Function reference • FLCore

All functions
`AIC(<FLModel>,<numeric>)`	Method AIC
`Arith(<numeric>,<FLArray>)` `Arith(<FLArray>,<numeric>)` `Arith(<FLArray>,<FLArray>)` `Arith(<FLPar>,<FLPar>)` `Arith(<FLArray>,<FLPar>)` `Arith(<FLPar>,<FLArray>)`	Arithmetic operators for FLCore classes
`BIC(<FLModel>)`	Method BIC Bayesian information criterion (BIC) method
`[`(<FLArray>,<ANY>,<ANY>,<ANY>) `[`(<FLArray>,<array>,<missing>,<missing>) `[<-`(<FLArray>,<ANY>,<ANY>,<ANY>) `[<-`(<FLArray>,<ANY>,<ANY>,<FLArray>) `$`(<FLQuant>) `[`(<FLQuantDistr>,<ANY>,<ANY>,<ANY>) `[`(<FLQuantDistr>,<array>,<missing>,<missing>) `[`(<FLPar>,<ANY>,<ANY>,<ANY>) `[`(<FLPar>,<array>,<missing>,<missing>) `[<-`(<FLPar>,<ANY>,<ANY>,<ANY>) `$`(<FLPar>) `$<-`(<FLPar>) `[`(<FLComp>,<ANY>,<ANY>,<ANY>) `[<-`(<FLComp>,<ANY>,<ANY>,<ANY>) `[`(<FLStock>,<ANY>,<ANY>,<ANY>) `[<-`(<FLStock>,<ANY>,<ANY>,<FLStock>) `[`(<FLI>,<ANY>,<ANY>,<ANY>) `[`(<predictModel>,<ANY>,<missing>,<ANY>) `[[<-`(<FLlst>,<ANY>,<missing>) `$<-`(<FLlst>) `[<-`(<FLlst>,<ANY>,<missing>,<ANY>) `[`(<FLlst>,<ANY>,<missing>,<ANY>)	Extract
`FLArray` `FLArray-class`	Class FLArray
`FLBiol()`	Class FLBiol
`FLBiols()`	Class FLBiols
`FLCohort()`	Class FLCohort
`FLCohorts()`	Class FLCohorts
`FLComp` `FLComp-class` `name,FLComp-method` `name` `desc,FLComp-method` `desc` `range,FLComp-method` `range`	Class FLComp
`FLComps` `FLComps-class`	Class FLComps
`FLI` `FLI-class`	Class FLI
`FLIndex()`	Class FLIndex
`FLIndexBiomass()`	Class FLIndexBiomass
`FLIndices()`	Class FLIndices
`FLModel()`	Class FLModel
`FLModelSim()`	Class FLModelSim
`FLModelSims()`	Class FLModelSims
`FLPar()`	Class FLPar
`FLParJK(<ANY>)` `orig(<FLParJK>)`	Class FLParJK
`FLPars()`	Class FLPars
`FLQuant()`	FLQuant class for numerical data
`FLQuantDistr()`	A class for samples of a probability distribution
`FLQuantJK(<ANY>)` `orig(<FLQuantJK>)` `orig(<FLQuants>)`	A class for jackknifing fisheries data
`FLQuantPoint()`	Class FLQuantPoint
`FLQuants()`	Class FLQuants
`FLS` `FLS-class`	Class FLS
`FLSR()`	Class FLSR
`FLSRs()`	`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.
