Drop an element from an FLSAM.control object

Drops multiple surveys or age groups from an FLSAM.control object

drop.from.control(object, fleets="missing",ages="missing")

Arguments

object: An FLSAM.control object
fleets: A vector containing the names of the fleets to be dropped
ages: A vector containing the names of the age groups to be dropped

Details

This function can be used to modify an FLSAM.control object by removing one or more fleets, or one or more age groups from the object. Changes in the sequence of bindings that may arise due to the removal of a fleet or age group are corrected for using the update function.

Value

An FLSAM.control object

Author

Mark R. Payne.

Examples

#Load assessment
library(FLSAM)
data(NSH)
#NSH.ctrl before dropping
NSH.ctrl
#> An object of class "FLSAM.control"
#> Slot "name":
#> [1] "North Sea Herring"
#> 
#> Slot "desc":
#> [1] "Imported from a VPA file. ( ./data/index.txt ).  Fri May  4 12:16:13 2012 + FLSAM: North Sea Herring"
#> 
#> Slot "range":
#>       min       max plusgroup   minyear   maxyear   minfbar   maxfbar 
#>         0         8         8      1992      2012         2         6 
#> 
#> Slot "fleets":
#> catch unique         SCAI        HERAS      IBTS-Q1        IBTS0 
#>            0            3            2            2            2 
#> 
#> Slot "plus.group":
#> plusgroup 
#>      TRUE 
#> 
#> Slot "states":
#>               age
#> fleet           0  1  2  3  4  5  6  7  8
#>   catch unique  0  1  2  3  4  5  6  7  7
#>   SCAI         -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS-Q1      -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0        -1 -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "logN.vars":
#> 0 1 2 3 4 5 6 7 8 
#> 0 1 1 1 1 1 1 1 1 
#> 
#> Slot "logP.vars":
#> numeric(0)
#> 
#> Slot "catchabilities":
#>               age
#> fleet           0  1  2  3  4  5  6  7  8
#>   catch unique -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   SCAI          0 -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1  1  2  3  4  5  6  7  7
#>   IBTS-Q1      -1  8 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0         9 -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "power.law.exps":
#>               age
#> fleet           0  1  2  3  4  5  6  7  8
#>   catch unique -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   SCAI         -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS-Q1      -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0        -1 -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "f.vars":
#>               age
#> fleet           0  1  2  3  4  5  6  7  8
#>   catch unique  0  0  0  0  0  0  0  0  0
#>   SCAI         -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS-Q1      -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0        -1 -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "obs.vars":
#>               age
#> fleet           0  1  2  3  4  5  6  7  8
#>   catch unique  0  0  0  0  0  0  0  0  0
#>   SCAI          1 -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1  2  2  2  2  2  2  2  2
#>   IBTS-Q1      -1  3 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0         4 -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "srr":
#> [1] 0
#> 
#> Slot "scaleNoYears":
#> [1] 0
#> 
#> Slot "scaleYears":
#> [1] NA
#> 
#> Slot "scalePars":
#>       age
#> years  0 1 2 3 4 5 6 7 8
#> 
#> Slot "cor.F":
#> [1] 2
#> 
#> Slot "cor.obs":
#>               age
#> fleet          0-1 1-2 2-3 3-4 4-5 5-6 6-7 7-8
#>   catch unique  NA  NA  NA  NA  NA  NA  NA  NA
#>   SCAI          -1  -1  -1  -1  -1  -1  -1  -1
