Package: FLCore 2.6.20.9204
![](https://github.com/flr/FLCore/raw/HEAD/man/figures/logo.png)
FLCore: Core Package of FLR, Fisheries Modelling in R
Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.
Authors:
FLCore_2.6.20.9204.tar.gz
FLCore_2.6.20.9204.zip(r-4.5)FLCore_2.6.20.9204.zip(r-4.4)FLCore_2.6.20.9204.zip(r-4.3)
FLCore_2.6.20.9204.tgz(r-4.4-any)FLCore_2.6.20.9204.tgz(r-4.3-any)
FLCore_2.6.20.9204.tar.gz(r-4.5-noble)FLCore_2.6.20.9204.tar.gz(r-4.4-noble)
FLCore_2.6.20.9204.tgz(r-4.4-emscripten)FLCore_2.6.20.9204.tgz(r-4.3-emscripten)
FLCore.pdf |FLCore.html✨
FLCore/json (API)
NEWS
# Install 'FLCore' in R: |
install.packages('FLCore', repos = c('https://ices-tools-prod.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/flr/flcore/issues
- nsher - FLCore datasets
- ple4 - FLCore datasets
- ple4.biol - FLCore datasets
- ple4.index - FLCore datasets
- ple4.indices - FLCore datasets
- ple4sex - FLCore datasets
fisheriesflrfisheries-modelling
Last updated 2 months agofrom:5dac55024c. Checks:OK: 1 WARNING: 6. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 10 2024 |
R-4.5-win | WARNING | Aug 10 2024 |
R-4.5-linux | WARNING | Aug 10 2024 |
R-4.4-win | WARNING | Aug 10 2024 |
R-4.4-mac | WARNING | Aug 10 2024 |
R-4.3-win | WARNING | Aug 10 2024 |
R-4.3-mac | WARNING | Aug 10 2024 |
Exports:%-%%^%%+%%++%%=%ababindabModelabParsacaccadjustageoptagesAICanappendapplyar1deviancesar1rlnormareaMeansareaSumsareaVarsArithas.data.frameas.FLBiolas.FLIndexas.FLQuantas.FLSRas.FLSRsas.FLStockaucbarchartbevholtbevholtAR1bevholtDabevholtsigbevholtss3bevholtSVbheqzbiasbiasedbiomassbiomass_endbiomass_spawnbkeybmsybreaksbubblesbwplotcatchcatch.ncatch.n<-catch.qcatch.q<-catch.selcatch.wtcatch.wt<-catch<-catchescatches<-catchInmaturecatchMaturecbind2ccostccplotcoercecombinecomparecomputeCatchcomputeDcomputeDiscardscomputeHarvestcomputeHessiancomputeLandingscomputeLogLikcomputeQcomputeStockcontrolcontrol<-cor2covcorrectedcostcovarcovar<-cpuecreateFLAccesorscushingcvdbinddensityplotdepletiondescdesc<-detailsdetails<-deviancesdeviances<-dimMeansdimsdimSumsdimVarsdiscardsdiscards.ndiscards.n<-discards.ratiodiscards.ratio<-discards.seldiscards.sel<-discards.wtdiscards.wt<-discards<-discardsRatiodistrdistr<-distributiondistribution<-dividedotplotdropee<-efforteffort<-evalPredictModelexpandfapexfbarfcostfcost<-fecfec<-ffwdfind.original.namefittedfitted<-FLBiolFLBiolsFLCohortFLCohortsFLIndexFLIndexBiomassFLIndicesFLlstFLModelFLModelSimFLModelSimsFLParFLParJKFLParPointFLParsFLQuantFLQuantDistrFLQuantJKFLQuantPointFLQuantsFLSRFLSRsFLStockFLStockLenFLStockRFLStocksfmlefmsyFunwantedFwantedfwdfwdWindowgeomeangetPluralgetSlotNamesClassgompertzgrgr<-grouphalfwidthharvestharvest.spwnharvest.spwn<-harvest<-hessianhessian<-histogramhriavibindifelseindexindex.qindex.q<-index.varindex.var<-index<-indicators.leninitialinitial<-intersectinvALKis.FLQuantis.FLStockiteriter<-iterCVsiterMeansiterMediansiterProbitersiterSumsiterVarsivonbertjackknifejackSummaryjoinknit_print.FLQuantl25l95landingslandings.nlandings.n<-landings.sellandings.sel<-landings.wtlandings.wt<-landings<-lapplylbarlc50leftboundlenquantilelenSamplesleslielmax5lmaxylmeanlmodelogerrorlogerror<-logllogl<-loglAR1logLiklogLik<-loptlowerlower<-lowesslowqlowq<-mm.spwnm.spwn<-m<-masemassmatmat<-mbarmcfmeanmean<-meanagemeanageCatchmeanLifespanmeanwtmeanwtCatchmedianmedian<-mergemetricsmidsmixedsrrmlcmodelmodel.framemodel<-mohnMatrixmsymvrnormnn<-namename<-nlsnoareanoseasonnounitorigparamsparams<-parscaleplotpmegapredictpredictModelpriceprice<-printproductionprofileprofitpropagatepropertiespvqapplyqbindqmaxqminquantquant<-quantilequantMeansquantSumsquantTotalsquantVarsrrange<-rbind2read.FLIndexread.FLIndicesreadADMBreadFLIndexreadFLIndicesreadFLStockreadMFCLreadVPA2BoxreadVPAFilereadVPAIntercatchrecrec.hatrec.obsrec<-recomputeHarvestrefptsrefpts<-residualsresiduals<-revenuergammarhorichardsrickerrickerAR1rickerCarickerSVrightboundrlnoiserlnormrlnormar1rlogrlogstandardrngagerngage<-rngyearrngyear<-rnoisernormrocrpoisrrawrSqrstandardrstudentrulesetrun.inforunstestrwalksbindsbmsysdseasonMeansseasonSumsseasonVarssegregsegregAR1sel.patternsel.pattern<-setPlusGroupsetquantsetunitsshepherdshepherdSVshowsigmasigma3simplifyslimslotssopspsplitsplomspr0spreadspwnspwn<-srsr<-SRModelNameSRNameCodessbssb_endssb_nextssb_startssb<-ssbpurecssfssnstandardUnitsstockstock.nstock.n<-stock.wtstock.wt<-stock<-stripplotsubsetsummarysurveysurvivorssurvprobsurvSRRsvsvModelsvParssweeptailtbteptransformtrimtStS<-tsbtsptypetype<-ubindunitMeansunitsunits<-unitSumsunitVarsuomuomUnitsupdateupperupper<-uppquppq<-varvar<-vbvcostvcost<-vcovvcov<-vecagevecyearverifyvonbertweighted.meanwindowwireframewriteADMBwriteFLStockwtwt<-xyplotybindyearMeansyearMediansyearSampleyearSumsyearTotalsyearVarszzbar
Dependencies:clicolorspacefansifarverggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
FLQuant arithmetic operators that extend objects | % %*%,FLPar,FLPar-method %*%,FLPar,FLQuant-method %*%,FLQuant,FLPar-method %*%,FLQuant,FLQuant-method %+% %+%,FLPar,FLPar-method %+%,FLPar,FLQuant-method %+%,FLQuant,FLPar-method %+%,FLQuant,FLQuant-method %+%-methods %-% %-%,FLPar,FLPar-method %-%,FLPar,FLQuant-method %-%,FLQuant,FLPar-method %-%,FLQuant,FLQuant-method %-%-methods %/%,FLPar,FLPar-method %/%,FLPar,FLQuant-method %/%,FLQuant,FLPar-method %/%,FLQuant,FLQuant-method %^% %^%,FLPar,FLPar-method %^%,FLPar,FLQuant-method %^%,FLQuant,FLPar-method %^%,FLQuant,FLQuant-method %^%-methods *,FLQuants,FLPar-method *,FLQuants,FLPars-method *,FLQuants,FLQuants-method +,FLQuants,FLQuants-method -,FLQuants,FLQuants-method /,FLQuants,FLPar-method /,FLQuants,FLPars-method /,FLQuants,FLQuants-method operators |
Catch curve estimates of total mortality at age (Z) | acc |
accessor and replacement methods for FLCore classes | accessors catch catch.n catch.n<- catch.q catch.q<- catch.wt catch.wt<- catch<- catch<-,FLS,FLQuants-method desc desc<- details details<- discards discards.n discards.n<- discards.sel discards.sel<- discards.wt discards.wt<- discards<- distr distr<- distribution distribution<- effort effort<- fec fec<- fitted fitted<- gr gr<- harvest harvest.spwn harvest.spwn<- harvest<- hessian hessian<- index index.q index.q<- index.var index.var<- index<- initial initial<- landings landings.n landings.n<- landings.sel landings.sel<- landings.wt landings.wt<- landings<- logerror logerror<- logl logl<- logLik logLik<- m m.spwn m.spwn<- m<- mat mat<- model model<- n n<- name name, name<- name<-<- params params, params<- params<-<- range<- rec rec.obs rec.obs<- rec<- residuals<- sel.pattern sel.pattern<- spwn spwn<- stock stock.n stock.n<- stock.wt stock.wt<- stock<- type type<- vcov vcov<- wt wt<- |
Recalculate to adjust abundances to F and M | adjust,FLStock-method |
Age at which a cohort reaches its maximum biomass, calculated by year | ageopt |
Method AIC | AIC AIC,FLModel,missing-method AIC,FLModel,numeric-method |
Append objects along the year dimension | append,FLStock,FLStock-method append-FLCore |
apply method for FLCore classes | apply,FLArray,numeric,function-method apply,FLPar,ANY,ANY-method apply,FLParJK,numeric,function-method apply,FLQuantJK,numeric,function-method |
Generates a time series of possible bias-corrected lognormal autocorrelated random values | ar1rlnorm |
Arithmetic operators for FLCore classes | Arith,FLArray,FLArray-method Arith,FLArray,FLPar-method Arith,FLArray,numeric-method Arith,FLPar,FLArray-method Arith,FLPar,FLPar-method Arith,numeric,FLArray-method |
Convert an FLStock into a list of one or FLSR objects. | as.FLSRs |
Bias of estimates through jackknife | bias bias,FLParJK-method |
