Software

Matching climate envelopes allows people to examine how potential invasive species may match habitats. This repository contains code for using the climatchR package for high-throughput calculations of climatch scores for species using GBIF data. Climatch is based upon the climatch algorithm as implemented through the climatchR package.

This repository contains code for the analysis of Wamboldt JJ, Nelson JE, Thomas LM, Steiner JN, Hebert JL, Erickson RA, Putnam JG. Quantitative method development to determine feed consumption using a dye. North American Journal of Aquaculture The purpose of the repository is to document what analysis was run for publication and is intended for an archive rather than a production or development

Hyperparameter optimization approaches were applied to improve performance and accuracy of groundwater flow models. Freely available new software, NWTOPT, is described that uses Tree of Parzen Estimators (TPE) and Random Search optimization algorithms to optimize MODFLOW-NWT’s solver settings. We ran 3500 trials on a steady-state and transient model. To quantify the performance of candidate solver

This is an R-package designed to create water-quality reports for either U.S. Fish and Wildlife Service (FWS) wildlife refuge boundaries, or user-specified Hydrologic Unit Code (HUC) boundaries (8 or 10 digit HUC services are available). Functions are included to take the user's geographical request, and find the sites that measure water-quality parameters, and retrieve that data. A workflow walks

The ToxMixtures R-package includes a set of functions to analyze, visualize, and organize measured chemical concentration data as it relates to chemical mixtures. ToxMixtures combines outputs from the R-package toxEval with open access sources on molecular biology to provide information on potential biological effects of chemicals detected in environmental matrices. To use ToxMixtures, the user wi

The repository contains code to analyze the differences in model results when nested design structures differ. The code for this project assumes the reader is familiar with R, nested designs, and mixed effects linear modeling.

occStan is an R package (R Core Team 2021) providing a collection of occpuancy Bayesian models written in the Stan language as called through RStan (Stan Development Team 2021). The package is a USGS software software release. The purpose of the package is to document these models for use in USGS projects and allow easy discrimination. The package assumes the user is familiar with R and occupancy

Matching climate envelopes of allows people to examine how potential invasive species may match habitats. The Australian government created Climatch to do allow for these comparisons. However, this webpage does not allow for readily scripting climate matching. Hence, the authors created climatchR, an R package (R Core Team 2020) implementing the climatch method in R. This was created to allow auto

The National Streamflow Statistics (NSS) Application is an online computer application that provides a simple method for applying regional flood-peak streamflow estimates and low flow frequency/duration streamflow estimates.

MetaIPM is a Python package (Python Software Foundation 2020) that models meta-population dynamics and continuous growth rates via an integral projection model (IPM) for species living in distinct habitat patches. The package stems from a model that compares invasive carp population control strategies. The package supports differing sex and any organisms living in distinct habitat patches.

fishstan is an R package for fitting common fisheries models using RStan

This code supports the manuscript "Refinement of eDNA as an early monitoring tool at the landscape-level: Study design considerations". The code fit a three-level occupancy model with two detection assays in the program Stan through R. We programmed this code for a specific project with the USFWS and it will likely not generalize to other situations. The primary purpose of releasing this code is t