Package: bbm 0.0.3

Leire Ibaibarriaga

bbm: FLR Implementation of a Two-Stage Stock Assessment Model

The two-stage biomass-based model for the Bay of Biscay anchovy (Ibaibarriaga et al., 2008).

Authors:Leire Ibaibarriaga [cre, aut], Sonia Sanchez [aut]

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bbm.pdf |bbm.html✨
bbm/json (API)
NEWS

# Install 'bbm' in R:

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

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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

On CRAN:

30 exports 0.00 score 38 dependencies 5 scripts

Last updated 2 years agofrom:c449fad0f3. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 07 2024
R-4.5-win-x86_64	WARNING	Sep 07 2024
R-4.5-linux-x86_64	WARNING	Sep 07 2024
R-4.4-win-x86_64	WARNING	Sep 07 2024
R-4.4-mac-x86_64	WARNING	Sep 07 2024
R-4.4-mac-aarch64	WARNING	Sep 07 2024
R-4.3-win-x86_64	WARNING	Sep 07 2024
R-4.3-mac-x86_64	WARNING	Sep 07 2024
R-4.3-mac-aarch64	WARNING	Sep 07 2024

Exports:AIC bbm bbmControl bbmFit bbmFitresiduals bbmFLPar BIC calcIndices calcPop convergence createInits fitSumm g indicesB indicesP inputs iter logLik message param.fix params.se periods plot qqmath residuals residuals.B residuals.P simIndices stock.bio vcov

Dependencies:cli colorspace cowplot data.table fansi farver FLCore ggplot2 ggplotFL ggrepel glue gridExtra gtable isoband iterators labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig R6 RColorBrewer Rcpp RcppEigen rlang scales tibble TMB utf8 vctrs viridisLite withr

Getting started with bbm package.

Leire Ibaibarriaga & Sonia Sanchez

Rendered frombbm_manual.Rmdusingknitr::rmarkdownon Sep 07 2024.

Last update: 2020-05-27
Started: 2018-09-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Method bbm	bbm bbm,FLQuant,FLIndices,FLIndices-method bbm,FLQuant,FLQuant,FLQuant-method bbm,FLStock,ANY,ANY-method bbm-method bbm-methods
bbmControl class	bbmControl bbmControl,missing-method bbmControl-class bbmControl-methods g,bbmControl-method param.fix,bbmControl-method
bbmFit class	+,FLStock,bbmFit-method AIC,bbmFit,ANY-method AIC,bbmFit-method bbmFit bbmFit,missing-method bbmFit-class bbmFit-methods BIC,bbmFit-method convergence,bbmFit-method fitSumm,bbmFit-method indicesB,bbmFit-method indicesP,bbmFit-method input,bbmFit-method iter,bbmFit-method logLik,bbmFit-method message,bbmFit-method params,bbmFit-method params.se,bbmFit-method plot,bbmFit-method residuals,bbmFit-method stock.bio,bbmFit-method vcov,bbmFit-method
bbmFitresiduals class	bbmFitresiduals bbmFitresiduals-class bbmFitresiduals-methods plot,bbmFitresiduals-method qqmath,bbmFitresiduals-method residualsB,bbmFitresiduals-method residualsP,bbmFitresiduals-method
Function to generate an FLPar for bbm function	bbmFLPar
Function to estimate fitted indices	calcIndices
Function to estimate abundances	calcPop
Method createInits	createInits createInits,FLQuant,FLIndices,FLIndices-method createInits,FLQuant,FLQuant,FLQuant-method createInits,FLQuant,FLQuants,FLQuants-method createInits,FLStock,ANY,ANY-method createInits,FLStock,FLQuant,FLQuant-method createInits-methods
bbm package datasets	ane datasets
Function to estimate the seasons	periods
Plot of Pearson residuals of survey indices	plot plot,bbmFit,missing-method plot,bbmFitresiduals,missing-method
Normal Q-Q Plot of surveys' indices	qqmath qqmath,bbmFitresiduals,missing-method qqplot
Method simIndices	simIndices simIndices,FLQuant-method simIndices,FLStock-method simIndices-methods