All functions

initialize(<FLiem>) iters(<FLiem>)

S4 class FLiem

FLmse() FLmse() om() `om<-`() tracking() `tracking<-`() control() `control<-`() oem() `oem<-`() args(<FLmse>) `args<-`(<FLmse>,<list>)

S4 class FLmse

FLoem() FLoem() observations() `observations<-`() deviances() `deviances<-`() show(<FLoem>) iter(<FLoem>) combine(<FLoem>,<FLoem>)

Specification for the observation error model (OEM).

FLom() FLom() stock(<FLom>) `stock<-`(<FLom>,<FLStock>) sr(<FLom>) `sr<-`() show(<FLom>) combine(<FLom>,<FLom>) `om<-`(<FLmse>,<FLo>) `tracking<-`(<FLmse>,<FLQuants>) `control<-`(<FLmse>,<mpCtrl>) `oem<-`(<FLmse>,<FLoem>)

A class for an operating model (OM)

bisect()

Bisection search for a forecast target providing a given performance statistic value.

catchSSB.hcr()

A HCR to set total catch based on SSB depletion level

computeFp05()

Calculates the Fbar value giving a maximum probability of ssb being Blim of 5%

cpue.hcr()

cpue.hcr

db()

Creates a single table of output from an FLmse object

debug() undebug(<mseCtrl>,<missing>) undebug(<mpCtrl>,<character>) undebug(<mpCtrl>,<missing>) undebug(<FLo>,<ANY>)

Debugging mse modules

effort.is()

effort implementation function

fixedC.hcr()

A fixed catch HCR

fixedF.hcr()

A fixed target f

fwd.om()

A method to project the operating model (OM)

expandGrid() gridList()

Functions to create grids and lists of model and simulation runs

ices.hcr()

The typical HCR used by ICES

index.hat(<FLIndexBiomass>,<FLStock>)

Predicted index of abundance from abundance estimates

indicator.hcr()

An indicator-based HCR

indicator.is()

indicator implementation function

kobestatistics

Kobe statistics

mcN()

Compute number of necessary Monte Carlo runs

movingF.hcr()

TODO:description

mp()

mp executes a single run of a Management Procedure

initialize(<mpCtrl>) est() `est<-`() phcr() `phcr<-`() hcr() `hcr<-`() isys() `isys<-`() tm() `tm<-`() show(<mpCtrl>) iters(<mpCtrl>) method(<mpCtrl>) `method<-`(<mpCtrl>,<`function`>) `args<-`(<mpCtrl>,<`function`>) debug(<mpCtrl>,<character>)

S4 class mpCtrl

initialize(<mseCtrl>) method() `method<-`() args() `args<-`() show(<mseCtrl>) exists()

S4 class mseCtrl

p4om

FLom object for North sea plaice

perfect.oem()

A perfect observation of catch and abundances-at-age.

perfect.sa()

A perfect 'estimate' of abundances, catches and harvest.

performance(<FLQuants>) performance(<FLStock>) performance(<FLStocks>) performance(<list>) performance(<FLom>)

Compute performance statistics

statistics

Example set of performance statistics

tac.is()

TAC implementation function

tune()

tune