Software

This software contains 3 separate R Markdown files and 1 R script file that comprise an analysis to 1. collate freshwater fish survey data from within the northeastern United States, 2. develop separate models to predict the probability of occurrence and the proportional abundance of 53 freshwater fish species, and 3. combine model results by fish species traits and habitat...

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...

Aftershock Forecaster is a GUI program that runs on the desktop and is used to compute ETAS-based aftershock forecasts.

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

This repository specifically contains code to reproduce analyses in: Rose, J.P., Nguyen, A.M., Jordan, A.C., Macias, D.A., Schoenig, E.J., Napolitano G.R., Kim, R., Ersan, J.S.M., Fulton, A.M., and Halstead, B.J. 2025. Rice cultivation supports growth and survival of a threatened semi-aquatic reptile. In review.

In this tutorial users will learn how to verify downloaded files by generating checksums and comparing them to those provided by different endpoints in the M2M API.

The USGS User Services, in collaboration with a NASA project, created this compositing workflow that produces Landsat composites for the Ucayali region in Peru. The Ucayali region is located in the heart of the Peruvian Amazon and spans approximately 102,400 square kilometers (39,537 square miles), making it the largest region in the country. The Ucayali experiences significant cloud...

This tutorial guides users on how to complete time series analysis in the cloud, with a focus on snow and glacial retreat at the South Cascade Glacier.

This tutorial teaches users how to combine multiple spectral bands for visualization and create annual composites using known temporal compositing techniques.

The code repository has been produced by the CONUS Ecological Flows project and contains scripts to run an analysis of fish body size relationships with flow regimes, functional traits, and land-use. This code can be run with the input dataset found from Woods (2025).

Anurans (frogs and toads) were surveyed using aural call surveys across the upper Midwest, United States from 2003 to 2008, and again in 2024. This code analyzes these data (from the associated data releases) using a multi-species occupancy model with imperfect detection, species traits, and species associations. It tests for relationships between covariates, occupancy, and detection...

This code cleans and analyzes historical King Rail (Rallus elegans) occurrence data in the Arkansas Delta to generate a multi-season spatial occupancy model. The data itself is publicly-available from Arkansas ​Game & Fish Commission.