Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
Filter Total Items: 962
Code for the effect of myiasis on Eastern Box Turtle (Terrapene carolina carolina) body condition, movement, and habitat use at Camp Edwards Code for the effect of myiasis on Eastern Box Turtle (Terrapene carolina carolina) body condition, movement, and habitat use at Camp Edwards
This software release contains one R script that reproduces all of the statistical analysis with objectives to (2) determine if myiasis affects Eastern Box Turtle body condition, (3) determine if myiasis affects Eastern Box Turtle shell temperature, (4) determine if myiasis affects Eastern Box Turtle habitat use, and (5) determine if myiasis affected turtles move shorter distances than...
Code release for simulated tag-return study for monitoring invasive fish removals Code release for simulated tag-return study for monitoring invasive fish removals
This repository is a code release to create and analyze simulated datasets to represent a tag-return study for the purposes of estimating annual removal rates of an invasive fish. The simulated scenarios cover ranges of parameters such as the number of fish tagged per year, magnitude of annual harvest rate, length of simulated study, probability of tag retention, probability of tag...
Code to analyze static occupancy of northwestern pond turtles (Actinemys marmorata) in timberland streams in the interior foothills of northern California Code to analyze static occupancy of northwestern pond turtles (Actinemys marmorata) in timberland streams in the interior foothills of northern California
The purpose of this study was to evaluate the distribution of northwestern pond turtles (Actinemys marmorata) and invasive American bullfrogs (Lithobates catesbeianus) in private timberland streams of interior northern California, USA. Fieldwork for the study occurred in 2021-2022 in Lassen, Plumas, Shasta, Tehama, and Trinity counties, California, and involved visual encounter surveys...
Code to evaluate the effect of the 2021 Dixie Fire on the occurrence of foothill yellow-legged frogs (Rana boylii) in northeastern California in 2022 Code to evaluate the effect of the 2021 Dixie Fire on the occurrence of foothill yellow-legged frogs (Rana boylii) in northeastern California in 2022
This repository contains code to fit a static occupancy model to time-to-detection data for foothill yellow-legged frogs (Rana boylii). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., and Rose, J.P., 2024, Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence: Journal of Fish and...
Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore
This repository contains code to fit Spatially-Explicit Capture Recapture (SECR) Models to trapping data for Peromyscus sonoriensis (deer mice) at Point Reyes National Seashore and reproduce analyses in the following manuscript: Rose, J.P., Parsons, L.S., Kleeman, P.M., and Halstead, B.J. 2024. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice)...
Code to Support Chinook Salmon Freshwater Habitat Potential Modeling and Mapping for the Yukon and Kuskokwim River Basins in Alaska Code to Support Chinook Salmon Freshwater Habitat Potential Modeling and Mapping for the Yukon and Kuskokwim River Basins in Alaska
Code to support the "Freshwater Habitat Potential for Chinook Salmon in the Yukon and Kuskokwim River Basins, Alaska" project dataset. These Python notebooks and scripts process synthetic stream networks and DEMs to create unique reach contributing areas (uRCAs) and uRCA valley bottoms (uRCA VBs). The Python notebooks are designed to be run within ESRI ArcPro software and utilize the...
Comparing maximum likelihood and Bayesian methods for fitting Hidden Markov Models to multi-state capture recapture data of invasive Silver Carp in the Illinois River Comparing maximum likelihood and Bayesian methods for fitting Hidden Markov Models to multi-state capture recapture data of invasive Silver Carp in the Illinois River
This repository contains the data, code for modeling and analysis, and publication markdown documents for a comparison of various methods for fitting multi-state models, including maximum likelihood and Bayesian approaches via R.
Conservation Efforts Database Batch Upload Template and User Manual (Cutthroat Trout Recovery Module) Conservation Efforts Database Batch Upload Template and User Manual (Cutthroat Trout Recovery Module)
This ArcGIS Pro project template is being provided to the public in support of scientists who wish to upload data to the Conservation Efforts Database (CED).
Conservation Efforts Database Batch Upload Template and User Manual (Gunnison Sage-grouse Recovery Module) Conservation Efforts Database Batch Upload Template and User Manual (Gunnison Sage-grouse Recovery Module)
This ArcGIS Pro project template is being provided to support scientists who wish to upload data to the Conservation Efforts Database (CED). This software release contains all of the source code and instructions to use the project template, including the tools that come with it, to upload large quantities of data to the CED.
Conservation Efforts Database Batch Upload Template and User Manual (Sagebrush Module) Conservation Efforts Database Batch Upload Template and User Manual (Sagebrush Module)
This ArcGIS Pro project template is being provided in support of scientists who wish to upload data to the Conservation Efforts Database (CED). This software release contains all of the source code and instructions to use the project template, including the tools that come with it, to upload large quantities of data to the CED.
covdetect - network covariance event detector (Version 0.0.0) covdetect - network covariance event detector (Version 0.0.0)
The codes presented here combine modifications to the standard CovSeisNet package (providing estimates of seismic network covariance) with image processing to detect and classify volcanic seismicity. The codes are Python implementations and should work with standard Python distributions. In this case we use Anaconda and have verified that the codes work with Python 3.9 and 3.10. The...
Creating a Polygon GeoJSON AOI File Creating a Polygon GeoJSON AOI File
This quick guide shows users how to create a GeoJSON Area of Interest (AOI) file for querying in the Landsat SpatioTemporal Asset Catalog (STAC) API to access Landsat datasets.