Software

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.

This is nimble model code for a hierarchical Bayesian analysis to estimate walrus herd density at multiple sites, where some surveys entailed counting walruses in a sample of grid cells overlain on the surveyed herd on shore; whereas, other surveys were censuses (complete counts.) The model code also predicts herd densities for new surveys taken at existing sites and a new site.

The code in this repository generates and analyzes directed acyclic graphs (DAGs) representing hypotheses about variables affecting the occurrence and surface availability of Plethodon salamanders in northern California; formats data from field surveys and GIS for analysis; and analyzes multi-scale occupancy models, including model selection, to evaluate the model and variables with the...

This repository contains code to fit open population models to capture-mark-recapture data for Sierra Nevada yellow-legged frogs (Rana sierrae). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., Rose, J.P., and Fellers, G.M. 2025. Climate-induced extirpation of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite...

This repository centralizes R code used to examine habitat selection and survival of greater sage-grouse (Centrocercus urophasianus) during multiple seasons and life stages, utilizing data collected from a wide range of study sites in Nevada and California, USA. The R script "selection_model.R" provides code for a GLMM framework with regularization within a Bayesian modeling environment...

Examinations of contact rates among white-tailed deer (Odocoileus virginianus; hereafter, deer) are important to applied management objectives given their societal value and disease transmission potential. This R script was used to curate the original GPS collar and capture data from Pennsylvania DMA2 in preparation for contact rates analysis.

The covCHICOTla repository contains primarily R and limited Mermaid, Perl, and Python language source code that collectively can be used for the construction of many tables of monthly groundwater levels (response variable) and predictor variables (covariates) intended to be inputs to statistical modeling of water levels in the Chicot aquifer system, southwestern Louisiana. The source...

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

D-Claw is a software library for the simulation of dense granular flows over spatially variable topography. D-Claw builds on clawpack, is written in Fortran, and has a python wrapper. The code is hosted on code.usgs.gov and mirrored on github. D-Claw is supported on Linux/Unix only.

This repository contains code for training and running the DeepFaune New England (DFNE) model for species classification in trail camera imagery. This model is a re-trained version of the DeepFaune model for classifying European species in trial cameras, fine-tuned to classify taxa from northeastern North America. The DFNE model takes as input cropped images of each animal, which can be...

DReAMER DReAMER: Depth Retrieval Algorithms for Mapping and Exploration of Rivers Description The software application made available through this repository is designed for mapping water depth in river channels from passive optical remotely sensed data. The program provides convenient access to a number of different methods for deriving bathymetric information from images and...

Code for implementation of the Dynamic Surface Water Extent algorithm in Google Earth Engine. Multiple scripts allow the creation of single-scene or composited Dynamic Surface Water Extent (DSWE) images from Landsat (updated for Collection 2 imagery) and MODIS data. All code is written for use in Google Earth Engine in the JavaScript API.