Package: FLa4a 1.8.3.9001
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:
FLa4a_1.8.3.9001.tar.gz
FLa4a_1.8.3.9001.zip(r-4.5)FLa4a_1.8.3.9001.zip(r-4.4)FLa4a_1.8.3.9001.zip(r-4.3)
FLa4a_1.8.3.9001.tgz(r-4.4-any)FLa4a_1.8.3.9001.tgz(r-4.3-any)
FLa4a_1.8.3.9001.tar.gz(r-4.5-noble)FLa4a_1.8.3.9001.tar.gz(r-4.4-noble)
FLa4a_1.8.3.9001.tgz(r-4.4-emscripten)FLa4a_1.8.3.9001.tgz(r-4.3-emscripten)
FLa4a.pdf |FLa4a.html✨
FLa4a/json (API)
NEWS
| # Install 'FLa4a' in R: |
| install.packages('FLa4a', repos = c('https://flr.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/flr/fla4a/issues
Datasets:
- hakeGSA7 - HakeGSA7
- hakeGSA7.idx - HakeGSA7.idx
- index_cd_len - Index_cd_len
- index_pt_len - Index_pt_len
- index_sp_len - Index_sp_len
- rfLen.stk - RfLen.stk
- rfTrawl.idx - RfTrawl.idx
- rfTrawlJmp.idx - RfTrawlJmp.idx
- rfTrawlTrd.idx - RfTrawlTrd.idx
- shake_len - Shake_len
Last updated 1 years agofrom:4bbe0d03bc. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 28 2024 |
| R-4.5-win | WARNING | Aug 28 2024 |
| R-4.5-linux | WARNING | Aug 28 2024 |
| R-4.4-win | WARNING | Aug 28 2024 |
| R-4.4-mac | WARNING | Aug 28 2024 |
| R-4.3-win | WARNING | Aug 28 2024 |
| R-4.3-mac | WARNING | Aug 28 2024 |
Exports:a4aFita4aFitMCMCa4aFitSAa4aFitSAsa4aGra4aMa4aSCAas.mcmcbreakptsbubblesburninclockcoefcoefficientscoefficients<-collapseSeasonscomputeCatchDiagnosticscovardefaultFmoddefaultN1moddefaultQmoddefaultSRmoddefaultVmoddimsdistrdistr<-fCovarfFrmlfitSummfmodelformulaformula<-fParsgenFLIndexgenFLQuantgenFLStockgetAcorgetADMBCallArgsgetADMBCovariancegetADMBHessiangetCovgetKgetNgetTPLgetXgetYidxgrInvModgrInvMod<-grModgrMod<-is.emptyiterl2alevellevel<-mmamodelmvrcopmvrnormmvrtrianglen1modelnitersparamsparams<-parspars2dimplotpredictqCovarqFrmlqmodelqParsqqmathreplaceZerosresidualsscasca.saSCAMCMCSCAParssep.sashapeshape<-simulatesrCovarsrFrmlsrmodelsrParsstdlogresstkmodelsubmodelsubmodelstrendtrend<-vCovarvFrmlvmodelvParswireframewt
Dependencies:ADGofTestassertthatclicodacolorspacecopuladeldirfansifarverFLCoreggplot2gluegridExtragslgtableinterpisobanditeratorsjpeglabelinglatticelatticeExtralifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmenumDerivpcaPPpillarpkgconfigpngpsplineR6RColorBrewerRcppRcppEigenrlangscalesstabledisttibbletriangleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| * 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 class | a4aGr 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 method | a4aInternal |
| Natural mortality class | a4aM 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 class | a4aStkParams 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 FLa4a | assorted 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 |
| Breakpoints | breakpts breakpts,numeric-method breakpts-methods |
| Bubbles plot of standardized log residuals | bubble plot of residuals bubbles,a4aFitResiduals,missing-method |
| Collapse seasons | collapseSeasons |
| Default sub-models | defaultFmod defaultN1mod defaultQmod defaultSRmod defaultSubModels defaultVmod |
| deprecated | a4aSCA deprecated |
| coefficients extract and replacement | coef 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 objects | genFLIndex genFLIndex,FLQuant-method genFLIndex-methods |
