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...

AMMonitor is an open source R package dedicated to collecting, storing, and analyzing AMU information in a way that 1) is cost-effective, 2) can efficiently process and store information, and 3) can take advantage of the vast and growing community of R analytics.

Matlab m-files that were used to generate performance tests and hindcasts for geomorphologic characteristics and piping plover habitat probabilities for Fire Island New York

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...

-R code to create and fit dynamic occupancy models to Dixie Valley Toad survey data in JAGS and produce useful summaries of model results. This script will perform the Gibbs Variable Selection (GVS) using the initial set of environmental covariates, and then fit the "final" model using only important environmental covariates. The dynamic occupancy model is adapted from the model...

This repository contains the source code for the oaftools package. The package creates visual tools to study aftershock behavior and the performance of the Operational Aftershock Forecasting system. The visual tools are: A global map, rendered by Leaflet to show the distribution of earthquakes with forecasts A local map, rendered by Leaflet to show the aftershock sequence and the...

Shinymgr is an R package that provides a unifying framework for managing and deploying Shiny applications that consist of modules. Developers use the shinymgr framework to write modules and seamlessly combine them into Shiny apps, and users of these apps can execute reproducible analyses that can be incorporated into reports for rapid dissemination. The package includes 11 instructional...

Scoops3D is software to analyze three-dimensional slope stability throughout a digital landscape.

Line-transect distance sampling (LTDS) surveys are commonly used to estimate abundance of animals or objects. In terrestrial LTDS surveys of gopher tortoise (Gopherus polyphemus) burrows, the presence of ground-level vegetation significantly decreases detection of burrows of all sizes, but no field or analytical methods exist to control for spatially heterogeneous vegetation obstruction...

The Hydrologic Analysis Package (HASP) can retrieve groundwater level and groundwater quality data, aggregate these data, plot them, and generate basic statistics. One of the benefits of HASP is its ability to aggregate two time-series of data into one record and generate statistics and graphics on hat record. By merging two data sets together, users can view and manipulate a much longer...

The code 'Keys Carbonate Budget Calculations', written in R (v.4.0.4; https://www.R-project.org/), uses benthic coral-reef survey data and fish survey data to calculate coral-reef carbonate budgets following the ReefBudget v2 methodology (http://geography.exeter.ac.uk/reefbudget/; Perry and Lange, 2019). The carbonate budgets include estimates (means +/- standard errors) of gross...