Skip to main content
U.S. flag

An official website of the United States government

Software

Software from the Alaska Science Center.

Filter Total Items: 18

Tests of multistate CJS models to estimate survival conditioned on a partially-observed latent state

Polar bears (Ursus maritimus) of the Southern Beaufort Sea (SBS) historically spent nearly the entire year on the sea ice but are increasingly using land habitat as sea ice becomes less available seasonally due to climate warming. The U.S. Geological Survey, Alaska Science Center maintains a research program on the SBS polar bear subpopulation and one important research question is whether habitat

Eelgrass Biomass Model

This code release contains R and JAGS code for estimating average eelgrass biomass at two lagoons (Izembek and Kinzarof) within the Izembek National Wildlife Refuge, Alaska, using data from point count surveys conducted by National Wildlife Refuge and U.S. Geological Survey (USGS) personnel. Biomass is estimated using a gamma hurdle model which models the probability of occurrence and eelgrass abu

Scripts to Analyze Altitude Selection in Migrating Pacific Flyway Geese

This code repo contains three scripts used in the associated manuscript to run the analyses (01_model_prob_flight.r; 02_model_altitude_selection.r) and the simulation used to make predictions (03_simulate_prob_fly_per_altitude.r). The analysis serves to evaluate conditions that affect 1) whether geese are in flight vs. resting on the water, 2) what altitude is selected by flying geese, and 3) what

Rayleigh Step-Selection Functions

This project aimed to find connections between step-selection functions (SSFs) and partial differential equation models of animal movement and, in doing so, improve the flexibility of SSFs. Please see the associated manuscript cited above for further details.

WiggleMatch: a spreadsheet for radiocarbon wiggle-matching

This spreadsheet enables statistical and visual wiggle-matching of sequential radiocarbon ages from a tree-ring chronology to the IntCal20 calibration curve. It will calculate and plot an optimal fit of the samples to the calibration curve and the user can then incrementally move the wiggle-match in time to see the effect in both goodness-of-fit statistics and visually on a graph. This is useful w

algaeClassify

The goal of algaeClassify is to facilitate the analysis of taxonomic and functional trait data for phytoplankton.

Bayesian Hierarchical Model of Whimbrel Survival

This model combines resighting data from Whimbrels breeding at Kanuti National Wildlife Refuge with known-fate data and pseudo-resighting history from Whimbrels breeding at the Colville River Delta ('colv'). All Whimbrels in the study (n = 76) were marked with a USGS metal band and a uniquely coded engraved leg flag. In addition, 15 Whimbrels at Kanuti were equipped with surgically implanted satel

Reproductive Success from Movement Data

This software release includes code to conduct analyses presented in the manuscript titled: A hierarchical modeling framework for estimating individual- and population-level reproductive success from movement data

SeaLog

SeaLog is a robust data-logging application designed to collect at-sea data of marine birds and mammals. This software was developed collaboratively with the U.S. Geological Survey, the National Park Service, the U.S. Fish and Wildlife Service, and ABR, Inc. SeaLog is Windows 10 compatible, is highly customizable, and provides user designed maps to allow visual feedback of observations.

QFASA Robustness to Assumption Violations: Computer Code

Quantitative fatty acid signature analysis (QFASA; Iverson et al. 2004) has become a common method of estimating diet composition, especially for marine mammals, but the performance of the method has received limited investigation. Bromaghin et al. (In press) used computer simulation to compare the bias of several QFASA estimators and developed recommendations regarding estimator selection. Simula

R scripts for analysis of fall photographic waterfowl surveys, Izembek NWR, Alaska, 2017-2019

This code repo contains three novel scripts used in Weiser et al. (2022): one to calculate the footprint of an aerial photo (01_function_photo_footprint.r), one to run a simulation to evaluate sample sizes for the photographic survey (02_photo_sample_size_sim.r), and one to run a simulation to evaluate sample sizes for the ocular survey (03_ocular_sample_size_sim.r). For more information on the ba

Code for analysis of polar bear maternal den abundance and distribution in four regions of northern Alaska and Canada within the Southern Beaufort Sea subpopulation boundary (1982-2015)

We have archived the derived data files and R/JAGS code for our analysis as a U.S. Geological Survey data release (link ). The code is divided into three R scripts: 1) pbdens_landdens_JWM.r contains R code for fitting hierarchical Bayesian models of polar bear maternal den abundance and distribution for the Southern Beaufort Sea (SBS) subpopulation, 1982-2015. This script requires the installation