Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
Filter Total Items: 962
ArrayAbundance: An R package to explore and model detection data from antenna arrays ArrayAbundance: An R package to explore and model detection data from antenna arrays
#ArrayAbundance: An R package to explore and model detection data from antenna arrays The goal of Rpackage is to help modelers format passive integrated transponder (PIT) tag array detection data for data exploration and for analysis with mark-recapture models. The package includes functions to categorize array detection data into movement categories (e.g., migratory movement versus...
Automated Walrus Haulout Cartography Automated Walrus Haulout Cartography
This pyQGIS script and adjoining QGIS layout templates and style specification generate maps from satellite imagery and any derived geospatial outline data that are inventoried and cross-referenced in a tabular inventory file. The maps are intended for mangers, decision makers, and researchers to support real-time decision making and to provide a graphical record that may be publicly...
Baydiff: Bayesian diffusion chronometry for volcanic systems Baydiff: Bayesian diffusion chronometry for volcanic systems
Diffusion chronometry is a powerful tool for estimating the time scales of magmatic processes. This MATLAB software can be used to estimate diffusion time scales using the forsterite content of olivine crystals. Estimates are obtained probabilistically, using a Bayesian framework, and account for uncertainties in data as well as any independent (prior) information.
Bayesian Composition Sampling Bayesian Composition Sampling
R Code to Run Composition Sampling for Cook et al. 2023 The aim of this software is to perform composition sampling on simulated disease observation data. Composition sampling is a valuable approach for statistical inference in data limited systems. This software implements composition sampling on simulated chronic wasting disease surveillance data in white-tailed deer in Michigan, U.S...
Caldera Collapse Earthquake Cycle Codes Caldera Collapse Earthquake Cycle Codes
This repository contains software files, codes, and data asociated with a publication on caldera collapse earthquake cycles.
CO2assessment R package CO2assessment R package
The CO2assessment package provides R functions and a Shiny application for CO2 storage resource assessment using 2013 USGS National Assessment of Geologic Carbon Dioxide Storage Resources methodology. Tools to facilitate estimation of CO2 storage resources in geologic formations include volumetric and thermodynamic equations and Monte Carlo simulation. The set of input parameters define
Code for a spatially interpolated integrated population model applied to simulations of spatially autocorrelated Greater Sage-Grouse (Centrocercus urophasianus) population data Code for a spatially interpolated integrated population model applied to simulations of spatially autocorrelated Greater Sage-Grouse (Centrocercus urophasianus) population data
This repository contains R code to: 1. Simulate spatially autocorrelated count and demographic data for 10 populations using mean and process variance estimates from a long-term (1938–2011), range-wide meta-analysis of Greater Sage-Grouse (Centrocercus urophasianus) population dynamics (Taylor et al., 2012). 2. Fit a spatially interpolated integrated population model (SIIPM) to the...
Code for Distance sampling accounting for density gradient and animal distribution Code for Distance sampling accounting for density gradient and animal distribution
Code to estimate animal density from line transect surveys where auxiliary data are available to model the distribution of animals near the survey line and the distribution of animals across the study area.
Code for Human activity drives establishment, but not invasion, of non-native plants on islands Code for Human activity drives establishment, but not invasion, of non-native plants on islands
This software release contains 7 R markdown files, the contents of which are described below. The raw data analyzed in these files is available at the following DOI: https://scholarworks.umass.edu/data/175/ 1. SEMs_Native.Rmd - Code for the piecewise structural equation model (pSEM) that predicts native plant richness on islands using the covariates described in the manuscript. -
Code for long-term monitoring reveals management effects on Prairie Warbler colonization, local extinction, and detection in a Massachusetts Pine Barren Code for long-term monitoring reveals management effects on Prairie Warbler colonization, local extinction, and detection in a Massachusetts Pine Barren
This repository contains all of the scripts to reproduce the analyses, figures, and tables associated with the manuscript Gordon et al. in prep. There is 1 R script that does the following: (1) format the data, (2) explores the data, and (3) goes through the analyses for each objective.
Code for multi-scale occupancy analysis of Temblor legless lizards, Anniella alexanderae Code for multi-scale occupancy analysis of Temblor legless lizards, Anniella alexanderae
This repository contains code to fit Multi-scale Occupancy Models to survey data for Temblor legless lizards (Anniella alexanderae) This repository specifically contains code to reproduce analyses in: Rose, J.P., Camp, S.M., Sheikh, Z.N., Johnson, C.B., Lei, S.H., Napolitano, G.R., Schoenig, E.J., Macias, D.A., Jordan, A.C., and Halstead, B.J. 2024. Multi-scale occupancy surveys reveal
Code for quantitative support for the benefits of proactive management for wildlife disease control Code for quantitative support for the benefits of proactive management for wildlife disease control
This software release contains the input data, R scripts, and Rmarkdown visualization scripts. This includes (i) aggregation code of expert elicited parameter estimates, (ii) simulation code using our develop dynamic multi-state occupancy model for no management, proactive management, and reactive management, (iii) code for probabilistic decision trees, and (iv) Rmarkdown scripts...