Software

This code supports land cover model building, validation and prediction for Alabama's Wildlife Management Areas using remote sensing and field data. It includes R scripts for data preprocessing, spectral indices calculation, model training, validation, and mapping, as well as GIS workflows for spatial alignment and analysis.

The North American Breeding Bird Survey (BBS) (https://www.pwrc.usgs.gov/bbs/) has counted birds annually for over fifty-five years. Survey 'routes' each consist of 50 'stops' (point counts) placed along a route path. Inter-stop distances and stop locations can vary from route to route and from year to year, and precise locations of each stop are not typically recorded. Burner et al....

This repository contains R scripts, YAML files, and BASH code to run simulations and evaluate the case study described in "Evaluating alternative methods for modeling trap efficiencies of outmigrating juvenile salmonids" (Walden and Som 2026), and depends on data files available in the accompanying data release https://doi.org/10.5066/P1PN4IHO. The R scripts can be run directly in R...

This code shows loading and formatting data, a series of functions to implement flow management constraints, a function to estimate parameters that drive daily discharge predictions, the optimization of the estimating function, and plotting code.

Greater sage-grouse (Centrocercus urophasianus) are landscape-scale sagebrush obligate species and an important gamebird and iconic species of the western United States. They occupy the sagebrush biome in western North America, extending east of the Sierra Nevada/Cascade Mountain ranges to the western regions of the Great Plains of the United States. Sage-grouse are one of the most...

Of all bird guilds in North America, grassland birds have experienced the sharpest declines since 1970. Here, we use the bbsBayes R package to estimate abundance of 50 species of grassland birds from 1984 - 2019 in the Plains states. To run these analyses, open the "GreatPlainsBirds.RProj" file, open the "GreatPlainsBirds_Analysis.R" script file, and run this script. NOTE: Running the...

The purpose of this code is to replicate the analyses associated with the manuscript: Parvin, L.K., V. Jirinec, M. Leu, and J.J. Valente. (in review). Survey protocols drive heterogeneity in occupancy estimates that cannot be standardized using post-hoc analyses. Ecological Solutions and Evidence.__ This manuscript simulates point count sampling of a simulated Wood Thrush (Hylocichla...

This code set is an R workflow for phenological date matching to provide an open-source solution for projects with limited funding to allow users to calculate Normalized Difference Vegetation Index (NDVI) from sentinel-2 imagery dates specified by a user supplied date raster (phenology raster) for mapping and forecasting geographic distributions of invasive plant species at large spatial...

This software release contains the core code and example data for generating animal movement simulations using step selection functions (SSFs). The approach is based on simulation methods used in a series of grizzly bear studies by Sells et al. (2022–2024). In general, an SSF is fit to animal movement data and associated environmental covariates, and the fitted model is used to simulate...

The PAMF Model is the foundation of the Phragmites Adaptive Management Framework. PAMF is an adaptive management and collective learning program that anyone managing Phragmites can join. Participants from around the Great Lakes basin submit Phragmites monitoring and management data to bolster the PAMF predictive model, which uses participant data to continually 'learn' more about which...

The purpose of this R software package is to build and fit an integrated species distribution model. Specifically, this package loads species and covariate data, builds a species region, sets up code, parameters, and specification for a NIMBLE model, and processes and plots NIMBLE output. This framework allows the inclusion of any number of count, detection/non-detection, and presence...

The code was used to analyze pollinator COI amplicon FASTQ sequence data in the paper titled "Development and validation of an eDNA assay for detection of the endangered Franklin’s bumble bee (Bombus franklini)" (IPDS number IP-175306, [DOI link]). The corresponding data release can be found here (IPDS number, [DOI link]). Although we use this code to analyze a pollinator COI dataset, it...