Add append method for FLombf to join two OMs at a year boundary

[Copilot]

FLombf lacked an append method, making it impossible to splice two operating models along the year axis (e.g. after running a simulation in pieces).

Changes

• R/FLombf-class.R — New setMethod("append", signature(x="FLombf", values="FLombf")):
  • Windows x up to after (default: dims(x)$maxyear) and values from after + 1
  • Appends biols via FLBiols(Map(append, x=biols(x), values=biols(values)))
  • Appends fisheries by chaining append on each FLFishery (effort etc.) then on each FLCatch within it
• NAMESPACE — Added "append" to exportMethods()
• NEWS.md — Documented under new version 2.5.0

Usage

om1 <- window(om, end=2020)
om2 <- window(om, start=2021)
om3 <- append(om1, om2, after=2020)
# om3 spans the full year range of om1 + om2

Original prompt

Summary

Add an append method for class FLombf that concatenates two FLombf objects along the year dimension: the first object up to (and including) a given after year, and the second object from the following year onwards.

Details

The method signature should follow the standard R append pattern:

append(x, values, after=dims(x)$maxyear)

where:

• x is the first FLombf object
• values is the second FLombf object
• after is the year up to which x is used (default: last year of x); values is taken from after + 1 onwards

Implementation

Add the following to R/FLombf-class.R (after the combine section, around line 865):

# append {{{

#' Append two FLombf objects along the year dimension
#'
#' Joins two \code{FLombf} objects along the year axis: the first object is
#' windowed to \code{after}, and the second from \code{after + 1} to its last
#' year. The two windowed pieces are then combined using \code{FLCore::append}
#' on the underlying \code{FLBiols} and \code{FLFisheries} slots.
#'
#' @param x An \code{FLombf} object, used up to year \code{after}.
#' @param values An \code{FLombf} object, used from year \code{after + 1}.
#' @param after Integer year. The last year taken from \code{x}. Defaults to
#'   the last year of \code{x}.
#'
#' @return A new \code{FLombf} object spanning the years of \code{x} up to
#'   \code{after} joined with the years of \code{values} from \code{after + 1}.
#'
#' @examples
#' # Split an FLombf at year 2020 and re-join
#' om1 <- window(om, end=2020)
#' om2 <- window(om, start=2021)
#' om3 <- append(om1, om2, after=2020)
#'
#' @rdname FLombf-class
#' @aliases append,FLombf,FLombf-method

setMethod("append", signature(x="FLombf", values="FLombf"),
  function(x, values, after=dims(x)$maxyear) {

    after <- as.integer(after)

    # WINDOW x up to 'after'
    x <- window(x, end=after)

    # WINDOW values from 'after + 1'
    values <- window(values, start=after + 1L)

    # APPEND biols
    biols(x) <- FLBiols(Map(append, x=biols(x), values=biols(values)))

    # APPEND fisheries: each FLFishery, then each FLCatch within
    fisheries(x) <- FLFisheries(Map(function(fx, fv) {
      # APPEND the FLFishery-level slots (effort, etc.)
      out <- append(fx, fv)
      # APPEND every FLCatch within the fishery
      out@.Data <- Map(append, x=fx@.Data, values=fv@.Data)
      names(out) <- names(fx)
      return(out)
    }, fx=fisheries(x), fv=fisheries(values)))

    return(x)
  }
) # }}}

Where to add it

Insert the new # append {{{ section after the existing # combine {{{ block (which ends around line 864 in R/FLombf-class.R) and before the # deviances {{{ block.

Export

Add "append" to the exportMethods() list in NAMESPACE (it is likely already exported via FLCore, but confirm it is listed or add it if missing).

Also add a short entry to NEWS.md under a new patch version:

## NEW FEATURES

- `append(FLombf, FLombf, after)` method to join two operating models at a year boundary.

The following is the prior conversation context from the user's chat exploration (may be truncated):

User: In flr/mse i need a function to append two objects of class FLombf, rthe first up to some year and the second from the next year

Assistant: Now I have a thorough understanding of the FLombf class. I'll create a append method that takes two FLombf objects and a year argument, taking the first object up to that year and the second from the next year. Looking at the existing window method and combine-based patterns in the code:

Assistant: I'm waiting for your confirmation to proceed with creating the pull request that adds the append method for FLombf.

This pull request was created from Copilot chat.

[iagomosqueira]

Default after should be the first year (minyear) of values.