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Software

An official USGS software project is code reviewed and approved at the bureau-level for distribution.

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MODFLOW 6: USGS Modular Hydrologic Model

MODFLOW is a popular open-source groundwater flow model distributed by the U.S. Geological Survey. 

ModelMuse Version 5.1.1

This version of ModelMuse fixes a serious bug in ModelMuse version 5.1.

ModelMuse: A Graphical User Interface for Groundwater Models

ModelMuse is a graphical user interface (GUI) for the U.S. Geological Survey (USGS) models MODFLOW 6, MODFLOW–2005, MODFLOW-LGR, MODFLOW-LGR2, MODFLOW-NWT, MODFLOW-CFP, MODFLOW-OWHM, MODPATH, ZONEBUDGET, PHAST, SUTRA 2.2, SUTRA 3.0,  MT3D-USGS, and WellFootprint and the non-USGS programs MT3DMS and PEST.

ReplicateChar package

The ReplicateChar package in R language provides functions for visualization and analysis of replicated charcoal counts within a discreet sedimentary horizon. The package consists of 1000+ lines of code and requires Windows OS for full functionality. It also integrates and automates the CharAnalysis.exe software (Higuera et.al) and allows for more efficient run times of high volumes of original an

ModelMuse Version 5.1: Software Release

ModelMuse version 5.1 updates version 5.0 by adding support for the groundwater transport process and time series files in MODFLOW 6.

American alligator growth simulation and integrated population model

The software consists of three scripts to be run in the R statistical program: 1) Alligator growth simulation; 2) alligator integrated population model file; and 3) data visualization script. Script #1 produces growth transition probabilities that are used in script #2. The second script uses the outputs from #1 as well as other data files to run an integrated population model. The last script (#

Integrated population model for red knot in Delaware Bay

This is code for an integrated population model developed to understand the effect of horseshoe crab abundance on population demographics of red knot, an Arctic-breeding shorebird. This model was developed as part of the revision to the Atlantic States Marine Fisheries Commission Adaptive Resource Management Plan for horseshoe crabs.

Optimal horseshoe crab harvest policies via approximate dynamic programming

Approximate Dynamic Programming relies on forward simulation of the system, so two population projection models are used, one for crabs and one for red knots. The two models are linked: HSC abundance is a predictor variable in the REKN model. Other useful outputs are produced as well, such as predictions of future harvest.

R scripts for analysis of fall photographic waterfowl surveys, Izembek NWR, Alaska, 2017-2019

This code repo contains three novel scripts used in Weiser et al. (2022): one to calculate the footprint of an aerial photo (01_function_photo_footprint.r), one to run a simulation to evaluate sample sizes for the photographic survey (02_photo_sample_size_sim.r), and one to run a simulation to evaluate sample sizes for the ocular survey (03_ocular_sample_size_sim.r). For more information on the ba

Behavioral and Reproductive Effects of the Lampricides TFM and TFM:1% Niclosamide on Native Freshwater Mussels - SPSS Code Release

This study continues our investigations into the effects of lampricides on mussels by extending research into potential effects on behavioral and reproductive endpoints on the mussel plain pocketbook (Lampsilis cardium). We hypothesized that TFM and TFM:NIC would reduce the viability of free glochidia in a dose-dependent manner, that older glochidia would be more sensitive than younger glochidia,

spatial_nsm: Spatial estimates of soil-climate properties using a modified Newhall simulation model

We developed a software framework to estimate high-resolution spatiotemporal soil moisture (monthly, annual, and seasonal) and temperature-moisture regimes. Our approach builds on the Newhall simulation model, allowing for the substitution of data and parameters, such as climate, snowmelt, soil properties, alternative potential evapotranspiration equations, and air-soil temperature offsets. The Ne

Spatial modeling of two mosquito vectors of West Nile virus using integrated nested Laplace approximation

This software involves R script to fit models of abundance of mosquito vectors (' Script_for_ECS22-0193_9_13_2215.R') to landscape and environmental covariates using INLA and SPDE. The dataset used for this analysis were originally provided by the Pennsylvania Department of Environmental Protection (DEP) with a confidentiality agreement. The majority of the data used in this study, however, have s