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