Method BIC Bayesian information criterion (BIC) method | BIC BIC,FLModel-method |
Method Bubbles plot | bubbles bubbles,formula,data.frame-method bubbles,formula,FLCohort-method bubbles,formula,FLQuant-method bubbles,formula,FLQuants-method bubbles-methods |
catch.n calculation method | catch.n,FLQuant-method |
Proportion of mature and inmature fish in the catch | catchInmature catchMature |
Convert Objects Between Classes | coerce-methods |
A method for comparing FLR objects | compare |
Methods to compute quantities | compute computeCatch computeCatch,FLS-method computeCatch,FLStock-method computeCatch,FLStockLen-method computeCatch-methods computeDiscards computeDiscards,FLS-method computeDiscards,FLStock-method computeDiscards-methods computeHarvest computeHarvest-methods computeLandings computeLandings,FLS-method computeLandings,FLStock-method computeLandings,FLStockLen-method computeLandings-methods computeStock computeStock,FLS-method computeStock,FLStock-method computeStock,FLStockLen-method computeStock-methods |
Computes fishing mortality from abundances, catches and natural mortality | computeHarvest,FLStock,missing-method |
cpue, a method to generate an observation of a CPUE index of abundance | cpue cpue,FLStock,missing-method cpue,FLStock-method cpue-methods |
Create accesor methods for a given class | createFLAccesors |
FLCore datasets | datasets nsher ple4 ple4.biol ple4.index ple4.indices ple4sex |
Methods for binding objects of array classes along a given dimension | abind dbind dbind,FLArray,FLArray-method dbind-methods ibind qbind sbind ubind ybind |
Method dims | dims dims,FLQuant-method dims-methods |
Summaries by dimension | areaMeans areaMeans,FLQuant-method areaMeans,FLQuantDistr-method areaSums areaSums,FLQuant-method areaSums,FLQuantDistr-method areaVars areaVars,FLQuant-method areaVars,FLQuantDistr-method dimMeans dimSummaries dimSums dimVars iterCVs iterCVs,FLQuant-method iterMeans iterMeans,FLPar-method iterMeans,FLQuant-method iterMeans,FLQuantDistr-method iterMedians iterMedians,FLPar-method iterMedians,FLQuant-method iterMedians,FLQuantDistr-method iterProb iterProb,FLQuant-method iterSums iterSums,FLPar-method iterSums,FLQuant-method iterVars iterVars,FLPar-method iterVars,FLQuant-method iterVars,FLQuantDistr-method quantMeans quantMeans,FLQuant-method quantSums quantSums,FLQuant-method quantSums-methods quantVars quantVars,FLQuant-method quantVars,FLQuantDistr-method seasonMeans seasonMeans,FLQuant-method seasonMeans,FLQuantDistr-method seasonSums seasonSums,FLQuant-method seasonSums,FLQuantDistr-method seasonVars seasonVars,FLQuant-method seasonVars,FLQuantDistr-method unitMeans unitMeans,FLQuant-method unitMeans,FLQuantDistr-method unitSums unitSums,FLQuant-method unitSums,FLQuantDistr-method unitVars unitVars,FLQuant-method unitVars,FLQuantDistr-method yearMeans yearMeans,FLQuant-method yearMeans,FLQuantDistr-method yearMedians yearMedians,FLQuant-method yearSums yearSums,FLQuant-method yearSums,FLQuantDistr-method yearVars yearVars,FLQuant-method yearVars,FLQuantDistr-method |
Compute the ratio of discards to total catch in numbers or weight | discardsRatio |
drop method for FLCore array-based classes | drop,FLArray-method drop,FLQuant-method |
Evaluates a predictModel slot inside the object cointaining it | evalPredictModel |
exp and log methods FLCore array-based classes | exp,FLQuant-method log,FLQuant-method |
Extract | $,FLPar-method $,FLQuant-method $<-,FLlst,ANY-method $<-,FLlst-method $<-,FLPar,ANY-method $<-,FLPar-method Extract [,FLArray,ANY,ANY,ANY-method [,FLArray,array,missing,missing-method [,FLComp,ANY,ANY,ANY-method [,FLI,ANY,ANY,ANY-method [,FLlst,ANY,missing,ANY-method [,FLPar,ANY,ANY,ANY-method [,FLPar,array,missing,missing-method [,FLQuantDistr,ANY,ANY,ANY-method [,FLQuantDistr,array,missing,missing-method [,FLStock,ANY,ANY,ANY-method [,predictModel,ANY,missing,ANY-method [<-,FLArray,ANY,ANY,ANY-method [<-,FLArray,ANY,ANY,FLArray-method [<-,FLComp,ANY,ANY,ANY-method [<-,FLlst,ANY,missing,ANY-method [<-,FLPar,ANY,ANY,ANY-method [<-,FLStock,ANY,ANY,FLStock-method [[<-,FLlst,ANY,missing,ANY-method [[<-,FLlst,ANY,missing-method `[<-,FLArray,ANY,ANY,ANY-method` `[<-,FLArray,ANY,ANY,FLArray-method` |
