Package: FLa4a 1.9.0

Ernesto Jardim

FLa4a: A Simple and Robust Statistical Catch at Age Model

A simple and robust statistical Catch at Age model that is specifically designed for stocks with intermediate levels of data quantity and quality.

Authors:Colin P. Millar [aut], Ernesto Jardim [aut, cre]

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NEWS

# Install 'FLa4a' in R:
install.packages('FLa4a', repos = c('https://flr.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/flr/fla4a/issues

Datasets:

On CRAN:

5.96 score 12 stars 2 packages 179 scripts 100 exports 49 dependencies

Last updated 30 days agofrom:cd8000eaf6. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-winWARNINGNov 22 2024
R-4.5-linuxWARNINGNov 22 2024
R-4.4-winWARNINGNov 22 2024
R-4.4-macWARNINGNov 22 2024
R-4.3-winWARNINGNov 22 2024
R-4.3-macWARNINGNov 22 2024

Exports:a4aFita4aFitMCMCa4aFitSAa4aFitSAsa4aGra4aMa4aSCAas.mcmcbreakptsbubblesburninclockcoefcoefficientscoefficients<-collapseSeasonscomputeCatchDiagnosticscovardefaultFmoddefaultN1moddefaultQmoddefaultSRmoddefaultVmoddimsdistrdistr<-fCovarfFrmlfitSummfmodelformulaformula<-fParsgenFLIndexgenFLQuantgenFLStockgetAcorgetADMBCallArgsgetADMBCovariancegetADMBHessiangetCovgetKgetNgetTPLgetXgetYidxgrInvModgrInvMod<-grModgrMod<-is.emptyiterl2alevellevel<-mmamodelmvrcopmvrnormmvrtrianglen1modelnitersparamsparams<-parspars2dimplotpredictqCovarqFrmlqmodelqParsqqmathreplaceZerosresidualsscasca.saSCAMCMCSCAParssep.sashapeshape<-simulatesrCovarsrFrmlsrmodelsrParsstdlogresstkmodelsubmodelsubmodelstrendtrend<-vCovarvFrmlvmodelvParswireframewt

