Tools for Running Management Strategy Evaluations using FLR

Documentation for package ‘mse’ version 2.2.1.9025

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-- A --

-- B --

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

-- C --

catchSSB.hcr	A HCR to set total catch based on SSB depletion level
combine-method	Specification for the observation error model (OEM).
combine-method	A class for an operating model (OM)
computeFp05	Calculates the Fbar value giving a maximum probability of ssb being below Blim of 5%
control	S4 class 'FLmse'
control-method	S4 class 'FLmse'
control-methods	S4 class 'FLmse'
control<-	S4 class 'FLmse'
control<--method	A class for an operating model (OM)
control<--methods	S4 class 'FLmse'
cpue.hcr	cpue.hcr

-- D --

db	Creates a single table of output from an FLmse object
debug-method	Debugging mse modules
debug-method	S4 class 'mpCtrl'
debug-mse	Debugging mse modules
deviances	Specification for the observation error model (OEM).
deviances-method	Specification for the observation error model (OEM).
deviances-methods	Specification for the observation error model (OEM).
deviances<-	Specification for the observation error model (OEM).
deviances<--method	Specification for the observation error model (OEM).
deviances<--methods	Specification for the observation error model (OEM).

-- E --

effort.is	effort implementation function
est	S4 class 'mpCtrl'
est-method	S4 class 'mpCtrl'
est-methods	S4 class 'mpCtrl'
est<-	S4 class 'mpCtrl'
est<--method	S4 class 'mpCtrl'
est<--methods	S4 class 'mpCtrl'
exists	S4 class 'mseCtrl'
exists-method	S4 class 'mseCtrl'
expandGrid	Functions to create grids and lists of model and simulation runs

-- F --

fixedC.hcr	A fixed catch HCR
fixedF.hcr	A fixed target f
FLiem	S4 class 'FLiem'
FLiem-class	S4 class 'FLiem'
FLiem-methods	S4 class 'FLiem'
FLmse	S4 class 'FLmse'
FLmse-class	S4 class 'FLmse'
FLmse-methods	S4 class 'FLmse'
FLoem	Specification for the observation error model (OEM).
FLoem-class	Specification for the observation error model (OEM).
FLoem-methods	Specification for the observation error model (OEM).
FLom	A class for an operating model (OM)
FLom-class	A class for an operating model (OM)
FLom-methods	A class for an operating model (OM)
fwd.om	A method to project the operating model (OM)

-- G --

grid	Functions to create grids and lists of model and simulation runs
gridList	Functions to create grids and lists of model and simulation runs

-- H --

-- I --

ices.hcr	The typical HCR used by ICES
index.hat-method	Predicted index of abundance from abundance estimates
indicator.hcr	An indicator-based HCR
indicator.is	indicator implementation function
initialize-method	S4 class 'FLiem'
initialize-method	S4 class 'mpCtrl'
initialize-method	S4 class 'mseCtrl'
isys	S4 class 'mpCtrl'
isys-method	S4 class 'mpCtrl'
isys-methods	S4 class 'mpCtrl'
isys<-	S4 class 'mpCtrl'
isys<--method	S4 class 'mpCtrl'
isys<--methods	S4 class 'mpCtrl'
iter-method	Specification for the observation error model (OEM).
iters-method	S4 class 'FLiem'
iters-method	S4 class 'mpCtrl'

-- K --

Kobe statistics

-- M --

mcN	Compute number of necessary Monte Carlo runs
method	S4 class 'mseCtrl'
method-method	S4 class 'mpCtrl'
method-method	S4 class 'mseCtrl'
method-methods	S4 class 'mseCtrl'
method<-	S4 class 'mseCtrl'
method<--method	S4 class 'mpCtrl'
method<--method	S4 class 'mseCtrl'
method<--methods	S4 class 'mseCtrl'
movingF.hcr	TODO:description
mp	mp executes a single run of a Management Procedure
mpCtrl	S4 class 'mpCtrl'
mpCtrl-class	S4 class 'mpCtrl'
mpCtrl-methods	S4 class 'mpCtrl'
mseCtrl	S4 class 'mseCtrl'
mseCtrl-class	S4 class 'mseCtrl'
mseCtrl-methods	S4 class 'mseCtrl'

-- O --

observations	Specification for the observation error model (OEM).
observations-method	Specification for the observation error model (OEM).
observations-methods	Specification for the observation error model (OEM).
observations<-	Specification for the observation error model (OEM).
observations<--method	Specification for the observation error model (OEM).
observations<--methods	Specification for the observation error model (OEM).
oem	S4 class 'FLmse'
oem-method	S4 class 'FLmse'
oem-methods	S4 class 'FLmse'
oem<-	S4 class 'FLmse'
oem<--method	A class for an operating model (OM)
oem<--methods	S4 class 'FLmse'
om	S4 class 'FLmse'
om-method	S4 class 'FLmse'
om-methods	S4 class 'FLmse'
om<-	S4 class 'FLmse'
om<--method	A class for an operating model (OM)
om<--methods	S4 class 'FLmse'

-- P --

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	Compute performance statistics
performance-method	Compute performance statistics
phcr	S4 class 'mpCtrl'
phcr-method	S4 class 'mpCtrl'
phcr-methods	S4 class 'mpCtrl'
phcr<-	S4 class 'mpCtrl'
phcr<--method	S4 class 'mpCtrl'
phcr<--methods	S4 class 'mpCtrl'

-- S --

sampling.oem	Samples from an operating model to obtain catch, biology and abundance data
show-method	Specification for the observation error model (OEM).
show-method	S4 class 'mpCtrl'
show-method	S4 class 'mseCtrl'
sr-method	A class for an operating model (OM)
sr<--method	A class for an operating model (OM)
statistics	Example set of performance statistics
stock-method	A class for an operating model (OM)
stock<--method	A class for an operating model (OM)

-- T --

tac.is	TAC implementation function
tm	S4 class 'mpCtrl'
tm-method	S4 class 'mpCtrl'
tm-methods	S4 class 'mpCtrl'
tm<-	S4 class 'mpCtrl'
tm<--method	S4 class 'mpCtrl'
tm<--methods	S4 class 'mpCtrl'
tracking	S4 class 'FLmse'
tracking-method	S4 class 'FLmse'
tracking-methods	S4 class 'FLmse'
tracking<-	S4 class 'FLmse'
tracking<--method	A class for an operating model (OM)
tracking<--methods	S4 class 'FLmse'
tune	tune

-- U --

Debugging mse modules