Function reference • FLCore

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