Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
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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.
occstanhm: Hierarchical occupancy models with correlated error structure occstanhm: Hierarchical occupancy models with correlated error structure
This repository contains a R package with 2-level and 3-level occupancy models. The package also contains a set of tutorials designed to help users understand how to use and code occupancy models in Stan. The models include a statistical hierarchy that allows for multi-species modeling and estimating correlations among species. The models may also be used as a more general "random-effect...
AMMonitor: Remote monitoring of biodiversity in an adaptive framework. Version 2.1 AMMonitor: Remote monitoring of biodiversity in an adaptive framework. Version 2.1
Amid climate change and rapidly shifting land uses, effective methods for monitoring wildlife are critical to support scientifically-informed resource management decisions. As such, monitoring is motivated by ecological hypotheses or natural resource management objectives. The practice of using Autonomous Monitoring Units (AMUs) such as trail cameras or audio recorders to monitor...
R code for identifying factors influencing the prevalence of hyperpigmented melanistic lesions in smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania R code for identifying factors influencing the prevalence of hyperpigmented melanistic lesions in smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania
Hyperpigmented melanistic lesions (HPMLs) are a visual anomaly documented on the skin of smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania and in numerous other geographical locations. Currently, there is a lack of information on environmental and fish characteristics that may influence the prevalence of HPMLs associated with a recently described...
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.
Analysis of occupancy surveys near Marbled Murrelet (Brachyramphus marmoratus) nest sites and random locations between 2018 and 2022 along the central Oregon coast, USA Analysis of occupancy surveys near Marbled Murrelet (Brachyramphus marmoratus) nest sites and random locations between 2018 and 2022 along the central Oregon coast, USA
These data were collected to test whether presence-absence surveys can aid in the identification of nesting sites for the Marbled Murrelet (Brachyramphus marmoratus), a threatened seabird that nests in older-aged forests along the Pacific Coast. The code presented here utilizes four data tables (csv documents) which are formatted according to tidy data principles. Those files are also...