Package: AgeingError 2.0.2
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:
AgeingError_2.0.2.tar.gz
AgeingError_2.0.2.zip(r-4.5)AgeingError_2.0.2.zip(r-4.4)AgeingError_2.0.2.zip(r-4.3)
AgeingError_2.0.2.tgz(r-4.4-x86_64)AgeingError_2.0.2.tgz(r-4.4-arm64)AgeingError_2.0.2.tgz(r-4.3-x86_64)AgeingError_2.0.2.tgz(r-4.3-arm64)
AgeingError_2.0.2.tar.gz(r-4.5-noble)AgeingError_2.0.2.tar.gz(r-4.4-noble)
AgeingError_2.0.2.tgz(r-4.4-emscripten)AgeingError_2.0.2.tgz(r-4.3-emscripten)
AgeingError.pdf |AgeingError.html✨
AgeingError/json (API)
NEWS
| # 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
Last updated 29 days agofrom:967a6fa4b9. Checks:OK: 1 WARNING: 8. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 17 2024 |
| R-4.5-win-x86_64 | WARNING | Sep 17 2024 |
| R-4.5-linux-x86_64 | WARNING | Sep 17 2024 |
| R-4.4-win-x86_64 | WARNING | Sep 17 2024 |
| R-4.4-mac-x86_64 | WARNING | Sep 17 2024 |
| R-4.4-mac-aarch64 | WARNING | Sep 17 2024 |
| R-4.3-win-x86_64 | WARNING | Sep 17 2024 |
| R-4.3-mac-x86_64 | WARNING | Sep 17 2024 |
| R-4.3-mac-aarch64 | WARNING | Sep 17 2024 |
Exports:ageing_comparisoncMxCreateDataCreateSpecsDoApplyAgeErrorestgrowth.vbfitminimizerplot_outputPlotOutputFnProcessResultsrMxrunRunFnSimulatorFnStepwiseFn
Dependencies:clievaluatefshighrknitrlatticeMatrixRcppRcppEigenTMBxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plot comparison of double age readings | ageing_comparison |
| Make a column matrix | cMx |
| Read the ageing error data | CreateData |
| Read the ageing error specifications | CreateSpecs |
| Determine the number of data sets in a data file | determine_n_sets |
| Run the ageing error optimization routine | DoApplyAgeError |
| Calculate von Bertanlaffy Growth Parameters from Lengths and Ages | estgrowth.vb |
| Fit an ageing error model using TMB | fit |
| Minimize the negative log likelihood | minimizer |
| Plot output | plot_output |
| Plot output | PlotOutputFn |
| Process results of the ageing error estimation | ProcessResults |
| Make a row matrix | rMx |
| Run ageing error routine | run |
| Run ageing error model | RunFn |
| Simulate double reading data | SimulatorFn |
| Step-wise model selection | StepwiseFn |
