find_f_b40: Find the Reference Removal Rate (RRR) 'bo_refpt' F_b0 which...

In pbs-assess/gfiscamutils: Provide functions for iSCAM models

Find the Reference Removal Rate (RRR) bo_refpt F_b0 which is the F value which will bring the Spawning biomass to bo_refpt B0 in one year within the tolerance of tol thousand tonnes.

Description

Find the Reference Removal Rate (RRR) bo_refpt F_b0 which is the F value which will bring the Spawning biomass to bo_refpt B0 in one year within the tolerance of tol thousand tonnes.

Usage

find_f_b40(
  model,
  bo_refpt = 0.4,
  init_catch = 6,
  spread = 0.5,
  root_dir = "d",
  tol = 0.1,
  max_iter = 10,
  burnin = 1000,
  proj_yrs = 50,
  iscam_path = "/usr/bin/gfiscam/build/dist/bin/iscam"
)

Arguments

model	An iscam model object (class mdl_cls)
bo_refpt	A fractional value of B0 to use as the reference point to approach in the calculation
init_catch	Initial catch value to run the model with
spread	Amount of catch +/- from the init_catch to allow the catch to wander in the search algorithm
root_dir	The root hard drive name, must be either 'c', 'C', 'd', or 'D'
tol	The catch tolerance in thousands of tonnes, default 0.5
max_iter	The maximum number of iterations to perform. If this is hit, a warning will be issued and the F value returned will be NA
burnin	The number of posterior samples to remove from the beginning of the list of posteriors
proj_yrs	The number of years to project
iscam_path	Full path to the ISCAM executable. To get this in Linux, type 'which iscam'. In Windows type 'where iscam'

Details

This is performed by an automated search for the catch level required to get the F value for the removal rate reference point. The initial catch is provided and should be based on the value in the decision table which is close to 0.5 probability that the biomass next year will drop below bo_refpt of B0. The initial value is placed as a catch TAC value in the projection file and the model mceval is run, then the biomass is compared with the 0.4B0 value and the tolerance is checked. If within the tolerance, tol, the F value is extracted and that is the RRR. If it is not within tolerance tol, the new catch becomes the current evaluated catch plus the difference between the estimated biomass and the B0 reference point biomass. This routine is continued until within the tolerance tol or the maximum number of iterations has taken place (max_iter).

The bash shell is used to run the ISCAM models. You must have bash available on your system. For Windows, you need to install WSL2 (Windows Subsystem for Linux) and install ISCAM on it to use this.

Install ISCAM: navigate to /usr/bin and clone the gfiscam GitHub repository. Type ⁠make -j 8 dist⁠. It should be at: ⁠/usr/bin/gfiscam/build/dist/bin/iscam⁠. This full path is necessary because the ⁠$PATH⁠ is not transferred through the system() call.

Value

A list of two items, the F and U values. Each of these are the length of the number of fleets

pbs-assess/gfiscamutils documentation built on Oct. 24, 2024, 1:37 p.m.