`FLStock()`	Class FLStock
`FLStockLen()`	Class FLStockLen
`FLStocks()`	Class FLStocks
`FLlst()`	Class FLlst
`Funwanted()`	Calculate the discards and landings-associated fishing mortalities
`ricker()` `bevholt()` `bevholtss3()` `segreg()` `geomean()` `shepherd()` `cushing()` `rickerSV()` `bevholtSV()` `shepherdSV()` `bevholtAR1()` `rickerAR1()` `segregAR1()` `rickerCa()` `survRec()` `bevholtsig()`	Stock-Recruitment models
`acc()`	Catch curve estimates of total mortality at age (Z)
`name()` `desc()` `range<-`() `catch()` `catch.n<-`() `catch.wt()` `discards()` `discards.n()` `discards.wt()` `landings()` `landings.n()` `landings.wt()` `m()` `stock()` `stock.n()` `stock.wt()` `m.spwn()` `harvest()` `harvest.spwn()` `mat()` `n()` `m()` `wt()` `fec()` `spwn()` `effort()` `type()` `distr()` `distribution()` `index()` `index.var()` `catch.n()` `catch.wt()` `sel.pattern()` `index.q()` `model()` `logl()` `gr()` `initial()` `logLik()` `vcov<-`() `hessian()` `logerror()` `details()` `residuals<-`() `fitted()` `rec()` `rec.obs()` `catch.q()` `discards.sel()` `landings.sel()` `params()` `catch<-`(<FLS>,<FLQuants>)	accessor and replacement methods for FLCore classes
`adjust(<FLStock>)`	Recalculate to adjust abundances to F and M
`append(<FLQuant>,<FLQuant>)` `append(<FLStock>,<FLStock>)`	Append objects along the year dimension
`apply,FLArray,numeric,function-method` `apply,FLPar,ANY,ANY-method` `apply,FLQuantJK,numeric,function-method` `apply,FLParJK,numeric,function-method`	apply method for FLCore classes
`ar1rlnorm()`	Generates a time series of possible bias-corrected lognormal autocorrelated random values
`bias(<FLQuantJK>)` `bias(<FLParJK>)`	Bias of estimates through jackknife
`bubbles(<formula>,<FLQuant>)` `bubbles(<formula>,<data.frame>)` `bubbles(<formula>,<FLCohort>)` `bubbles(<formula>,<FLQuants>)`	Method Bubbles plot
`catch.n(<FLQuant>)`	catch.n calculation method
`coerce-methods`	Convert Objects Between Classes
`compare()`	A method for comparing FLR objects
`computeLandings()` `computeDiscards()` `computeCatch()` `computeStock()` `computeLandings()` `computeDiscards()` `computeCatch()` `computeStock()`	Methods to compute quantities
`cpue()` `survey()`	cpue, a method to generate an observation of a CPUE index of abundance
`createFLAccesors()`	Create accesor methods for a given class
`datasets` `ple4` `ple4sex` `ple4.biol` `ple4.index` `ple4.indices` `nsher`	FLCore datasets
`dbind()` `qbind()` `ybind()` `ubind()` `sbind()` `abind()` `ibind()`	Methods for binding objects of array classes along a given dimension
`quantSums()` `yearSums()` `unitSums()` `seasonSums()` `areaSums()` `iterSums()` `dimSums()` `quantMeans()` `yearMeans()` `unitMeans()` `seasonMeans()` `areaMeans()` `iterMeans()` `dimMeans()` `quantVars()` `yearVars()` `unitVars()` `seasonVars()` `areaVars()` `iterVars()` `dimVars()` `iterMedians()` `iterCVs()` `iterProb()`	Summaries by dimension
`dims()` `dims()`	Method dims
`drop(<FLArray>)`	drop method for FLCore array-based classes
`evalPredictModel()`	Evaluates a predictModel slot inside the object cointaining it
`exp(<FLQuant>)` `log(<FLQuant>)`	exp and log methods FLCore array-based classes
`getSlotNamesClass()`	Names of slots of a given class
`group` `group,FLQuant,function-method`	Group objects over some index by applying a function over a single dimension
`vonbert()` `ivonbert()` `gompertz()` `richards()`	Growth models
`iav()`	Compute the inter-annual variability of a time series
`intersect(<FLArray>,<FLArray>)`	Returns FLR objects trimmed to their shared dimensions.