Dependencies:ADGofTestassertthatclicodacolorspacecopuladeldirfansifarverFLCoreggplot2gluegridExtragslgtableinterpisobanditeratorsjpeglabelinglatticelatticeExtralifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmenumDerivpcaPPpillarpkgconfigpngpsplineR6RColorBrewerRcppRcppEigenrlangscalesstabledisttibbletriangleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
* methods* *,FLIndices,a4aFitSA-method *,FLIndices,SCAPars-method *,FLStock,a4aFitSA-method *,FLStock,SCAPars-method
S4 class 'a4aFit'a4aFit a4aFit-class a4aFit-methods catch.n,a4aFit-method clock clock,a4aFit-method clock-methods computeCatchDiagnostics,a4aFit-method fitSumm fitSumm,a4aFit-method fitSumm-methods harvest,a4aFit,ANY-method index,a4aFit-method iter,a4aFit-method logLik,a4aFit-method show,a4aFit-method stock.n,a4aFit-method
S4 class 'a4aFitCatchDiagn'a4aFitCatchDiagn a4aFitCatchDiagn-class a4aFitCatchDiagn-methods computeCatchDiagnostics
S4 class 'a4aFitMCMC'a4aFit,a4aFitMCMC-method a4aFitMCMC a4aFitMCMC-class a4aFitMCMC-methods a4aFitSA,a4aFitMCMC-method as.mcmc as.mcmc,a4aFitMCMC-method as.mcmc-methods burnin burnin,a4aFitMCMC-method burnin-methods
S4 class 'a4aFitResiduals'a4aFitResiduals a4aFitResiduals-class a4aFitResiduals-methods residuals,a4aFit-method
S4 class 'a4aFitSA'a4aFit,a4aFitSA-method a4aFitSA a4aFitSA-class a4aFitSA-methods a4aFitSAs a4aFitSAs,a4aFitSA-method a4aFitSAs,list-method a4aFitSAs,missing-method a4aFitSAs-class a4aFitSAs-methods fmodel,a4aFitSA-method iter,a4aFitSA-method m,a4aFitSA-method n1model,a4aFitSA-method pars pars,a4aFitSA-method pars-methods qmodel,a4aFitSA-method show,a4aFitSA-method srmodel,a4aFitSA-method stkmodel,a4aFitSA-method submodels,a4aFitSA-method vmodel,a4aFitSA-method wt,a4aFitSA-method
Individual growth classa4aGr a4aGr,missing-method a4aGr-class a4aGr-methods distr,a4aGr-method distr<-,a4aGr,character-method grInvMod grInvMod,a4aGr-method grInvMod-methods grInvMod<- grInvMod<-,a4aGr,formula-method grInvMod<--methods grMod grMod,a4aGr-method grMod-methods grMod<- grMod<-,a4aGr,formula-method grMod<--methods params,a4aGr-method params<-,a4aGr,FLPar-method vcov,a4aGr-method vcov<-,a4aGr,numeric-method
Stock assessment model advanced methoda4aInternal
Natural mortality classa4aM a4aM,missing-method a4aM-class a4aM-methods level level,a4aM-method level-methods level<- level<-,a4aM-method level<--methods shape shape,a4aM-method shape-methods shape<- shape<-,a4aM-method shape<--methods show,a4aM-method trend trend,a4aM-method trend-methods trend<- trend<-,a4aM-method trend<--methods
Stock parameters classa4aStkParams a4aStkParams,missing-method a4aStkParams-class a4aStkParams-methods coefficients coefficients,a4aStkParams-method coefficients-methods coefficients<- coefficients<-,a4aStkParams,FLPar-method coefficients<--methods distr,a4aStkParams-method distr<-,a4aStkParams,character-method fMod fMod,a4aStkParams-method fMod-methods fMod<- fMod<-,a4aStkParams,formula-method fMod<--methods iter,a4aStkParams-method m,a4aStkParams-method mat,a4aStkParams-method n1Mod n1Mod,a4aStkParams-method n1Mod-methods n1Mod<- n1Mod<-,a4aStkParams,formula-method n1Mod<--methods params,a4aStkParams-method params<-,a4aStkParams,FLPar-method propagate,a4aStkParams-method rMod-methods srMod srMod,a4aStkParams-method srMod<- srMod<-,a4aStkParams,formula-method srMod<--methods vcov,a4aStkParams-method vcov<-,a4aStkParams,array-method wt,a4aStkParams-method
+ methods+,FLIndices,a4aFit-method +,FLStock,a4aFit-method +,FLStock,a4aFitSA-method addition
Assorted methods needed by FLa4aassorted methods dims,a4aStkParams-method getYidx getYidx,FLQuant-method getYidx-methods is.empty niters niters,a4aGr-method niters,FLModelSim-method niters-methods replaceZeros replaceZeros,FLIndex-method replaceZeros,FLIndices-method replaceZeros,FLQuant-method replaceZeros,FLStock-method replaceZeros-methods
Breakpointsbreakpts breakpts,numeric-method breakpts-methods
Bubbles plot of standardized log residualsbubble plot of residuals bubbles,a4aFitResiduals,missing-method
Collapse seasonscollapseSeasons
Default sub-modelsdefaultFmod defaultN1mod defaultQmod defaultSRmod defaultSubModels defaultVmod
deprecateda4aSCA deprecated
coefficients extract and replacementcoef coef,a4aFitSA-method coef,a4aFitSA-methods coef,a4aStkParams-method coef,SCAPars-method coef,submodel-method coef,submodels-method coef<- coef<-,a4aFitSA,numeric-method coef<-,a4aFitSA-methods coef<-,a4aStkParams,FLPar-method coef<-,a4aStkParams,matrix-method coef<-,a4aStkParams,numeric-method coef<-,SCAPars,numeric-method coef<-,submodel,FLPar-method coef<-,submodel,numeric-method coef<-,submodels,numeric-method formula<- formula<-,submodel,formula-method
Methods to generate FLIndex objectsgenFLIndex genFLIndex,FLQuant-method genFLIndex-methods
Methods to generate FLQuant objectsgenFLQuant genFLQuant,a4aStkParams-method genFLQuant,FLQuant-method genFLQuant,submodel-method genFLQuant,submodels-method genFLQuant-methods
