`R/iSCAM2OM.R`

`iSCAM2OM.Rd`

Functions for importing an iSCAM assessment. From a fitted model, `iSCAM2OM`

populates the various slots of an operating model and `iSCAM2Data`

generates a Data object.
These functions rely on several functions written by Chris Grandin (DFO PBS).

iSCAM2OM( iSCAMdir, nsim = 48, proyears = 50, mcmc = FALSE, Name = "iSCAM model", Source = "No source provided", length_timestep = 1, nyr_par_mu = 2, Author = "No author provided", report = FALSE, silent = FALSE ) iSCAM2Data( iSCAMdir, Name = "iSCAM assessment", Source = "No source provided", length_timestep = 1, Author = "No author provided" )

iSCAMdir | A folder with iSCAM input and output files in it. Alternatively, a list returned by load.iscam.files. |
---|---|

nsim | The number of simulations to take for parameters with uncertainty (for OM@cpars custom parameters) |

proyears | The number of MSE projection years |

mcmc | Logical, whether to use mcmc samples to create custom parameters cpars. Alternatively, a list returned by read.mcmc. Set the seed for the function to sub-sample the mcmc samples. |

Name | The name of the operating model |

Source | Reference to assessment documentation e.g. a url |

length_timestep | How long is a model time step in years (e.g. a quarterly model is 0.25, a monthly model 1/12) (currently only uses annual time step) |

nyr_par_mu | integer, the number of recent years to estimate vulnerability over for future projections |

Author | Who did the assessment |

report | logical should a numbers at age reconstruction plot be produced? |

silent | logical should progress reporting be printed to the console? |

The function calls `model <- load.iscam.files(iSCAMdir)`

and grabs the following matrices:

`model$mpd$d3_weight_mat`

- fecundity (product of weight and maturity at age)`model$mpd$ma`

- maturity at age

The function calls `model <- load.iscam.files(iSCAMdir)`

and then grabs the following matrices:

`model$mpd$N`

- abundance at age`model$mpd$F`

- fishing mortality at age`model$mpd$M`

- natural mortality at age

If a delay-difference model is recognized, then the following is used instead:

`model$mpd$F_dd`

- fishing mortality at age`model$mpd$M_dd`

- natural mortality at age

Abundance at age is reconstructed using `model$mpd$rt`

(recruitment) and projected with `F_dd`

and
`M_dd`

to match `model$mpd$numbers`

.

If `mcmc = TRUE`

the function calls `mcmc_model <- read.mcmc(iSCAMdir)`

, and grabs `nsim`

sub-samples of the MCMC output
through the following arrays:

`mcmc_model$params`

and`mcmc_model$ft`

- fishing mortality at age from the fleet selectivity parameters and apical F's`mcmc_model$m`

- year-specific natural mortality at age`mcmc_model$params$rinit`

and`mcmc_model$rt`

- recruitment and abundance

While the iSCAM start age can be greater than zero, abundance at age is back-calculated to age zero using the M at the start age.

These arrays are then passed to `VPA2OM`

to generate the operating model.

iSCAM calculates the stock-recruit relationship and subsequently a single set of MSY and unfished reference points using R0, steepness, and unfished spawners per recruit from the mean M, fecundity, and growth (mean with respect to time).

R0 and h are recalculated for the operating model by obtaining the stock-recruit alpha and beta from the
iSCAM parameters and the mean unfished spawners per recruit in the first `ageM`

(age of 50% maturity) years.
R0 is also back calculated to age zero.

T. Carruthers, Q. Huynh