Package: AgeingError 2.2.0

Ian G. Taylor

AgeingError: Estimating ageing error with 'TMB' from double reads

Implements Generalized Linear Mixed Effect Models (GLMMs) using TMB to estimate ageing error from double reads of otoliths. The original analysis (Punt et al. 2008; <doi:10.1139/F08-111>) was written in ADMB and focused on estimating imprecision and bias. The newer version of the software allows for random effects using TMB.

Authors:Andre E. Punt [aut], Kelli F. Johnson [aut], James T. Thorson [ctb, cph], Ian G. Taylor [aut, cre], Paul Burch [aut], Ian J. Stewart [ctb], Melissa A. Haltuch [ctb]

AgeingError_2.2.0.tar.gz
AgeingError_2.2.0.zip(r-4.7)AgeingError_2.2.0.zip(r-4.6)AgeingError_2.2.0.zip(r-4.5)
AgeingError_2.2.0.tgz(r-4.6-x86_64)AgeingError_2.2.0.tgz(r-4.6-arm64)AgeingError_2.2.0.tgz(r-4.5-x86_64)AgeingError_2.2.0.tgz(r-4.5-arm64)
AgeingError_2.2.0.tar.gz(r-4.7-arm64)AgeingError_2.2.0.tar.gz(r-4.7-x86_64)AgeingError_2.2.0.tar.gz(r-4.6-arm64)AgeingError_2.2.0.tar.gz(r-4.6-x86_64)
AgeingError_2.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AgeingError/json (API)

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

Bug tracker:https://github.com/pfmc-assessments/ageingerror/issues

Pkgdown/docs site:https://pfmc-assessments.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

5.00 score 11 stars 10 scripts 22 exports 66 dependencies

Last updated from:5f2b755117. Checks:11 ERROR, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR195
linux-devel-x86_64ERROR194
source / vignettesOK333
linux-release-arm64ERROR187
linux-release-x86_64ERROR184
macos-release-arm64ERROR105
macos-release-x86_64ERROR234
macos-oldrel-arm64ERROR143
macos-oldrel-x86_64ERROR272
windows-develERROR141
windows-releaseERROR149
windows-oldrelERROR164
wasm-releaseOK176

Exports:ageing_comparisoncMxCreateDataCreateSpecsDoApplyAgeErrorestgrowth.vbfitload_dataload_specsminimizerplot_outputPlotOutputFnProcessResultsrMxrunRunFnSimulatorFnStepwiseFntally_repeatswrite_data_filewrite_fileswrite_specs_file

Dependencies:base64encbitbit64bslibcachemclicliprcpp11crayonDiagrammeRdigestdplyrevaluatefarverfastmapfontawesomefsgenericsgluehighrhmshtmltoolshtmlwidgetsigraphjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMatrixmemoisemimepillarpkgconfigprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppEigenreadrrlangrmarkdownrstudioapisassscalesstringistringrtibbletidyrtidyselecttinytexTMBtzdbutf8vctrsviridisLitevisNetworkvroomwithrxfunyaml

Estimating ageing error using the TMB model written by André Punt
Introduction | R package | Input files | Data file | Separate Data Sets | Combined Data Set | Other Considerations | Specifications file | Bias options | Sigma options | Example Specifications file | Examples | Blue Grenadier | Bight Redfish | School Whiting | Sablefish | Trouble Shooting | Acknowledgements | References
Rendered fromgetting_started.Rmdusinglitedown::vignette

Last update: 2026-06-17
Started: 2024-05-29

R-based workflow for the AgeingError package
Helper functions in AgeingError | Writing the data file | Writing the specifications file | Convenience wrapper: write_files() | Running the model
Rendered fromhelper_functions.Rmdusinglitedown::vignette

Last update: 2026-06-17
Started: 2026-06-17