscapes. Stan code and documentation to provide access and adaptation for other wildlife disease applications.

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.

The aqtsra package in the R language provides a light-weight utility for merging U.S. Geological Survey National Water Information System (NWIS) flat-file tables of raw and approved unit-value time-series data from the AQUARIUS Time-Series software. Provision is made for parsing time stamps, insertion of the day fraction into the year, and days since last site visit among other limited...

This model combines resighting data from Whimbrels breeding at Kanuti National Wildlife Refuge with known-fate data and pseudo-resighting history from Whimbrels breeding at the Colville River Delta ('colv'). All Whimbrels in the study (n = 76) were marked with a USGS metal band and a uniquely coded engraved leg flag. In addition, 15 Whimbrels at Kanuti were equipped with surgically...

Climate data allow people to examine species distributions and possible distributions. This script takes ERA5-Land climate estimates (https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era5) for precipitation and lake temperature and processes them to create summary climate layers for use with biological organisms in lakes. This code could be modified to use a different...

Estimating High Resolution Multi-Cropped Irrigated Land Use Using a Pesticide Use Reporting Database in California Estimating the amount of water needed for agriculture is vital for food and water security. These estimates rely on maps of crop type and acreage that have limited ground-truthing or represent multiple years or regional cropping patterns. In regions where crops change...

We present two change-point models for identifying singular changes in movement behavior: a location-based change-point model (LCPM) and a movement metric-based change-point model (MMCPM). This software includes R scripts to: 1) run both the LCPM and MMCPM on telemetry data in a Bayesian hierarchical framework using NIMBLE (mmcpm.R and lcpm.R), 2) generate realistic movement behavior...