Software

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...

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...

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...

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...

This application was developed to estimate the vertical withdrawal zone and overall mixed release water temperature using a user-provided vertical temperature profile and flow rates of selective withdrawal features at eight dams within the Willamette Valley Project that are operated by the U.S. Army Corps of Engineers - Portland District. The application was developed using a macro...

This code can be used to rapidly create an annotated bibliography that will help users navigate and synthesize a large body of literature. Users can input a set of PDF or DOCX files that they have identified as relevant to their question as well as lists of relevant search terms. This code will convert the input documents into TXT files, trim the files to exclude extraneous text such as...

The purpose of this R software package is to easily download and process climate, anthropological, and environmental covariate data for specified areal units to use primarily in an integrated species distribution model. The package contains wrapper functions for the `geodata` R package and externally downloaded datasets.

The purpose of this R software package is to easily download and clean species data from the Global Biodiversity Information Facility (GBIF). This package relies on functions in the `rgif` package and contains wrappers to download and format data for the purposes of building an integrated species distribution model.

This geospatial tool is designed to calculate an estimated volume of mine waste using a polygon outline of the mine waste and elevation data obtained from remote sensing. The tool is developed to run as a toolbox in the ESRI ArcGIS Pro application. It calculates the volume using the geospatial data and a linear regression method described in the accompanying publication. This tool has...