Package: bycatch 1.0.10

Eric Ward

bycatch: Fit Bayesian Models to Bycatch Data

Fits models to bycatch data, and can expand to fleet-wide estimates, like in situations when fisheries are observed with less than 100% observer coverage.

Authors:Eric Ward [aut, cre], Jason Jannot [aut], Kate Richerson [aut], Kayleigh Somers [aut], Tina Lyu [ctb], Trustees of Columbia University [cph]

bycatch_1.0.10.tar.gz
bycatch_1.0.10.zip(r-4.7-x86_64)bycatch_1.0.10.zip(r-4.7-arm64)bycatch_1.0.10.zip(r-4.6-x86_64)bycatch_1.0.10.zip(r-4.6-arm64)bycatch_1.0.10.zip(r-4.5-x86_64)
bycatch_1.0.10.tgz(r-4.6-x86_64)bycatch_1.0.10.tgz(r-4.6-arm64)bycatch_1.0.10.tgz(r-4.5-x86_64)bycatch_1.0.10.tgz(r-4.5-arm64)
bycatch_1.0.10.tar.gz(r-4.7-arm64)bycatch_1.0.10.tar.gz(r-4.7-x86_64)bycatch_1.0.10.tar.gz(r-4.6-arm64)bycatch_1.0.10.tar.gz(r-4.6-x86_64)
bycatch_1.0.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
bycatch/json (API)

# Install 'bycatch' in R:
install.packages('bycatch', repos = c('https://noaa-fisheries-integrated-toolbox.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ericward-noaa/bycatch/issues

Pkgdown/docs site:https://ericward-noaa.github.io

Uses libs:
  • onetbb– Parallelism library for C++
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

onetbbcpp

5.11 score 3 stars 18 scripts 9 exports 48 dependencies

Last updated from:52615d336e. Checks:15 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK239
linux-devel-x86_64OK298
source / vignettesOK404
linux-release-arm64OK239
linux-release-x86_64OK292
macos-release-arm64OK198
macos-release-x86_64OK497
macos-oldrel-arm64OK216
macos-oldrel-x86_64OK527
windows-devel-arm64OK365
windows-devel-x86_64OK342
windows-release-arm64OK348
windows-release-x86_64OK211
windows-oldrel-x86_64OK289
wasm-releaseOK159

Exports:extract_log_lik_for_loofit_bycatchget_expandedget_fittedget_stream_summaryget_totalplot_expandedplot_fittedplot_pred_distribution

Dependencies:abindbackportsBHcallrcheckmateclicpp11descdistributionalfarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglifecycleloomagrittrmatrixStatsnumDerivotelpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsS7scalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr

Diagnosing errors
Load data | Simple model with constant bycatch, no covariates
Rendered froma04_diagnosing_problems.Rmdusingknitr::rmarkdown

Last update: 2026-09-03
Started: 2023-02-15

Fitting models with the bycatch package
Load data | Simple model with constant bycatch, no covariates | Make plots | Extracting model selection information (LOOIC) | Negative binomial example | Zero - inflated example | Continuous models | Example with covariates | Fit model with time-varying effects | Fit model with no bycatch events
Rendered froma02_fitting_models.Rmdusingknitr::rmarkdown

Last update: 2026-09-03
Started: 2021-05-05

Plotting the predicted bycatch distribution
Load data | Fit a model | Plot the prediction distribution for a single year
Rendered froma06_more_plots.Rmdusingknitr::rmarkdown

Last update: 2026-09-03
Started: 2026-09-03

Expanding bycatch estimates
Load data | Simple model with constant bycatch, no covariates | Make table of expanded bycatch estimates | Make table of total bycatch estimates | Derived quantities | Simulating future values
Rendered froma03_expanding_estimates.Rmdusingknitr::rmarkdown

Last update: 2026-03-13
Started: 2021-05-05

Multi-stream monitoring
Overview | Simple two-stream example | Fitting a multi-stream model | Plotting results | Stream-specific summaries | Three-stream example | Comparing to pooled data | Different distributions | Adding covariates | Time-varying effects
Rendered froma05_multistream.Rmdusingknitr::rmarkdown

Last update: 2026-02-13
Started: 2026-01-06

Overview of bycatch package
Overview | Other families | Fixed effect covariates | Time varying parameters | Expanding estimates
Rendered froma01_overview.Rmdusingknitr::rmarkdown

Last update: 2026-01-06
Started: 2021-05-05