Project forward an FLStock for a fbar target | ffwd |
Class FLArray | FLArray FLArray-class |
Class FLBiol | desc,FLBiol-method desc<-,FLBiol,character-method fec,FLBiol-method fec<-,FLBiol,FLQuant-method FLBiol FLBiol,FLQuant-method FLBiol,missing-method FLBiol-class FLBiol-methods FLBiolcpp-class m,FLBiol-method m<-,FLBiol,FLQuant-method n,FLBiol-method n<-,FLBiol,FLQuant-method name,FLBiol-method name<-,FLBiol,character-method range,FLBiol-method range<-,FLBiol,numeric-method spwn,FLBiol-method spwn<-,FLBiol,FLQuant-method wt,FLBiol-method wt<-,FLBiol,FLQuant-method |
Class FLBiols | FLBiols FLBiols,FLBiol-method FLBiols,list-method FLBiols,missing-method FLBiols-class FLBiols-methods |
Class FLCohort | FLCohort FLCohort,array-method FLCohort,FLCohort-method FLCohort,FLQuant-method FLCohort,missing-method FLCohort,vector-method FLCohort-class FLCohort-methods |
Class FLCohorts | FLCohorts FLCohorts,ANY-method FLCohorts,FLCohorts-method FLCohorts,list-method FLCohorts,missing-method FLCohorts-class FLCohorts-methods |
Class FLComp | desc,FLComp-method desc<-,FLComp,character-method FLComp FLComp-class name,FLComp-method name<-,FLComp,character-method range,FLComp-method range<-,FLComp,numeric-method |
Class FLComps | FLComps FLComps-class |
Class FLI | FLI FLI-class |
Class FLIndex | catch.n,FLIndex-method catch.n<-,FLIndex,FLQuant-method catch.n<-,FLIndex,numeric-method catch.wt,FLIndex-method catch.wt<-,FLIndex,FLQuant-method catch.wt<-,FLIndex,numeric-method desc,FLIndex-method desc<-,FLIndex,character-method distribution,FLIndex-method distribution<-,FLIndex,character-method effort,FLIndex-method effort<-,FLIndex,FLQuant-method FLIndex FLIndex,FLQuant-method FLIndex,missing-method FLIndex-class FLIndex-methods index,FLIndex-method index.q,FLIndex-method index.q<-,FLIndex,FLQuant-method index.q<-,FLIndex,numeric-method index.var,FLIndex-method index.var<-,FLIndex,FLQuant-method index.var<-,FLIndex,numeric-method index<-,FLIndex,FLQuant-method index<-,FLIndex,numeric-method name,FLIndex-method name<-,FLIndex,character-method range,FLIndex-method range<-,FLIndex,numeric-method sel.pattern,FLIndex-method sel.pattern<-,FLIndex,FLQuant-method sel.pattern<-,FLIndex,numeric-method type,FLIndex-method type<-,FLIndex,character-method |
Class FLIndexBiomass | catch.n,FLIndexBiomass-method catch.n<-,FLIndexBiomass,FLQuant-method catch.n<-,FLIndexBiomass,numeric-method catch.wt,FLIndexBiomass-method catch.wt<-,FLIndexBiomass,FLQuant-method catch.wt<-,FLIndexBiomass,numeric-method desc,FLIndexBiomass-method desc<-,FLIndexBiomass,character-method distribution,FLIndexBiomass-method distribution<-,FLIndexBiomass,character-method effort,FLIndexBiomass-method effort<-,FLIndexBiomass,FLQuant-method FLIndexBiomass FLIndexBiomass,FLQuant-method FLIndexBiomass,missing-method FLIndexBiomass-class FLIndexBiomass-methods index,FLIndexBiomass-method index.q,FLIndexBiomass-method index.q<-,FLIndexBiomass,FLQuant-method index.q<-,FLIndexBiomass,numeric-method index.var,FLIndexBiomass-method index.var<-,FLIndexBiomass,FLQuant-method index.var<-,FLIndexBiomass,numeric-method index<-,FLIndexBiomass,FLQuant-method index<-,FLIndexBiomass,numeric-method name,FLIndexBiomass-method name<-,FLIndexBiomass,character-method range,FLIndexBiomass-method range<-,FLIndexBiomass,numeric-method sel.pattern,FLIndexBiomass-method sel.pattern<-,FLIndexBiomass,FLQuant-method sel.pattern<-,FLIndexBiomass,numeric-method |