#>   HERAS         -1  NA  NA  NA  NA  NA  NA  NA
#>   IBTS-Q1       -1  -1  -1  -1  -1  -1  -1  -1
#>   IBTS0         -1  -1  -1  -1  -1  -1  -1  -1
#> 
#> Slot "cor.obs.Flag":
#> [1] ID ID ID ID ID
#> Levels: ID AR US
#> 
#> Slot "biomassTreat":
#> [1] -1  0 -1 -1 -1
#> 
#> Slot "timeout":
#> [1] 3600
#> 
#> Slot "likFlag":
#> [1] LN LN LN LN LN
#> Levels: LN ALN
#> 
#> Slot "fixVarToWeight":
#> [1] FALSE
#> 
#> Slot "simulate":
#> [1] FALSE
#> 
#> Slot "residuals":
#> [1] TRUE
#> 
#> Slot "sumFleets":
#> logical(0)
#> 
#Drop MLAI index
drop.from.control(NSH.ctrl,fleets="MLAI")
#> An object of class "FLSAM.control"
#> Slot "name":
#> [1] "North Sea Herring"
#> 
#> Slot "desc":
#> [1] "Imported from a VPA file. ( ./data/index.txt ).  Fri May  4 12:16:13 2012 + FLSAM: North Sea Herring"
#> 
#> Slot "range":
#>       min       max plusgroup   minyear   maxyear   minfbar   maxfbar 
#>         0         8         8      1992      2012         2         6 
#> 
#> Slot "fleets":
#> catch unique         SCAI        HERAS      IBTS-Q1        IBTS0 
#>            0            3            2            2            2 
#> 
#> Slot "plus.group":
#> plusgroup 
#>      TRUE 
#> 
#> Slot "states":
#>               age
#> fleet           0  1  2  3  4  5  6  7  8
#>   catch unique  0  1  2  3  4  5  6  7  7
#>   SCAI         -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS-Q1      -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0        -1 -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "logN.vars":
#> 0 1 2 3 4 5 6 7 8 
#> 0 1 1 1 1 1 1 1 1 
#> 
#> Slot "logP.vars":
#> numeric(0)
#> 
#> Slot "catchabilities":
#>               age
#> fleet           0  1  2  3  4  5  6  7  8
#>   catch unique -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   SCAI          0 -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1  1  2  3  4  5  6  7  7
#>   IBTS-Q1      -1  8 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0         9 -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "power.law.exps":
#>               age
#> fleet           0  1  2  3  4  5  6  7  8
#>   catch unique -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   SCAI         -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS-Q1      -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0        -1 -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "f.vars":
#>               age
#> fleet           0  1  2  3  4  5  6  7  8
#>   catch unique  0  0  0  0  0  0  0  0  0
#>   SCAI         -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS-Q1      -1 -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0        -1 -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "obs.vars":
#>               age
#> fleet           0  1  2  3  4  5  6  7  8
#>   catch unique  0  0  0  0  0  0  0  0  0
#>   SCAI          1 -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1  2  2  2  2  2  2  2  2
#>   IBTS-Q1      -1  3 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0         4 -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "srr":
#> [1] 0
#> 
#> Slot "scaleNoYears":
#> [1] 0
#> 
#> Slot "scaleYears":
#> [1] NA
#> 
#> Slot "scalePars":
#>       age
#> years  0 1 2 3 4 5 6 7 8
#> 
#> Slot "cor.F":
#> [1] 2
#> 
#> Slot "cor.obs":
#>               age
#> fleet          0-1 1-2 2-3 3-4 4-5 5-6 6-7 7-8
#>   catch unique  NA  NA  NA  NA  NA  NA  NA  NA
#>   SCAI          -1  -1  -1  -1  -1  -1  -1  -1
#>   HERAS         -1  NA  NA  NA  NA  NA  NA  NA
#>   IBTS-Q1       -1  -1  -1  -1  -1  -1  -1  -1
#>   IBTS0         -1  -1  -1  -1  -1  -1  -1  -1
