A class for FLXSA control options

Runs of the FLXSA method require a number of parameter to be set. Most of them change the behaviour of the solution-searching algorithm Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque eleifend odio ac rutrum luctus. Aenean placerat porttitor commodo. Pellentesque eget porta libero. Pellentesque molestie mi sed orci feugiat, non mollis enim tristique. Suspendisse eu sapien vitae arcu lobortis ultrices vitae ac velit. Curabitur id

FLXSA.control(
  x = NULL,
  tol = 1e-09,
  maxit = 30,
  min.nse = 0.3,
  fse = 0.5,
  rage = 0,
  qage = 10,
  shk.n = TRUE,
  shk.f = TRUE,
  shk.yrs = 5,
  shk.ages = 5,
  window = 100,
  tsrange = 20,
  tspower = 3,
  vpa = FALSE
)

Slots

x

An object of class FLXSA. If provided, the 'FLXSA.control' is initialized with the corresponding values of an XSA analysis stored in the object. This is useful for getting the same initial sloteters for successive analyses. Specifying one or more of the other arguments supersedes default values, or values obtained from this FLXSA object

tol

The covergence tolerance, i.e. difference between two successive iterations must be lower, to declare convergence of the model.

maxit

The maximum number of iterations allowed

min.nse

The minimum value of SE permitted in estimate of N hat

fse

User set SE of F when shrinking to mean F

rage

The oldest age for which the two parameter model is used for catchability at age. Note that this value should be one less than the value used in the executable version of XSA

qage

The age after which catchability is no longer estimated. q at older ages set to the value at this age

shk.n

If TRUE, shrinkage to mean N

shk.f

If TRUE, shrinkage to mean F

shk.yrs

The number of years to be used for shrinkage to F for terminal year

shk.ages

The number of ages to be used for shrinkage to F for terminal age

window

The time window to consider in the model

tsrange

The number of years to be used in the time series weighting

tspower

The power to be used in the time series taper weighting

vpa

If FALSE use cohort analysis, otherwise, use VPA

Validity

VALIDITY

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You can inspect the class validity function by using getValidity(getClassDef('FLCatch'))

Accessors

All slots in the class have accessor and replacement methods defined that allow retrieving and substituting individual slots.

The values passed for replacement need to be of the class of that slot. A numeric vector can also be used when replacing FLQuant slots, and the vector will be used to substitute the values in the slot, but not its other attributes.

Constructor

A construction method exists for this class that can take named arguments for any of its slots. All slots are then created to match the requirements of the class validity.

See also

FLComp

Author

Laurence Kell & Philippe Grosjean

Examples

  # To create a new FLXSA.control object with default parameters:
  my.xsa.control <- FLXSA.control()
  my.xsa.control
#> tol 		 1e-09 
#> maxit 		 30 
#> min.nse 		 0.3 
#> fse 		 0.5 
#> rage 		 0 
#> qage 		 10 
#> shk.n 		 TRUE 
#> shk.f 		 TRUE 
#> shk.yrs 		 5 
#> shk.ages 		 5 
#> window 		 100 
#> tsrange 		 20 
#> tspower 		 3 
#> vpa 		 FALSE 
  # Same, but changing values of some parameters
  my.xsa.control <- FLXSA.control(maxit=50, shk.f=FALSE)
  my.xsa.control
#> tol 		 1e-09 
#> maxit 		 50 
#> min.nse 		 0.3 
#> fse 		 0.5 
#> rage 		 0 
#> qage 		 10 
#> shk.n 		 TRUE 
#> shk.f 		 FALSE 
#> shk.yrs 		 5 
#> shk.ages 		 5 
#> window 		 100 
#> tsrange 		 20 
#> tspower 		 3 
#> vpa 		 FALSE