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>) `[`(<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

Class FLArray

FLBiol()

Class FLBiol

FLBiols()

Class FLBiols

FLCohort()

Class FLCohort

FLCohorts()

Class FLCohorts

FLComp

Class FLComp

FLComps

Class FLComps

FLI

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

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

ricker() bevholt() bevholtss3() segreg() geomean() shepherd() cushing() rickerSV() bevholtSV() shepherdSV() bevholtAR1() rickerAR1() segregAR1() rickerCa() survRec()

Stock-Recruitment models

name() desc() `range<-`() `units<-`() 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

flq() flqp() flqd() flc() flp() fls() flsl() fli() flib() flsr() flqs() flcs() flss() flis() flps() flb() flbs() flms() flmss() pm()

Short aliases for most FLCore classes construction methods

apply(<FLArray>,<numeric>,<function>) apply(<FLPar>,<ANY>,<ANY>) apply(<FLQuantJK>,<numeric>,<function>) apply(<FLParJK>,<numeric>,<function>)

apply method for FLCore classes

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

coerce-methods

Convert Objects Between Classes

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

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

iter()

Methods iter

jackknife(<FLQuant>) jackknife(<FLQuants>) jackknife(<FLModel>)

Method jackknife

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

metrics()

Extract simply-defined metrics from compex objects

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>)

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(<FLQuants>,<formula>) predictModel(<FLQuants>,<missing>) predictModel(<FLQuants>,<character>) predictModel(<FLQuants>,<function>) predictModel(<missing>,<ANY>)

A class for model prediction

quant() `quant<-`(<FLArray>,<character>)

Method quant

quantTotals()

Methods quantTotals

rnoise(<numeric>,<FLQuant>)

Random noise with different frequencies

ruleset()

Set of verify rules for an FLR class

show(<FLArray>)

Method show

simplify()

Aggregate or select along unwanted dimensions

slim()

Drop unnecesary 'iters'

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

summary(<FLArray>) summary(<FLQuantPoint>) summary(<FLPar>) summary(<FLComp>) summary(<FLQuants>) summary(<predictModel>) summary(<FLBiol>) summary(<FLModel>) summary(<FLlst>)

Method summary

sweep(<FLArray>) sweep(<FLPar>)

Method sweep for FLCore classes

trim()

Method trim

units(<FLArray>)

Method units

uom() uomUnits()

uom 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