Class FLIndices | FLIndices FLIndices,FLI-method FLIndices,list-method FLIndices,missing-method FLIndices-class FLIndices-methods |
Class FLlst | FLlst FLlst,ANY-method FLlst,list-method FLlst,missing-method FLlst-class FLlst-methods |
Class FLModel | FLModel FLModel,character-method FLModel,formula-method FLModel,function-method FLModel,missing-method FLModel-class FLModel-methods |
Class FLModelSim | FLModelSim FLModelSim,character-method FLModelSim,formula-method FLModelSim,function-method FLModelSim,missing-method FLModelSim-class FLModelSim-methods |
Class FLModelSims | FLModelSims FLModelSims,ANY-method FLModelSims,FLModelSims-method FLModelSims,list-method FLModelSims,missing-method FLModelSims-class FLModelSims-methods |
Class FLPar | FLPar FLPar,array-method FLPar,FLPar-method FLPar,missing-method FLPar,vector-method FLPar-class FLPar-methods |
Class FLParJK | FLParJK FLParJK,ANY-method FLParJK-class orig,FLParJK-method |
Class FLPars | FLPars FLPars,ANY-method FLPars,FLPars-method FLPars,list-method FLPars,missing-method FLPars-class FLPars-methods |
FLQuant class for numerical data | FLQuant FLQuant,array-method FLQuant,FLQuant-method FLQuant,matrix-method FLQuant,missing-method FLQuant,vector-method FLQuant-class FLQuant-methods |
A class for samples of a probability distribution | FLQuantDistr FLQuantDistr,ANY,ANY-method FLQuantDistr,FLQuant,FLQuant-method FLQuantDistr-class FLQuantDistr-methods |
A class for jackknifing fisheries data | FLQuantJK FLQuantJK,ANY-method FLQuantJK-class orig,FLQuantJK-method orig,FLQuants-method |
Class FLQuantPoint | FLQuantPoint FLQuantPoint,FLQuant-method FLQuantPoint,missing-method FLQuantPoint-class FLQuantPoint-methods lowq,FLQuantPoint-method lowq<-,FLQuantPoint,FLQuant-method mean,FLQuantPoint-method mean<-,FLQuantPoint,FLQuant-method median,FLQuantPoint-method median<-,FLQuantPoint,FLQuant-method n,FLQuantPoint-method quantile,FLQuantPoint-method uppq,FLQuantPoint-method uppq<-,FLQuantPoint,FLQuant-method var,FLQuantPoint-method var<-,FLQuantPoint,FLQuant-method |
Class FLQuants | FLQuants FLQuants,ANY-method FLQuants,FLComp-method FLQuants,FLQuants-method FLQuants,list-method FLQuants,missing-method FLQuants-class FLQuants-methods |
Class FLS | FLS FLS-class |
Class FLSR | covar,FLSR-method covar<-,FLSR,FLQuants-method desc,FLSR-method desc<-,FLSR,character-method details,FLSR-method details<-,FLSR,list-method distribution,FLSR-method distribution<-,FLSR,character-method distribution<-,FLSR,factor-method fitted,FLSR-method fitted<-,FLSR,FLArray-method fitted<-,FLSR,numeric-method FLSR FLSR,ANY-method FLSR,missing-method FLSR-class FLSR-methods gr,FLSR-method gr<-,FLSR,function-method hessian,FLSR-method hessian<-,FLSR,array-method initial,FLSR-method initial<-,FLSR,function-method logl,FLSR-method logl<-,FLSR,function-method logLik,FLSR-method logLik<-,FLSR,logLik-method logLik<-,FLSR,numeric-method model,FLSR-method model<-,FLSR,character-method model<-,FLSR,formula-method model<-,FLSR,function-method model<-,FLSR,list-method name,FLSR-method name<-,FLSR,character-method params,FLSR-method params<-,FLSR,FLPar-method range,FLSR-method range<-,FLSR,numeric-method rec,FLSR-method rec<-,FLSR,FLQuant-method rec<-,FLSR,numeric-method residuals,FLSR-method residuals<-,FLSR,FLArray-method residuals<-,FLSR,numeric-method ssb,FLSR-method ssb<-,FLSR,FLQuant-method ssb<-,FLSR,numeric-method vcov,FLSR-method vcov<-,FLSR,array-method |
'FLSRS' is a class that extends 'list' through 'FLlst' but implements a set of features that give a little bit more structure to list objects. The elements of 'FLSRs' must all be of class 'FLSR'. It implements a lock mechanism that, when turned on, does not allow the user to increase or decrease the object length. | FLSRs FLSRs,ANY-method FLSRs,FLSR-method FLSRs,list-method FLSRs,missing-method FLSRs-class FLSRs-methods |
