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-x86_64)AgeingError_2.2.0.zip(r-4.7-arm64)AgeingError_2.2.0.zip(r-4.6-x86_64)AgeingError_2.2.0.zip(r-4.6-arm64)AgeingError_2.2.0.zip(r-4.5-x86_64)
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

5.12 score 11 stars 10 scripts 23 exports 66 dependencies

Last updated from:4589e73549. Checks:13 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING162
linux-devel-x86_64WARNING175
source / vignettesOK347
linux-release-arm64WARNING144
linux-release-x86_64WARNING171
macos-release-arm64WARNING157
macos-release-x86_64WARNING274
macos-oldrel-arm64WARNING167
macos-oldrel-x86_64WARNING448
windows-devel-arm64WARNING245
windows-devel-x86_64WARNING226
windows-release-arm64WARNING237
windows-release-x86_64WARNING163
windows-oldrel-x86_64WARNING140
wasm-releaseOK141

Exports:ageing_comparisonageing_error_matrix_to_fimscMxCreateDataCreateSpecsDoApplyAgeErrorestgrowth.vbfitload_dataload_specsminimizerplot_outputPlotOutputFnProcessResultsrMxrunRunFnSimulatorFnStepwiseFntally_repeatswrite_data_filewrite_fileswrite_specs_file

Dependencies:base64encbitbit64bslibcachemclicliprcpp11crayonDiagrammeRdigestdplyrevaluatefarverfastmapfontawesomefsgenericsgluehighrhmshtmltoolshtmlwidgetsigraphjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMatrixmemoisemimepillarpkgconfigprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppEigenreadrrlangrmarkdownrstudioapisassscalesstringistringrtibbletidyrtidyselecttinytexTMBtzdbutf8vctrsviridisLitevisNetworkvroomwithrxfunyaml

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 | Adding data to an SS3 or FIMS model
Rendered fromhelper_functions.Rmdusinglitedown::vignette

Last update: 2026-10-08
Started: 2026-06-17

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