Package: a4adiags 0.1.5.9001

Iago Mosqueira

a4adiags: Additional Diagnostics for FLa4a stock Assessment Models

A series of extra diagnostics for the FLa4a model, including prediction skill through restrospective prediction of model inputs and runs tests. Contains ggplot-based plot funtions of diagnostics outputs.

Authors:Iago Mosqueira [aut, cre], Henning Winker [aut], European Union [fnd, cph]

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NEWS

# Install 'a4adiags' in R:

install.packages('a4adiags', repos = c('https://flr.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/flr/a4adiags/issues

Datasets:

indices - Data from the 2020 ICES stock assessment of North Sea sole
sol274fit - Data from the 2020 ICES stock assessment of North Sea sole
stock - Data from the 2020 ICES stock assessment of North Sea sole

On CRAN:

2.70 score 7 scripts 6 exports 58 dependencies

Last updated 5 days agofrom:1855f20035. Checks:1 OK, 8 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 04 2025
R-4.5-win	WARNING	Mar 04 2025
R-4.5-mac	WARNING	Mar 04 2025
R-4.5-linux	WARNING	Mar 04 2025
R-4.4-win	WARNING	Mar 04 2025
R-4.4-mac	WARNING	Mar 04 2025
R-4.4-linux	WARNING	Mar 04 2025
R-4.3-win	WARNING	Mar 04 2025
R-4.3-mac	WARNING	Mar 04 2025

Exports:a4aBioidx a4ahcxval plota4aBioidx plotRunstest plotXval2 runstest

Dependencies:ADGofTest assertthat cli coda codetools colorspace copula cowplot data.table deldir fansi farver FLa4a FLasher FLCore FLFishery foreach ggplot2 ggplotFL ggrepel glue gridExtra gsl gtable interp isoband iterators jpeg labeling lattice latticeExtra lifecycle magrittr MASS Matrix mgcv munsell mvtnorm nlme numDeriv pcaPP pillar pkgconfig png pspline R6 RColorBrewer Rcpp RcppEigen rlang scales stabledist tibble triangle utf8 vctrs viridisLite withr

Model Diagnostics for FLa4a

Iago MOSQUEIRA (WMR), Henning WINKER (EC JRC)

Rendered froma4adiags.Rmdusingknitr::rmarkdownon Mar 04 2025.

Last update: 2021-01-29
Started: 2020-12-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
a4aBioidx Computes observed and expected FLIndexBiomass from a4a fits	a4aBioidx
Compute a retrospective hindcast cross-validation of a4a stock and indices	a4ahcxval
plota4aBioidx Computes observed and expected FLIndexBiomass from a4a fits plota4aBioidx(stock, fit, indices) \itemstockInput FLStock object. \itemfitobject a4a fit . \itemindicesInput FLIndices object. \itemnyearsNumber if years for retrospective, defaults to 5. \itemnsqNumber of years for average biology and selectivity, defaults to 3. \itemfixed.ksIs the number of knots is splines with 'year' constant? ggplot plota4aBioidx Computes observed and expected FLIndexBiomass from a4a fits data(sol274) # models fmod <- ~te(replace(age, age > 8, 8), year, k = c(4, 22)) + s(replace(age, age > 8, 8), k=4) + s(year, k=22, by=as.numeric(age==1)) qmod <- list(~s(age, k=3), ~s(age, k=3)) vmod <- list(~s(age, k=3), ~s(age, k=3), ~s(age, k=3)) srmod <- ~factor(year) # RUN a4a fit <- sca(stock, indices, fmodel=fmod, qmodel=qmod, vmodel=vmod,sr=srmod) idxs = a4aBioidx(stock,fit,indices) plota4aBioidx(stock,fit,indices)	plota4aBioidx
plotRunstest Plot the runs test result for one or more time series	plotRunstest,a4aFitSA,FLIndices-method
Plot of FLIndices cross-validation by retrospective hindcast	plotXval2
Computes Runs Test p-values	runstest,a4aFitSA,FLIndices-method
Data from the 2020 ICES stock assessment of North Sea sole (sol.27.4)	indices sol274 sol274fit stock