Class FLStock | catch,FLStock-method catch.n,FLStock-method catch.n<-,FLStock,FLQuant-method catch.n<-,FLStock,numeric-method catch.wt,FLStock-method catch.wt<-,FLStock,FLQuant-method catch.wt<-,FLStock,numeric-method catch<-,FLStock,FLQuant-method catch<-,FLStock,FLQuants-method catch<-,FLStock,numeric-method desc,FLStock-method desc<-,FLStock,character-method discards,FLStock-method discards.n,FLStock-method discards.n<-,FLStock,FLQuant-method discards.n<-,FLStock,numeric-method discards.wt,FLStock-method discards.wt<-,FLStock,FLQuant-method discards.wt<-,FLStock,numeric-method discards<-,FLStock,FLQuant-method discards<-,FLStock,numeric-method FLStock FLStock,FLQuant-method FLStock,FLQuants-method FLStock,missing-method FLStock-class FLStock-methods harvest,FLStock-method harvest.spwn,FLStock-method harvest.spwn<-,FLStock,FLQuant-method harvest.spwn<-,FLStock,numeric-method harvest<-,FLStock,character-method harvest<-,FLStock,FLQuant-method harvest<-,FLStock,numeric-method landings,FLStock-method landings.n,FLStock-method landings.n<-,FLStock,FLQuant-method landings.n<-,FLStock,numeric-method landings.wt,FLStock-method landings.wt<-,FLStock,FLQuant-method landings.wt<-,FLStock,numeric-method landings<-,FLStock,FLQuant-method landings<-,FLStock,numeric-method m,FLStock-method m.spwn,FLStock-method m.spwn<-,FLStock,FLQuant-method m.spwn<-,FLStock,numeric-method m<-,FLStock,FLQuant-method m<-,FLStock,numeric-method mat,FLStock-method mat<-,FLStock,FLQuant-method mat<-,FLStock,numeric-method name,FLStock-method name<-,FLStock,character-method range,FLStock-method range<-,FLStock,numeric-method stock,FLStock-method stock.n,FLStock-method stock.n<-,FLStock,FLQuant-method stock.n<-,FLStock,numeric-method stock.wt,FLStock-method stock.wt<-,FLStock,FLQuant-method stock.wt<-,FLStock,numeric-method stock<-,FLStock,FLQuant-method stock<-,FLStock,numeric-method |
Class FLStockLen | catch,FLStockLen-method catch.n,FLStockLen-method catch.n<-,FLStockLen,FLQuant-method catch.n<-,FLStockLen,numeric-method catch.wt,FLStockLen-method catch.wt<-,FLStockLen,FLQuant-method catch.wt<-,FLStockLen,numeric-method catch<-,FLStockLen,FLQuant-method catch<-,FLStockLen,numeric-method desc,FLStockLen-method desc<-,FLStockLen,character-method discards,FLStockLen-method discards.n,FLStockLen-method discards.n<-,FLStockLen,FLQuant-method discards.n<-,FLStockLen,numeric-method discards.wt,FLStockLen-method discards.wt<-,FLStockLen,FLQuant-method discards.wt<-,FLStockLen,numeric-method discards<-,FLStockLen,FLQuant-method discards<-,FLStockLen,numeric-method FLStockLen FLStockLen,FLQuant-method FLStockLen,missing-method FLStockLen-class FLStockLen-methods halfwidth,FLStockLen-method halfwidth<-,FLStockLen,-method harvest,FLStockLen-method harvest.spwn,FLStockLen-method harvest.spwn<-,FLStockLen,FLQuant-method harvest.spwn<-,FLStockLen,numeric-method harvest<-,FLStockLen,character-method harvest<-,FLStockLen,FLQuant-method harvest<-,FLStockLen,numeric-method landings,FLStockLen-method landings.n,FLStockLen-method landings.n<-,FLStockLen,FLQuant-method landings.n<-,FLStockLen,numeric-method landings.wt,FLStockLen-method landings.wt<-,FLStockLen,FLQuant-method landings.wt<-,FLStockLen,numeric-method landings<-,FLStockLen,FLQuant-method landings<-,FLStockLen,numeric-method m,FLStockLen-method m.spwn,FLStockLen-method m.spwn<-,FLStockLen,FLQuant-method m.spwn<-,FLStockLen,numeric-method m<-,FLStockLen,FLQuant-method m<-,FLStockLen,numeric-method mat,FLStockLen-method mat<-,FLStockLen,FLQuant-method mat<-,FLStockLen,numeric-method name,FLStockLen-method name<-,FLStockLen,character-method range,FLStockLen-method range<-,FLStockLen,numeric-method stock,FLStockLen-method stock.n,FLStockLen-method stock.n<-,FLStockLen,FLQuant-method stock.n<-,FLStockLen,numeric-method stock.wt,FLStockLen-method stock.wt<-,FLStockLen,FLQuant-method stock.wt<-,FLStockLen,numeric-method stock<-,FLStockLen,FLQuant-method stock<-,FLStockLen,numeric-method |