#> 
#> Slot "cor.obs.Flag":
#> factor(0)
#> Levels: ID AR US
#> 
#> Slot "biomassTreat":
#> numeric(0)
#> 
#> Slot "timeout":
#> [1] 3600
#> 
#> Slot "likFlag":
#> factor(0)
#> Levels: LN ALN
#> 
#> Slot "fixVarToWeight":
#> [1] FALSE
#> 
#> Slot "simulate":
#> [1] FALSE
#> 
#> Slot "residuals":
#> [1] TRUE
#> 
#> Slot "sumFleets":
#> logical(0)
#> 
#Drop ages 8 and 9
drop.from.control(NSH.ctrl,ages=8:9)
#> An object of class "FLSAM.control"
#> Slot "name":
#> [1] "North Sea Herring"
#> 
#> Slot "desc":
#> [1] "Imported from a VPA file. ( ./data/index.txt ).  Fri May  4 12:16:13 2012 + FLSAM: North Sea Herring"
#> 
#> Slot "range":
#>       min       max plusgroup   minyear   maxyear   minfbar   maxfbar 
#>         0         8         8      1992      2012         2         6 
#> 
#> Slot "fleets":
#> catch unique         SCAI        HERAS      IBTS-Q1        IBTS0 
#>            0            3            2            2            2 
#> 
#> Slot "plus.group":
#> plusgroup 
#>      TRUE 
#> 
#> Slot "states":
#>               age
#> fleet           0  1  2  3  4  5  6  7
#>   catch unique  0  1  2  3  4  5  6  7
#>   SCAI         -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS-Q1      -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0        -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "logN.vars":
#> 0 1 2 3 4 5 6 7 
#> 0 1 1 1 1 1 1 1 
#> 
#> Slot "logP.vars":
#> numeric(0)
#> 
#> Slot "catchabilities":
#>               age
#> fleet           0  1  2  3  4  5  6  7
#>   catch unique -1 -1 -1 -1 -1 -1 -1 -1
#>   SCAI          0 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1  1  2  3  4  5  6  7
#>   IBTS-Q1      -1  8 -1 -1 -1 -1 -1 -1
#>   IBTS0         9 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "power.law.exps":
#>               age
#> fleet           0  1  2  3  4  5  6  7
#>   catch unique -1 -1 -1 -1 -1 -1 -1 -1
#>   SCAI         -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS-Q1      -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0        -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "f.vars":
#>               age
#> fleet           0  1  2  3  4  5  6  7
#>   catch unique  0  0  0  0  0  0  0  0
#>   SCAI         -1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS-Q1      -1 -1 -1 -1 -1 -1 -1 -1
#>   IBTS0        -1 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "obs.vars":
#>               age
#> fleet           0  1  2  3  4  5  6  7
#>   catch unique  0  0  0  0  0  0  0  0
#>   SCAI          1 -1 -1 -1 -1 -1 -1 -1
#>   HERAS        -1  2  2  2  2  2  2  2
#>   IBTS-Q1      -1  3 -1 -1 -1 -1 -1 -1
#>   IBTS0         4 -1 -1 -1 -1 -1 -1 -1
#> 
#> Slot "srr":
#> [1] 0
#> 
#> Slot "scaleNoYears":
#> [1] 0
#> 
#> Slot "scaleYears":
#> [1] NA
#> 
#> Slot "scalePars":
#>       age
#> years  0 1 2 3 4 5 6 7
#> 
#> Slot "cor.F":
#> [1] 2
#> 
#> Slot "cor.obs":
#>               age
#> fleet          0-1 1-2 2-3 3-4 4-5 5-6 6-7
#>   catch unique  NA  NA  NA  NA  NA  NA  NA
#>   SCAI          -1  -1  -1  -1  -1  -1  -1
#>   HERAS         -1  NA  NA  NA  NA  NA  NA
#>   IBTS-Q1       -1  -1  -1  -1  -1  -1  -1
#>   IBTS0         -1  -1  -1  -1  -1  -1  -1
#> 
#> Slot "cor.obs.Flag":
#> [1] ID ID ID ID ID
#> Levels: ID AR US
#> 
#> Slot "biomassTreat":
#> [1] -1  0 -1 -1 -1
#> 
#> Slot "timeout":
#> [1] 3600
#> 
#> Slot "likFlag":
#> [1] LN LN LN LN LN
#> Levels: LN ALN
#> 
#> Slot "fixVarToWeight":
#> [1] FALSE
#> 
#> Slot "simulate":
#> [1] FALSE
#> 
#> Slot "residuals":
#> [1] TRUE
#> 
#> Slot "sumFleets":
#> logical(0)
#>

Arguments

Details

Value

Author

See also

Examples