Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet)

Functions that uses the file location or the r4ss output list of a fitted SS3 model including input files to populate the various slots of an MOM or OM object. SS2MOM and SS2OM mainly populates the Stock and Fleet components components of the operating model. SS2MOM creates a 2-sex model and multiple fleets with discarding behavior. SS2OM returns a single sex (either male, female, or averaged biological parameters) and single fleet (aggregate selectivity and mortality, no explicit discarding modeled). For either, the user still needs to parameterize most of the observation and implementation portions. SSMOM2OM is the internal function that simplifies the MOM object to an OM object. plot_SS2OM generates a markdown report to compare the OM and SS output.

Usage

SS2MOM(
  SSdir,
  nsim = 48,
  proyears = 50,
  reps = 1,
  maxF = 3,
  seed = 1,
  interval = 1,
  pstar = 0.5,
  Obs = MSEtool::Generic_Obs,
  Imp = MSEtool::Perfect_Imp,
  silent = FALSE,
  Name = "MOM generated by SS2MOM",
  Source = "No Source provided",
  ...
)

plot_SS2MOM(
  x,
  SSdir,
  gender = 1:2,
  filename = "SS2MOM",
  dir = tempdir(),
  open_file = TRUE,
  silent = FALSE,
  ...
)

SS2OM(
  SSdir,
  nsim = 48,
  proyears = 50,
  reps = 1,
  maxF = 3,
  seed = 1,
  interval = 1,
  pstar = 0.5,
  Obs = MSEtool::Generic_Obs,
  Imp = MSEtool::Perfect_Imp,
  import_mov = TRUE,
  gender = 1:2,
  seasons_to_years = TRUE,
  model_discards = TRUE,
  silent = FALSE,
  Name = "OM generated by SS2OM function",
  Source = "No source provided",
  Author = "No author provided",
  report = FALSE,
  filename = "SS2OM",
  dir = tempdir(),
  open_file = TRUE,
  ...
)

SSMOM2OM(
  MOM,
  SSdir,
  gender = 1:2,
  import_mov = TRUE,
  seed = 1,
  silent = FALSE,
  model_discards = TRUE
)

plot_SS2OM(
  x,
  SSdir,
  gender = 1:2,
  filename = "SS2OM",
  dir = tempdir(),
  open_file = TRUE,
  silent = FALSE,
  ...
)

MOM_agg_fleets(MOM)

Arguments

SSdir: A folder with Stock Synthesis input and output files in it.
nsim: The number of simulations to take for parameters with uncertainty (for OM@cpars custom parameters).
proyears: The number of projection years for MSE
reps: The number of stochastic replicates within each simulation in the operating model.
maxF: The maximum allowable F in the operating model.
seed: The random seed for the operating model.
interval: The interval at which management procedures will update the management advice in multiMSE, e.g., 1 = annual updates.
pstar: The percentile of the sample of the management recommendation for the MP/MMP.
Obs: The observation model (class Obs). These functions do not update implementation parameters.
Imp: The implementation model (class Imp). These functions do not update implementation parameters.
silent: Whether to silence messages to the console.
Name: The name of the operating model
Source: Reference to assessment documentation e.g. a url
...: Arguments to pass to SS_output.
x: For plot_SS2OM, an object of either class OM or Hist. For plot_SS2MOM, an object of either class MOM or multiHist.
gender: An integer that indexes the sex for importing life history parameters (1 = usually female, 2 = usually male, 1:2 = mean across both sexes). Only used for SS2OM only in a 2-sex model.
filename: If report = TRUE, character string for the name of the markdown and HTML files.
dir: If report = TRUE, the directory in which the markdown and HTML files will be saved.
open_file: If report = TRUE, whether the HTML document is opened after it is rendered.
import_mov: Logical. Import movement matrix?
seasons_to_years: Logical, when season is the time step, whether to convert OM from a seasonal model to annual model.
model_discards: Logical, how to simplify a multi-fleet SS model to an OM object. If TRUE, OM will still model discards using the mean retention across fleets (weighted by fleet F). Otherwise, no discards are modeled and all fishing removals are calculated in the OM from the SS F-at-age matrix.
Author: Who did the assessment
report: Logical, if TRUE, the function will run runMSE to generate the Hist object from the operating model to compare against SS output. A markdown report will be generated.
MOM: MOM object

Value

SS2MOM returns an object of class MOM. SS2OM returns an object of class OM.

Functions

MOM_agg_fleets(): Aggregate all fleets in an MOM object.

Note

Currently tested on r4ss version 1.38.1-40.0 and SS 3.30.14.

Author

Q. Huynh