Class FLStocks | FLStocks FLStocks,ANY-method FLStocks,FLStock-method FLStocks,list-method FLStocks,missing-method FLStocks-class FLStocks-methods |
Extract and modify the recruitment time series | FUNCTION |
Calculate the discards and landings-associated fishing mortalities | Funwanted |
Extend a FLR object along the year dimension and set future assumed values | fwdWindow fwdWindow,FLStock,missing-method |
Names of slots of a given class | getSlotNamesClass |
Group objects over some index by applying a function over a single dimension | group group,FLQuant,function-method |
Compute the inter-annual variability of a time series | iav |
Calculate quantile(s) of length distribution | bheqz indicators.len l25 l95 lbar lc50 lenquantile lmax5 lmaxy lmean lmode pmega |
Returns FLR objects trimmed to their shared dimensions. | intersect |
Methods iter | iter iter,FLArray-method iter,FLCohort,ANY-method iter,FLQuant,ANY-method iter-methods |
Method jackknife | jackknife jackknife,FLModel-method jackknife,FLQuant-method jackknife,FLQuants-method jackknife-methods |
Joins objects along a dimensions where dimnames differ | join join,FLQuant,FLQuant-method join,FLQuants,missing-method |
Lattice methods | barchart,formula,FLComp-method barchart,formula,FLQuant-method bwplot,formula,FLComp-method bwplot,formula,FLQuant-method densityplot,formula,FLPar-method dotplot,formula,FLComp-method dotplot,formula,FLQuant-method histogram,formula,FLComp-method histogram,formula,FLQuant-method histogram,formula,FLQuants-method lattice lattice-FLCore stripplot,formula,FLComp-method stripplot,formula,FLQuant-method xyplot,formula,FLCohort-method xyplot,formula,FLComp-method xyplot,formula,FLQuant-method xyplot,formula,FLQuants-method |
Compute mean absolute scaled error (MASE) | mase mase,FLIndices,list-method mase,FLQuant,FLQuants-method |
Computes the mean natural mortality acros the fully selected ages | mbar |
Calculate the mean age in the stock and catch | meanage meanageCatch |
Calculate the mean weight in stock and catch | meanwt meanwtCatch |
Extract simply-defined metrics from compex objects | metrics metrics,FLComp,list-method metrics,FLS,missing-method metrics-methods |
Generate a matrix to compute Mohn's rho for a single metric | mohnMatrix |
msy: A series of methods to extract or compute MSY-based reference points | bmsy bmsy-methods fmsy fmsy-methods msy msy-methods sbmsy sbmsy-methods |
Method names | names names,FLArray-method names,FLPar-method names<-,FLPar,character-method |
Method plot | plot plot,FLBiol,missing-method plot,FLCohort,missing-method plot,FLIndex,missing-method plot,FLIndices,missing-method plot,FLPar,missing-method plot,FLQuant,missing-method plot,FLQuantPoint,missing-method plot,FLSR,missing-method plot,FLStock,missing-method plot,FLStocks,FLPar-method plot,FLStocks,missing-method |
A class for model prediction | predictModel predictModel,FLQuants,character-method predictModel,FLQuants,formula-method predictModel,FLQuants,function-method predictModel,FLQuants,list-method predictModel,FLQuants,missing-method predictModel,missing,ANY-method predictModel-class predictModel-methods |
Returns the computed yearly production | production production,FLStock-method |
Method propagate | propagate propagate,FLQuant-method propagate-methods |
Returns a series of properties of the fisheries element represented by the class. | properties |
Method quant | quant quant,FLArray-method quant-methods quant<-,FLArray,character-method |
Methods quantTotals | quantTotals quantTotals-methods yearTotals yearTotals-methods |