| Methods to generate FLQuant objects | genFLQuant genFLQuant,a4aStkParams-method genFLQuant,FLQuant-method genFLQuant,submodel-method genFLQuant,submodels-method genFLQuant-methods |
| Methods to generate FLStock objects | genFLStock genFLStock,FLStock,FLQuant,FLQuant,missing-method genFLStock,FLStock,FLQuant,missing,FLQuant-method genFLStock,FLStock,missing,FLQuant,FLQuant-method genFLStock-methods |
| compute log-correlation matrix | getAcor getAcor,FLQuant-method getAcor-methods |
| Get ADMB Hessian | getADMBCovariance getADMBHessian |
| Get covariance matrix | getCov |
| Get K | getK getK,a4aGr-method getK-methods |
| Get TPL with ADMB code | getTPL |
| Get model matrix | getX getX,formula-method getX-methods |
| hakeGSA7 | hakeGSA7 |
| hakeGSA7.idx | hakeGSA7.idx |
| index_cd_len | index_cd_len |
| index_pt_len | index_pt_len |
| index_sp_len | index_sp_len |
| Method to convert length-based data to age-based | l2a l2a,FLIndex,a4aGr-method l2a,FLQuant,a4aGr-method l2a,FLStockLen,a4aGr-method l2a-methods |
| natural mortality | m m,a4aM-method |
| Model averaging (experimental) | ma ma,a4aFitSAs-method ma-methods |
| natural mortality | mvnorm mvrnorm,numeric,a4aM,missing,missing,missing,missing-method |
| Simulation using copula models | mvrcop mvrcop,numeric,FLModelSim-method |
| mvrcop | mvrcop for a4aGr mvrcop,numeric,a4aGr-method |
| mvrnorm | mvrnorm for a4aGR mvrnorm,numeric,a4aGr,ANY,ANY,ANY,ANY-method mvrnorm,numeric,a4aGr-method |
| Simulation with a copula model and triangular distributions | mvrtriangle mvrtriangle,numeric,FLModelSim-method |
| mvrtriangle | mvrtriangle 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-age | plot for fitted catch-at-age plot,a4aFit,FLStock-method |
| testing | plot for fitted indices-at-age plot,a4aFit,FLIndices-method |
| Plot of standardized log residuals | plot of residuals plot,a4aFitResiduals,missing-method |
| predict for 'a4aGr' | predict for a4aGr predict,a4aGr-method |
| Predict methods for SCA | predict for sca predict,a4aFitSA-method predict,SCAPars-method |
| qqplot of standardized log residuals | qqmath,a4aFitResiduals,missing-method qqplot of residuals |
| range for a4aM objects | range<-,a4aM,ANY,numeric-method |
| redfish length data | rfLen |
| rfLen.stk | rfLen.stk |
| rfTrawl.idx | rfTrawl.idx |
| rfTrawlJmp.idx | rfTrawlJmp.idx |
| rfTrawlTrd.idx | rfTrawlTrd.idx |
| Statistical catch-at-age method | sca sca,FLStock,FLIndex-method sca,FLStock,FLIndices-method sca-methods |
| Call sca inside the mp function | sca.sa |
| MCMC settings class | getADMBCallArgs 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 class | fCovar 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 function | sep.sa |
| shake_len | shake_len |
| Simulation methods for SCA | simulate simulate,a4aFitSA-method simulate,a4aStkParams-method simulate,SCAPars-method simulate,submodel-method simulate,submodels-method |
| Southern hake length data | southernHakeLen |
| Standardized log residuals | stdlogres stdlogres,FLQuant,FLQuant-method stdlogres-methods |
| Submodel class | formula,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 matrix | vcov 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 FLQuant | wireframe plot for FLQuant wireframe,FLQuant,missing-method wireframe,FLQuant-method |