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AIC(<FLModel>,<numeric>)
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Method AIC |
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Arith(<numeric>,<FLArray>) Arith(<FLArray>,<numeric>) Arith(<FLArray>,<FLArray>) Arith(<FLPar>,<FLPar>) Arith(<FLArray>,<FLPar>) Arith(<FLPar>,<FLArray>)
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Arithmetic operators for FLCore classes |
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BIC(<FLModel>)
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Method BIC
Bayesian information criterion (BIC) method |
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`[`(<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>)
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Extract |
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FLArray
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Class FLArray |
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FLBiol()
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Class FLBiol |
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FLBiols()
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Class FLBiols |
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FLCohort()
|
Class FLCohort |
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FLCohorts()
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Class FLCohorts |
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FLComp
|
Class FLComp |
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FLComps
|
Class FLComps |
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FLI
|
Class FLI |
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FLIndex()
|
Class FLIndex |
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FLIndexBiomass()
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Class FLIndexBiomass |
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FLIndices()
|
Class FLIndices |
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FLModel()
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Class FLModel |
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FLModelSim()
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Class FLModelSim |
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FLModelSims()
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Class FLModelSims |
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FLPar()
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Class FLPar |
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FLParJK(<ANY>) orig(<FLParJK>)
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Class FLParJK |
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FLPars()
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Class FLPars |
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FLQuant()
|
FLQuant class for numerical data |
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FLQuantDistr()
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A class for samples of a probability distribution |
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FLQuantJK(<ANY>) orig(<FLQuantJK>) orig(<FLQuants>)
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A class for jackknifing fisheries data |
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FLQuantPoint()
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Class FLQuantPoint |
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FLQuants()
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Class FLQuants |
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FLS
|
Class FLS |
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FLSR()
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Class FLSR |
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FLSRs()
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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.
|
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FLStock()
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Class FLStock |
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FLStockLen()
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Class FLStockLen |
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FLStocks()
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Class FLStocks |
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FLlst()
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Class FLlst |
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Funwanted()
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Calculate the discards and landings-associated fishing mortalities |
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ricker() bevholt() bevholtss3() segreg() geomean() shepherd() cushing() rickerSV() bevholtSV() shepherdSV() bevholtAR1() rickerAR1() segregAR1() rickerCa() survRec()
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Stock-Recruitment models |
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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>)
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accessor and replacement methods for FLCore classes |
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adjust(<FLStock>)
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Recalculate to adjust abundances to F and M |
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append(<FLQuant>,<FLQuant>) append(<FLStock>,<FLStock>)
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Append objects along the year dimension |
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apply(<FLArray>,<numeric>,<`function`>) apply(<FLPar>,<ANY>,<ANY>) apply(<FLQuantJK>,<numeric>,<`function`>) apply(<FLParJK>,<numeric>,<`function`>)
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apply method for FLCore classes |
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ar1rlnorm()
|
Generates a time series of possible bias-corrected lognormal autocorrelated random values |
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bias(<FLQuantJK>) bias(<FLParJK>)
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Bias of estimates through jackknife |
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bubbles(<formula>,<FLQuant>) bubbles(<formula>,<data.frame>) bubbles(<formula>,<FLCohort>) bubbles(<formula>,<FLQuants>)
|
Method Bubbles plot |
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catch.n(<FLQuant>)
|
catch.n calculation method |
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coerce-methods
|
Convert Objects Between Classes |
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compare()
|
A method for comparing FLR objects |
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computeLandings() computeDiscards() computeCatch() computeStock() computeLandings() computeDiscards() computeCatch() computeStock()
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Methods to compute quantities |
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cpue() survey()
|
cpue, a method to generate an observation of a CPUE index of abundance |
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createFLAccesors()
|
Create accesor methods for a given class |
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datasets
|
FLCore datasets |
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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()
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Summaries by dimension |
|
dims() dims()
|
Method dims |
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drop(<FLArray>)
|
drop method for FLCore array-based classes |
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evalPredictModel()
|
Evaluates a predictModel slot inside the object cointaining it |
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exp(<FLQuant>) log(<FLQuant>)
|
exp and log methods FLCore array-based classes |
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getSlotNamesClass()
|
Names of slots of a given class |
|
iav()
|
Compute the inter-annual variability of a time series |
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intersect(<FLArray>,<FLArray>)
|
Returns FLR objects trimmed to their shared dimensions. |
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iter()
|
Methods iter |
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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 |
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mase()
|
Compute mean absolute scaled error (MASE) |
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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(<FLQuants>,<formula>) predictModel(<FLQuants>,<missing>) predictModel(<FLQuants>,<character>) predictModel(<FLQuants>,<`function`>) predictModel(<FLQuants>,<list>) predictModel(<missing>,<ANY>)
|
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(<FLArray>) `units<-`(<FLArray>,<character>) units(<FLPar>) `units<-`(<FLPar>,<character>) units(<FLComp>) `units<-`(<FLComp>,<list>) `units<-`(<FLComp>,<character>) `units<-`(<FLComp>,<`function`>)
|
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 |