Reads a single file with one year of data in VPA format as output by ICES Intercatch | readVPAIntercatch |
residuals | residuals-FLQuant |
Random noise with different frequencies | rlnoise rlnoise,numeric,FLQuant-method rlnoise,numeric,missing-method rlnoise-method rnoise rnoise,numeric,FLQuant-method rnoise,numeric,missing-method rnoise-method |
Receiver Operating Characteristic (ROC) | auc roc |
Set of verify rules for an FLR class | ruleset ruleset,FLStock-method |
Computes Runs Test p-values | runstest runstest,FLQuant,FLQuant-method runstest,FLQuant,missing-method runstest,FLQuants,FLQuants-method runstest,FLQuants,missing-method runstest,numeric,missing-method runstest,numeric,numeric-method |
Generate a random walk time series from a starting point | rwalk |
Method show | show show,FLArray-method show,FLPar-method show,FLQuants-method |
Aggregate or select along unwanted dimensions | simplify simplify,FLStock-method simplify-methods |
Drop unnecesary 'iters' | slim slim,FLComp-method slim-methods |
splits _x_ along the _iter_ dimension into the groups defined by _f_. | split,FLComp,vector-method split-methods |
Method splom | splom splom,FLPar,missing-method |
A function to make available list elements inside a function or method | spread |
Stock-Recruitment models | ab2sv bevholt bevholt.ar1 bevholt.c.a bevholt.c.b bevholt.d bevholt.ndc Bevholt.SV bevholt.sv bevholtAR1 bevholtDa bevholtsig bevholtss3 bevholtSV cushing geomean logl.ar1 mixedsrr ricker ricker.ar1 ricker.c.a ricker.c.b ricker.d Ricker.SV ricker.sv rickerAR1 rickerCa rickerSV segreg segregAR1 shepherd shepherd.ar1 shepherd.d shepherd.d.ar1 shepherd.ndc shepherd.ndc.ar1 shepherdSV SRModels survRec survSRR sv2ab |
Calculate or return the Spawning Stock Biomass | ssb ssb,FLBiol-method ssb,FLStock-method ssb-FLBiol,method ssb-methods |
Calculate next yera's SSB from survivors and Fbar | ssb_next |
Standard units of measurement for a complex class object | standardUnits standardUnits,character-method standardUnits,FLBiol-method standardUnits,FLS-method |
Method summary | summary,FLArray-method summary,FLBiol-method summary,FLComp-method summary,FLlst-method summary,FLlst-methods summary,FLModel-method summary,FLPar-method summary,FLQuantPoint-method summary,FLQuants-method summary,FLQuants-methods summary,predictModel-method |
A method to generate observations of abundance at age. | survey survey,FLStock,FLIndex-method survey,FLStock,FLIndexBiomass-method survey,FLStock,FLIndices-method survey,FLStock,missing-method |
Calculate the survivors of a stock to the next year. | survivors |
Method sweep for FLCore classes | sweep,FLArray-method sweep,FLPar-method |
Returns the first and last parts of an FLQuant. | head,FLQuant-method tail,FLQuant-method |
Method trim | trim trim,FLArray-method trim,FLBiol-method trim,FLComp-method trim,FLS-method trim-methods |
Method units | setunits units,FLArray-method units,FLComp-method units,FLPar-method units-FLCore units<-,FLArray,character-method units<-,FLComp,character-method units<-,FLComp,function-method units<-,FLComp,list-method units<-,FLPar,character-method |
uom Units of Measurement | uom uomUnits |
Table for conversions and operations between units of measurement | uomTable |
Extract and modify the _lower_ and _upper_ FLModel attibutes. | lower lower,FLModel-method lower-methods lower<- lower<-,FLModel,numeric-method lower<--methods upper upper,FLModel-method upper-methods upper<- upper<-,FLModel,numeric-method upper<--methods upperlower |
Verify FLR objects | verify verify,FLComp-method verify,FLStock-method |
Growth models | gompertz ivonbert richards vonbert |
Weighted means along a FLQuants. | weighted.mean,FLQuants,FLQuants-method |
Method wireframe | wireframe wireframe,FLQuant-method |
Samples along the year dimension | yearSample |
Total mortality z | z z,FLS-method z-methods |