`iter()`	Methods iter
`jackknife(<FLQuant>)` `jackknife(<FLQuants>)` `jackknife(<FLModel>)`	Method jackknife
`join()`	Joins objects along a dimensions where dimnames differ
`xyplot(<formula>,<FLQuant>)` `xyplot(<formula>,<FLCohort>)` `xyplot(<formula>,<FLQuants>)` `xyplot(<formula>,<FLComp>)` `bwplot(<formula>,<FLQuant>)` `bwplot(<formula>,<FLComp>)` `dotplot(<formula>,<FLQuant>)` `dotplot(<formula>,<FLComp>)` `barchart(<formula>,<FLQuant>)` `barchart(<formula>,<FLComp>)` `stripplot(<formula>,<FLQuant>)` `stripplot(<formula>,<FLComp>)` `histogram(<formula>,<FLQuant>)` `histogram(<formula>,<FLComp>)` `histogram(<formula>,<FLQuants>)` `densityplot(<formula>,<FLPar>)`	Lattice methods
`indicators.len()` `lenquantile()` `lmax5()` `l95()` `l25()` `lc50()` `lmode()` `lbar()` `lmean()` `lmaxy()` `pmega()` `bheqz()`	Calculate quantile(s) of length distribution
`mase()`	Compute mean absolute scaled error (MASE)
`mbar()`	Computes the mean natural mortality acros the fully selected ages
`metrics()`	Extract simply-defined metrics from compex objects
`mohnMatrix()`	Generate a matrix to compute Mohn's rho for a single metric
`msy()` `bmsy()` `sbmsy()` `fmsy()`	msy: A series of methods to extract or compute MSY-based reference points
`names(<FLArray>)` `names(<FLPar>)` `names<-`(<FLPar>,<character>)	Method names
`%+%` `%-%` `%^%` `%%`(<FLQuant>,<FLQuant>) `%/%`(<FLQuant>,<FLQuant>) `%%`(<FLPar>,<FLQuant>) `%/%`(<FLPar>,<FLQuant>) `%%`(<FLQuant>,<FLPar>) `%/%`(<FLQuant>,<FLPar>) `%%`(<FLPar>,<FLPar>) `%/%`(<FLPar>,<FLPar>) `/`(<FLQuants>,<FLPar>) ``(<FLQuants>,<FLPar>) `/`(<FLQuants>,<FLPars>) ``(<FLQuants>,<FLPars>) `/`(<FLQuants>,<FLQuants>) `*`(<FLQuants>,<FLQuants>) `+`(<FLQuants>,<FLQuants>) `-`(<FLQuants>,<FLQuants>)	FLQuant arithmetic operators that extend objects
`plot(<FLQuant>,<missing>)` `plot(<FLStock>,<missing>)` `plot(<FLBiol>,<missing>)` `plot(<FLIndex>,<missing>)` `plot(<FLSR>,<missing>)` `plot(<FLPar>,<missing>)`	Method plot
`predictModel` `predictModel-methods` `predictModel-class` `predictModel,FLQuants,formula-method` `predictModel,FLQuants,missing-method` `predictModel,FLQuants,character-method` `predictModel,FLQuants,function-method` `predictModel,FLQuants,list-method` `predictModel,missing,ANY-method`	A class for model prediction
`production()`	Returns the computed yearly production
`propagate()`	Method propagate
`properties()`	Returns a series of properties of the fisheries element represented by the class.
`quant()` `quant<-`(<FLArray>,<character>)	Method quant
`quantTotals()`	Methods quantTotals
`readVPAIntercatch()`	Reads a single file with one year of data in VPA format as output by ICES Intercatch
`residuals(<FLQuant>)`	residuals
`rnoise(<numeric>,<FLQuant>)` `rnoise(<numeric>,<missing>)` `rlnoise(<numeric>,<FLQuant>)`	Random noise with different frequencies
`ruleset()`	Set of verify rules for an FLR class
`runstest()`	Computes Runs Test p-values
`show(<FLArray>)`	Method show
`sigma3()`	Compute the 3-sigma limits and the corresponding p-value
`simplify()`	Aggregate or select along unwanted dimensions
`slim()`	Drop unnecesary 'iters'
`split(<FLQuant>,<vector>)` `split(<FLComp>,<vector>)`	splits x along the iter dimension into the groups defined by f.
`splom(<FLPar>,<missing>)`	Method splom
`spread()`	A function to make available list elements inside a function or method
`ssb()`	Calculate or return the Spawning Stock Biomass
`ssb_next()`	Calculate next yera's SSB from survivors and Fbar
`standardUnits()`	Standard units of measurement for a complex class object
`summary(<FLArray>)` `summary(<FLQuantPoint>)` `summary(<FLPar>)` `summary(<FLComp>)` `summary(<FLQuants>)` `summary(<predictModel>)` `summary(<FLBiol>)` `summary(<FLModel>)` `summary(<FLlst>)`	Method summary
`survivors()`	Calculate the survivors of a stock to the next year.
`sweep(<FLArray>)` `sweep(<FLPar>)`	Method sweep for FLCore classes
`tail(<FLQuant>)` `head(<FLQuant>)`	Returns the first and last parts of an FLQuant.
`trim()`	Method trim
`units-FLCore` `units,FLArray-method` `units` `units,FLPar-method` `units` `units,FLComp-method` `units` `units` `units`	Method units
`uom()` `uomUnits()`	uom Units of Measurement
`uomTable`	Table for conversions and operations between units of measurement
`lower()` `upper(<FLModel>)`	Extract and modify the lower and upper FLModel attibutes.
`verify()`	Verify FLR objects
`wireframe(<formula>,<FLQuant>)`	Method wireframe
`z()`	Total mortality z

Reference

All functions