Package: FLCore 2.6.20.9204

Iago Mosqueira

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:Iago Mosqueira [cre], Laurence T. Kell [aut], Philippe Grosjean [aut]

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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

Datasets:

nsher - FLCore datasets
ple4 - FLCore datasets
ple4.biol - FLCore datasets
ple4.index - FLCore datasets
ple4.indices - FLCore datasets
ple4sex - FLCore datasets

On CRAN:

fisheries flr fisheries-modelling

477 exports 14 stars 4.22 score 29 dependencies 23 dependents 650 scripts 61 downloads

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:%-%%^%%+%%++%%=%ab abind abModel abPars ac acc adjust ageopt ages AIC an append apply ar1deviances ar1rlnorm areaMeans areaSums areaVars Arith as.data.frame as.FLBiol as.FLIndex as.FLQuant as.FLSR as.FLSRs as.FLStock auc barchart bevholt bevholtAR1 bevholtDa bevholtsig bevholtss3 bevholtSV bheqz bias biased biomass biomass_end biomass_spawn bkey bmsy breaks bubbles bwplot catch catch.n catch.n<-catch.q catch.q<-catch.sel catch.wt catch.wt<-catch<-catches catches<-catchInmature catchMature cbind2 ccost ccplot coerce combine compare computeCatch computeD computeDiscards computeHarvest computeHessian computeLandings computeLogLik computeQ computeStock control control<-cor2cov corrected cost covar covar<-cpue createFLAccesors cushing cv dbind densityplot depletion desc desc<-details details<-deviances deviances<-dimMeans dims dimSums dimVars discards discards.n discards.n<-discards.ratio discards.ratio<-discards.sel discards.sel<-discards.wt discards.wt<-discards<-discardsRatio distr distr<-distribution distribution<-divide dotplot drop e e<-effort effort<-evalPredictModel expand fapex fbar fcost fcost<-fec fec<-ffwd find.original.name fitted fitted<-FLBiol FLBiols FLCohort FLCohorts FLIndex FLIndexBiomass FLIndices FLlst FLModel FLModelSim FLModelSims FLPar FLParJK FLParPoint FLPars FLQuant FLQuantDistr FLQuantJK FLQuantPoint FLQuants FLSR FLSRs FLStock FLStockLen FLStockR FLStocks fmle fmsy Funwanted Fwanted fwd fwdWindow geomean getPlural getSlotNamesClass gompertz gr gr<-group halfwidth harvest harvest.spwn harvest.spwn<-harvest<-hessian hessian<-histogram hr iav ibind ifelse index index.q index.q<-index.var index.var<-index<-indicators.len initial initial<-intersect invALK is.FLQuant is.FLStock iter iter<-iterCVs iterMeans iterMedians iterProb iters iterSums iterVars ivonbert jackknife jackSummary join knit_print.FLQuant l25 l95 landings landings.n landings.n<-landings.sel landings.sel<-landings.wt landings.wt<-landings<-lapply lbar lc50 leftbound lenquantile lenSamples leslie lmax5 lmaxy lmean lmode logerror logerror<-logl logl<-loglAR1 logLik logLik<-lopt lower lower<-lowess lowq lowq<-m m.spwn m.spwn<-m<-mase mass mat mat<-mbar mcf mean mean<-meanage meanageCatch meanLifespan meanwt meanwtCatch median median<-merge metrics mids mixedsrr mlc model model.frame model<-mohnMatrix msy mvrnorm n n<-name name<-nls noarea noseason nounit orig params params<-parscale plot pmega predict predictModel price price<-print production profile profit propagate properties pv qapply qbind qmax qmin quant quant<-quantile quantMeans quantSums quantTotals quantVars r range<-rbind2 read.FLIndex read.FLIndices readADMB readFLIndex readFLIndices readFLStock readMFCL readVPA2Box readVPAFile readVPAIntercatch rec rec.hat rec.obs rec<-recomputeHarvest refpts refpts<-residuals residuals<-revenue rgamma rho richards ricker rickerAR1 rickerCa rickerSV rightbound rlnoise rlnorm rlnormar1 rlog rlogstandard rngage rngage<-rngyear rngyear<-rnoise rnorm roc rpois rraw rSq rstandard rstudent ruleset run.info runstest rwalk sbind sbmsy sd seasonMeans seasonSums seasonVars segreg segregAR1 sel.pattern sel.pattern<-setPlusGroup setquant setunits shepherd shepherdSV show sigma sigma3 simplify slim slots sop sp split splom spr0 spread spwn spwn<-sr sr<-SRModelName SRNameCode ssb ssb_end ssb_next ssb_start ssb<-ssbpurec ssf ssn standardUnits stock stock.n stock.n<-stock.wt stock.wt<-stock<-stripplot subset summary survey survivors survprob survSRR sv svModel svPars sweep tail tb tep transform trim tS tS<-tsb tsp type type<-ubind unitMeans units units<-unitSums unitVars uom uomUnits update upper upper<-uppq uppq<-var var<-vb vcost vcost<-vcov vcov<-vecage vecyear verify vonbert weighted.mean window wireframe writeADMB writeFLStock wt wt<-xyplot ybind yearMeans yearMedians yearSample yearSums yearTotals yearVars z zbar

Dependencies:cli colorspace fansi farver ggplot2 glue gtable isoband iterators labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig R6 RColorBrewer rlang scales tibble utf8 vctrs viridisLite withr

Citation

Development and contributors

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