Chapter 12 Modifying the OM

It is often desirable to created modified versions of an OM for testing purposes such as series of robustness tests or to evaluate whether an MP is performing as expected under ideal conditions.

DLMtool includes several functions for this purpose.

12.1 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 built-in OM Components:

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

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

OM@Perr # recruitment process error

## [1] 0.15 0.30

OM@Linfgrad # gradient in Linf

## numeric(0)

OM@Cobs # error in observations

## [1] 0.2 0.6

OM@TACFrac # implementation error in TAC

## [1] 1.1 1.2

By default 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@Linfgrad # no gradient in Linf

## [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, proc, and grad 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.

12.2 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