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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

Mercury Condition Index Tool

The Mercury Condition Index Tool uses existing data of mercury concentrations in invertebrates, fish, and birds within national parks to estimate a park level Condition Index (and associated uncertainty) for mercury, based on its potential risk to fish and wildlife health. The tool employs a series of logic steps to convert provided data into standardized units, based upon both basic stoichiometr

Mojave Seed Menus: a new spatial tool for restoration software release v1.0

Mojave Seed Menus is a spatial decision-support tool designed to help land managers create suitable seed mixes for restoration sites, such as a burned area or other mapped spatial feature. The application provides coverage for the Mojave Desert ecoregion. Seed menus are based on a combination of habitat suitability models for 50 priority restoration plant species. Species are selected based on the

CWDsims version v0.2.2

This is a repository with R code for CWD simulation models and interactive Shiny applications. Currently there are deterministic and stochastic models that are intended to model hunting scenarios for a 5 to 10 year time horizon. The models are sex and age structured with direct and indirect transmission.

occStan: Occupancy models with RStan

occStan is an R package (R Core Team 2021) providing a collection of occpuancy Bayesian models written in the Stan language as called through RStan (Stan Development Team 2021). The package is a USGS software software release. The purpose of the package is to document these models for use in USGS projects and allow easy discrimination. The package assumes the user is familiar with R and occupancy

climatchR: An implementation of Climatch in R

Matching climate envelopes of allows people to examine how potential invasive species may match habitats. The Australian government created Climatch to do allow for these comparisons. However, this webpage does not allow for readily scripting climate matching. Hence, the authors created climatchR, an R package (R Core Team 2020) implementing the climatch method in R. This was created to allow auto

Data analysis and figures for Differences in Rhizosphere Microbial Communities Between Native and Non-Native Phragmites australis May Depend on Stand Density

This repository holds the code to reproduce the data analyses and figures found in "Differences in Rhizosphere Microbial Communities Between Native and Non-Native Phragmites australis May Depend on Stand Density" published in Ecology and Evolution written by Wesley A. Bickford, Donald R. Zak, Kurt P. Kowalski, and Deborah E. Goldberg.


MetaIPM is a Python package (Python Software Foundation 2020) that models meta-population dynamics and continuous growth rates via an integral projection model (IPM) for species living in distinct habitat patches. The package stems from a model that compares invasive carp population control strategies. The package supports differing sex and any organisms living in distinct habitat patches.

Bighorn Sheep Risk of Contact Tool

The Risk of Contact Tool (RoCT) is an R-based implementation of the Risk of Contact model described in O'Brien et al. (2014). It uses a variety of spatial inputs (including telemetry point data, a core herd home range (CHHR) polygon, a habitat raster model, and a set of active domestic sheep allotments) together with estimates of bighorn sheep foray behavior to estimate the probability and rate of

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

Data and Software for Space matters: host spatial structure and model plague transmission dynamics and pathways

This software release contains the code descriped in Russell, R.E., Walsh, D.P., Samuel, M.D., Grunnill, M.D., and Rocke, T.E., 2021, Space matters: host spatial structure and the dynamics of plague transmission: Ecological Modelling,Volume 443,

Annual Management Unit Summary Code

The Phragmites Adaptive Management Framework (PAMF) is an adaptive management program created to improve the efficacy and efficiency of Phragmites management efforts throughout the Great Lakes region. Managers enroll Phragmites stands, report the management techniques they used, and monitor the invasion status of Phragmites on their site (management unit - MU). Through a systematic approach, PAMF