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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() n(<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
rec(<FLStock>)
Extract and modify the recruitment time series
Funwanted()
Calculate the discards and landings-associated fishing mortalities
ricker() bevholt() bevholtDa() bevholtss3() segreg() geomean() shepherd() cushing() rickerSV() bevholtSV() shepherdSV() bevholtAR1() rickerAR1() segregAR1() rickerCa() survRec() bevholtsig() mixedsrr()
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
ageopt(<FLStock>)
Age at which a cohort reaches its maximum biomass, calculated by year
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
as.FLSRs()
Convert an FLStock into a list of one or FLSR objects.
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
catchInmature() catchMature()
Proportion of mature and inmature fish in the catch
coerce-methods
Convert Objects Between Classes
compare()
A method for comparing FLR objects
computeLandings() computeDiscards() computeCatch() computeStock() computeHarvest() computeLandings() computeDiscards() computeCatch() computeStock()
Methods to compute quantities
computeHarvest(<FLStock>,<missing>)
Computes fishing mortality from abundances, catches and natural mortality
cpue()
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() yearMedians() yearMeans() unitMeans() seasonMeans() areaMeans() iterMeans() dimMeans() quantVars() yearVars() unitVars() seasonVars() areaVars() iterVars() dimVars() iterMedians() iterCVs() iterProb()
Summaries by dimension
dims() dims()
Method dims
discardsRatio()
Compute the ratio of discards to total catch in numbers or weight
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
ffwd()
Project forward an FLStock for a fbar target
fwdWindow()
Extend a FLR object along the year dimension and set future assumed values
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
meanage() meanageCatch()
Calculate the mean age in the stock and catch
meanwt() meanwtCatch()
Calculate the mean weight in stock and catch
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
roc() auc()
Receiver Operating Characteristic (ROC)
ruleset()
Set of verify rules for an FLR class
runstest()
Computes Runs Test p-values
rwalk()
Generate a random walk time series from a starting point
show(<FLArray>)
Method show
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
survey()
A method to generate observations of abundance at age.
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 setunits 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
weighted.mean(<FLQuants>,<FLQuants>)
Weighted means along a FLQuants.
wireframe(<formula>,<FLQuant>)
Method wireframe
yearSample()
Samples along the year dimension
z()
Total mortality z