The tinyErr function

The tinyErr function can be used to remove observation, implementation, and process error, as well as any gradients in life-history parameters. For example, we first create an Operating Model using some example Stock, Fleet, Obs, and Imp objects :

OM <- new("OM", Albacore, Generic_IncE, Imprecise_Biased, Overages)

Notice that our OM includes process error in the life-history parameters, as well as observation and implementation error:

OM@Perr # recruitment process error

## [1] 0.15 0.30

OM@Msd  # inter-annual variability in M

## [1] 0.0 0.1

OM@Cobs # error in observations

## [1] 0.2 0.6

OM@TACFrac # implementation error in TAC

## [1] 1.1 1.2

The tinyErr function will remove all sources of uncertainty and variability:

OM2 <- tinyErr(OM)

## Removing all Observation Error

## Removing all Implementation Error

## Removing all Process Error

## Removing all Gradients

OM2@Perr # no recruitment process error

## [1] 0 0

OM2@Msd  # no inter-annual variability in M

## [1] 0 0

OM2@Cobs # very low observation error

## [1] 0.00 0.05

OM2@TACFrac # no implementation error 

## [1] 1 1

The obs, imp, and proc arguments to the tinyErr function can be used to control which sources of error and variability to remove from the OM. See ?tinyErr for more details.

The Replace function

The can be used to replace individual Stock, Fleet, Obs, or Imp components in an Operating Model.

For example, to replace the Stock object in an OM we provide Replace with a new Stock object:

 OM1 <- new("OM", Albacore, Generic_DecE, Generic_Obs, Overages)
 OM2 <- Replace(OM1, Blue_shark, Name="Blue_shark OM based on OM1")

## Replacing sub-model: Stock

Likewise, to replace any of the other OM components:

 OM1 <- new("OM", Albacore, Generic_DecE, Generic_Obs, Overages)
 OM2 <- Replace(OM1, Generic_IncE, Name="OM1 with new Fleet")

## Replacing sub-model: Fleet

 OM3 <- Replace(OM2, Perfect_Info, Name="OM2 with new Obs")

## Replacing sub-model: Obs

 OM4 <- Replace(OM3, Perfect_Imp, Name="OM2 with new Imp")

## Replacing sub-model: Imp