Description
ObsCovgTools provides tools for evaluating fishery observer coverage, particularly with respect to documenting and estimating rare bycatch. Current functionality includes evaluating observer coverage in terms of
- probabilities of observing a bycatch event and of any bycatch occurring in total effort, given mean bycatch rate, dispersion index (variance to mean ratio in the bycatch rate), and total fishery effort;
- upper confidence limit of bycatch when none was observed, given total fishery effort and dispersion index; and
- bycatch estimation CV (coefficient of variation), given bycatch rate, dispersion index, and total fishery effort.
Estimates in all cases are based directly on the corresponding Poisson or negative binomial probability distribution.
Caveat
The ObsCovgTools package assumes that
- observer coverage is representative,
- bycatch is in terms of individuals (not weight) per unit effort, and
- the specified dispersion index reflects the highest level of any hierarchical variance (e.g., using dispersion index at trip level if greater than that at set level).
Violating these assumptions may result in negatively biased projections of observer coverage required to meet specific objectives. Users may want to explore uncertainty in dispersion index and in bycatch per unit effort by varying those inputs.
Shiny app
This package has been implemented as a Shiny web application, coauthored by Howard Coleman, which can be accessed at https://connect.fisheries.noaa.gov/ObsCovg/
(If you encounter an error at that link, you can also try https://kacurtis.shinyapps.io/obscov/)
Installation
You can install or update {ObsCovgTools} from GitHub with:
# install.packages("devtools")
devtools::install_github("kacurtis/ObsCovgTools")Citation
If you use ObsCovgTools results in publications or talks, please cite the primary citation:
Curtis K. A., Carretta J. V. 2020. ObsCovgTools: Assessing observer coverage needed to document and estimate rare event bycatch. Fisheries Research, 225: 105493. https://doi.org/10.1016/j.fishres.2020.105493
You can also cite the package, updating the version number and year if you use a more recent version:
Curtis K. A. 2020. ObsCovgTools: Evaluate Fishery Observer Coverage for Bycatch Estimation. R package version 3.1.1. https://kacurtis.github.io/ObsCovgTools
Funding
Development of the ObsCovgTools package and the Shiny application was supported by a grant from the National Marine Fisheries Service (NMFS) Office of Science and Technology, through a contract to Ocean Associates, Inc.
Disclaimer This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
U.S. Department of Commerce | National Oceanographic and Atmospheric Administration | NOAA Fisheries
