Software

"Max spots" or "maxspots" refers to the locations of the local maxima of the horizontal gradient of potential fields such as gravity or magnetic anomalies. Because maxspots mark locations of abrupt change in the anomalies, they can be used to identify the edges of subsurface features with significant contrasts in density and/or magnetization, such as faults, intrusions, or lithologic...

Pysochron is a Python-based tool designed to calculate isochron burial ages from in-situ cosmogenic 26Al and 10Be data. It uses orthogonal distance regressions to fit isochron lines to 1000 Monte Carlo simulations of nuclide concentration measurements to account for uncertainty, and allows the user to modify various aspects of the fitting process, including constants relating to the...

This software release consists of two tools for filtering and reformatting geochemical data from the associated data release of Granitto and others, 2025. They are provided as a Python toolbox for use in ArcGIS Pro, and scripts that can be used in the open-source software QGIS. Inputs to the ArcGIS tools should be stored in the file geodatabase or GeoPackage formats. The QGIS tools can...

Using a 36-year dataset of smallmouth bass length-at-age, we assess the effect of population density, average critical period temperature, and average spring flow rate on early life growth rate. We also looked at how a disease outbreak in 2004 impacted early life growth rates in reaches with and without the disease. The code in this release provides the R scripts to perform this analysis...

This script simulates data under an example scenario and applies a model to the simulated dataset to estimate trend, thus evaluating the power to detect the trend. The study was designed to evaluate various scenarios (sampling designs, as well as biological parameters that differ between the two study lagoons).

The script in this code repository simulates point-count data under an example scenario, sets up model input, and runs an N-mixture model with two components of detection (availability and perceptibility) to estimate the population trend. This simulation and analysis were developed to evaluate the consequences of changing spring phenology for estimating population trend of breeding bird

The script (habitat_density_model.r) in this code repository filters data, sets up model input, and runs an N-mixture model with two components of detection (availability and perceptibility) to estimate bird density from point-count data. This analysis was developed to evaluate covariates of population density for three species of boreal birds: Lesser Yellowlegs, Olive-sided Flycatcher...

Brook trout are a recreationally important fish species that need cold water for survival. The objective of this study was to quantify within- and among-population variability in HSP47 and CIRBP expression in four wild populations of brook trout (Salvelinus fontinalis) to quantify seasonal changes in gene expression. The code release contains a R script for the analysis of brook trout...

Aquatic invasive species can influence mercury methylation and bioaccumulation in lake ecosystems by altering chemical and biological pathways and dynamics. Invasive zebra mussels Dreissena polymorpha, which have invaded lakes and rivers throughout North America, may amplify mercury bioavailability by disrupting food webs and altering biogeochemical processes. This potential...

This "software technical note" (`TECHNOTE.md`) provides extensive details involving the construction of typical well-depth grids from research-grade statistical study of the Chicot aquifer system. The README also within this directory is designed and intended to parallel the documentation of individual covariate construction as part of the primal feature of the **covCHICOTla** software...

This is the repository for an R Shiny App that allows users to create sea ice records for the Bering and Chukchi seas from diatom data. Users will upload a data set of diatom percentages and the app will return predictions of spring (March, April, May, June_ sea ice concentrations based on a generalized additive model of surface sediment assemblages in the Bering and Chukchi Seas. Please...

Code for R Shiny application to visualize and download sea otter population survey data in Alaska. The Sea Otter Survey Data Visualization Tool was developed by the U.S. Geological Survey (USGS) to facilitate visualizing and downloading sea otter population survey data in an interactive mapping application. Numerous survey efforts have occurred over the years. Sea otter survey data can...