Methods to generate FLStock objectsgenFLStock genFLStock,FLStock,FLQuant,FLQuant,missing-method genFLStock,FLStock,FLQuant,missing,FLQuant-method genFLStock,FLStock,missing,FLQuant,FLQuant-method genFLStock-methods
compute log-correlation matrixgetAcor getAcor,FLQuant-method getAcor-methods
Get ADMB HessiangetADMBCovariance getADMBHessian
Get covariance matrixgetCov
Get KgetK getK,a4aGr-method getK-methods
Get TPL with ADMB codegetTPL
Get model matrixgetX getX,formula-method getX-methods
hakeGSA7hakeGSA7
hakeGSA7.idxhakeGSA7.idx
index_cd_lenindex_cd_len
index_pt_lenindex_pt_len
index_sp_lenindex_sp_len
Method to convert length-based data to age-basedl2a l2a,FLIndex,a4aGr-method l2a,FLQuant,a4aGr-method l2a,FLStockLen,a4aGr-method l2a-methods
natural mortalitym m,a4aM-method
Model averaging (experimental)ma ma,a4aFitSAs-method ma-methods
Run several stock assessments in a single runmultisca
natural mortalitymvnorm mvrnorm,numeric,a4aM,missing,missing,missing,missing-method
Simulation using copula modelsmvrcop mvrcop,numeric,FLModelSim-method
mvrcopmvrcop for a4aGr mvrcop,numeric,a4aGr-method
mvrnormmvrnorm for a4aGR mvrnorm,numeric,a4aGr,ANY,ANY,ANY,ANY-method mvrnorm,numeric,a4aGr-method
Simulation with a copula model and triangular distributionsmvrtriangle mvrtriangle,numeric,FLModelSim-method
mvrtrianglemvrtriangle for a4aGr mvrtriangle,numeric,a4aGr-method
Check that the second dimension in params is "iter"pars2dim pars2dim,FLModelSim-method pars2dim,FLPar-method pars2dim-methods
plot for fitted catch-at-ageplot for fitted catch-at-age plot,a4aFit,FLStock-method
testingplot for fitted indices-at-age plot,a4aFit,FLIndices-method
Plot of standardized log residualsplot of residuals plot,a4aFitResiduals,missing-method
predict for 'a4aGr'predict for a4aGr predict,a4aGr-method
Predict methods for SCApredict for sca predict,a4aFitSA-method predict,SCAPars-method
qqplot of standardized log residualsqqmath,a4aFitResiduals,missing-method qqplot of residuals
range for a4aM objectsrange<-,a4aM,ANY,numeric-method
redfish length datarfLen
rfLen.stkrfLen.stk
rfTrawl.idxrfTrawl.idx
rfTrawlJmp.idxrfTrawlJmp.idx
rfTrawlTrd.idxrfTrawlTrd.idx
Statistical catch-at-age methodsca sca,FLStock,FLIndex-method sca,FLStock,FLIndices-method sca-methods
Call sca inside the mp functionsca.sa
MCMC settings classgetADMBCallArgs getADMBCallArgs,SCAMCMC-method getADMBCallArgs-methods getN getN,SCAMCMC-method getN-methods mcmc mcmc,SCAMCMC-method mcmc-methods SCAMCMC SCAMCMC,missing-method SCAMCMC-class SCAMCMC-methods
Model parameters classfCovar fCovar,SCAPars-method fCovar-methods fFrml fFrml,SCAPars-method fFrml-methods fmodel fmodel,SCAPars-method fmodel-methods fPars fPars,SCAPars-method fPars-methods iter,SCAPars-method m,SCAPars-method n1model n1model,SCAPars-method n1model-methods propagate,SCAPars-method qCovar qCovar,SCAPars-method qCovar-methods qFrml qFrml,SCAPars-method qFrml-methods qMod qMod,SCAPars-method qMod-methods qmodel qmodel,SCAPars-method qmodel-methods qPars qPars,SCAPars-method qPars-methods SCAPars SCAPars,missing-method SCAPars-class SCAPars-methods srCovar srCovar,SCAPars-method srCovar-methods srFrml srFrml,SCAPars-method srFrml-methods srmodel srmodel,SCAPars-method srmodel-methods srPars srPars,SCAPars-method srPars-methods stkmodel stkmodel,SCAPars-method stkmodel-methods vCovar vCovar,SCAPars-method vCovar-methods vFrml vFrml,SCAPars-method vFrml-methods vMod vMod,SCAPars-method vMod-methods vmodel vmodel,SCAPars-method vmodel-methods vPars vPars,SCAPars-method vPars-methods wt,SCAPars-method
Call a separable SA inside the mp functionsep.sa
shake_lenshake_len
Simulation methods for SCAsimulate simulate,a4aFitSA-method simulate,a4aStkParams-method simulate,SCAPars-method simulate,submodel-method simulate,submodels-method
Southern hake length datasouthernHakeLen
Standardized log residualsstdlogres stdlogres,FLQuant,FLQuant-method stdlogres-methods
Submodel classformula,submodel-method iter,submodel-method params,submodel-method propagate,submodel-method sMod sMod,submodel-method sMod-methods submodel submodel,missing-method submodel-class submodel-methods
Submodels class$<-,submodels,submodel-method corBlock-methods corBlocks corBlocks,submodels-method corBlocks<- corBlocks<-,submodels,list-method formula,submodels-method iter,submodels-method params,submodels-method propagate,submodels-method sMod,submodels-method submodels submodels-class submodels-methods [[<-,submodels,character,missing-method [[<-,submodels,numeric,missing-method
Variance-covariance matrixvcov vcov,a4aFitSA-method vcov,SCAPars-method vcov,submodel-method vcov,submodels-method vcov<-,a4aFitSA,numeric-method vcov<-,a4aStkParams,numeric-method vcov<-,SCAPars,numeric-method vcov<-,submodel,array-method vcov<-,submodel,matrix-method vcov<-,submodel,numeric-method
wireframe plot for FLQuantwireframe plot for FLQuant wireframe,FLQuant,missing-method wireframe,FLQuant-method