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

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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

StreamStats Channel Width Weighting Services

This software release contains Python functions for weighting multiple non-independent estimates of a variable. Weighting is determined by the standard error of prediction of each estimate and the correlation between the estimation methods. The methodology for weighting estimates from either two or three different methods is described in Chase and others (2020). A function is also included to han

Predicting climate change impacts on poikilotherms

This software involves files to fit the physiologically-guided abundance (PGA) model ('fish_predictions_pga.R'), a naive model ('fish_predictions_naive.R'), and a PGA model using simulated data ('PGA_sim.R'). Each R file calls as associated .stan file that contains the model code that is executed by stan when running the R code ('fish_prediction.stan', 'fish_prediction_naive.stan', and 'fish_predi

High-throughput calculations of climatch scores

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.

Analysis code for Quantitative method development to determine feed consumption using a dye

This repository contains code for the analysis of a 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 type repository.

AMMonitor

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.

LinkedBNs_4Habitat - Matlab files to link Bayesian networks to generate habitat predictions

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

NWTOPT

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 p

Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021

-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 publishe