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Software

Software from the Alaska Science Center.

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

Nest Survival Bias Analysis

This R script will run one replicate of one scenario used by Weiser (in review) to quantify biases in estimates of nest survival when nests are not found at the beginning of the nesting interval (age 0). The script simulates nest monitoring histories based on input parameters, applies models with or without an age effect to estimate daily survival rates, and calculates nest survival (to the end of

Arctic Shorebird Population Model

R script to run one example of the stochastic matrix models run by Weiser et al. to simulate shorebird population trends and elasticities.

USGS ISO Content Specifications

A repository for USGS ISO metadata content specifications. Content specifications define documentation requirements for various USGS data and software products. These specs are used to guide authors in developing robust standardized metadata using the ISO 19115 suite of metadata standards. The repository is used for development, testing and implementation of content spec modules. It contains guida

Python Scripts for Bioinformatics, 2017

Bioinformatics software repository containing python scripts intended for search and download of genetic information obtained from GenBank NCBI genetics data resources in support of developing PCR primers, targeted genetic databases, genetic analyses, and data interpretation. Includes multiple functions to streamline this process. This repository represents an effort to strengthen the software c

USGS Sea Ice Mail, 2017

Daily sea ice imagery and charting benefits logistics and navigational planning in the Alaskan Arctic waters, yet access to these data often requires high bandwidth data access and substantial GIS processing. This software script acquires, processes and delivers these data in a format that may be manipulated by openly available virtual globe software, be visualized by software commonly installed

qfasar: Quantitative Fatty Acid Signature Analysis in R

Knowledge of predator diets provides numerous insights into their ecology. Diet estimation therefore remains an active area of research in quantitative ecology. Quantitative Fatty Acid Signature Analysis (QFASA) is a method of estimating the diet composition of predators. The fundamental unit of information in QFASA is a fatty acid signature (signature), which is a vector of proportions describing