Appendix B — Overview of Major Changes

This section is primarily relevant to readers who have been working with openMSE in the past and are interested in learning about the technical differences between openMSE 2.0 and earlier versions of the packages.

The majority of the new developments have occurred in the MSEtool package. The most significant changes are the development of new object classes and new accessor and assignment functions related to those objects.

B.1 New Object Classes

Table B.1 provides on overview of the new object classes, and some examples of the accessor and assignment functions that operate on those objects.

The new object classes have been defined with lowercase names, however the accessor and assignment functions use either uppercase for acronyms (e.g., OM()) or regular case (e.g., Stock()).

The function examples in Table B.1 are primarily intended for demonstration purposes. In practice, these functions, particularly the assignment functions, may require additional arguments. Consult the help documentation for the respective object class (e.g., ?OM ) for further information.

The new object classes and related functions are described in more detail elsewhere in this manual.

Table B.1: A brief description of the primary new object classes developed for openMSE 2.0

New Class	Description	Key Functions Examples	Deprecated Class
`om`	S4 object containing the operating model information. Used for both single-stock/fleet and multi-stock/fleet models.	`OM()`: Create new `om`-class object	`OM` `MOM`
`stock`	S4 object containing information relating to the biological characteristics of a stock.	`Stock()` : Create a new `stock`-class object `Stock(OM)` : Access a `stock`-class object from an `om`-class object `Stock(OM) <- Stock()` : Assign a `stock`-class object to an `om`-class object	`Stock`
`fleet`	S4 object containing information relating to the exploitation characteristics of a stock.	`Fleet()` : Create a new `fleet`-class object `Fleet(OM`): Access a `fleet`-class object from an `om`-class object `Fleet(OM) <- Fleet()` : Assign a `fleet`-class object to an `om`-class object	`Fleet`
`obs`	S4 object containing information related to the observation model used to generate fishery data.	`Obs()` : Create a new `obs`-class object `Obs(OM`): Access an `obs`-class object from an `om`-class object `Obs(OM) <- Obs()` : Assign an `obs`-class object to an `om`-class object	`Obs`
`imp`	S4 object containing information related to the implementation error for management advice produced by management procedures. Note: Implementation error is currently not implemented in `openMSE 2.0` .	`Imp()` : Create a new `imp`-class object `Imp(OM`): Access an `imp`-class object from an `om`-class object `Imp(OM) <- Imp()` : Assign an `imp`-class object to an `om`-class object	`Imp`
`data`	S4 object containing information related to fishery data. A `data`-class object contains the data from all fleets in an `OM` . Each `OM` has a `data`-class object for each `Stock` , or for each stock complex.	`Data()` : Create a new `data`-class object `Data(OM`): Access a `data`-class object from an `om`-class object `Data(OM) <- Data()` : Assign a `data`-class object to an `om`-class object	`Data`
`mp`	Function that takes a `data` -class object and returns an `advice`-class object.	`MyMP <- function(Data, ...) { Advice() } class(MyMP) <- 'mp'`	`MP`
`advice`	S4 object returned by a `mp`-class function and containing information related management advice.	`Advice()`: Create a new `advice`-class object	`Rec`
`hist`	S4 object containing the simulated historical fishery and information for future population dynamics. Used for both single-stock/fleet and multi-stock/fleet models.	`Hist(MSE)` : return historical time series information from an `mse`-class object. Note: The object returned by `Hist(MSE)` is not a complete `hist`-class object, but only contains the historical time series data. Other information in `hist`-class objects is stored elsewhere in `mse`-class objects	`Hist` `multiHist`
`mse`	S4 object containing all information from the historical and projection periods. Used for both single-stock/fleet and multi-stock/fleet models.	Used by performance metric and summary table functions. Note: performance metric functions have not yet been developed for `mse`-class objects.	`MSE` `MMSE`