Package: bycatch 1.0.9

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], Trustees of Columbia University [cph]

bycatch_1.0.9.tar.gz
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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:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

4.87 score 3 stars 14 scripts 8 exports 50 dependencies

Last updated from:f2aeebe60b. Checks:11 NOTE, 1 OK, 1 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE376
linux-devel-x86_64NOTE317
source / vignettesOK407
linux-release-arm64NOTE288
linux-release-x86_64NOTE363
macos-release-arm64NOTE245
macos-release-x86_64NOTE459
macos-oldrel-arm64NOTE208
macos-oldrel-x86_64NOTE497
windows-develNOTE331
windows-releaseNOTE353
windows-oldrelNOTE348
wasm-releaseFAIL169

Exports:extract_log_lik_for_loofit_bycatchget_expandedget_fittedget_stream_summaryget_totalplot_expandedplot_fitted

Dependencies:abindbackportsBHcallrcheckmateclicpp11descdistributionaldplyrfarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglifecycleloomagrittrmatrixStatsnumDerivotelpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsS7scalesStanHeaderstensorAtibbletidyselectutf8vctrsviridisLitewithr

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

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

Last update: 2026-02-13
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: 2026-02-13
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