gadget.fit: Gadget fit
In gadget-framework/rgadget: Tools to Create and Maintain Gadget Models

gadget.fit

R Documentation

Gadget fit

Description

gadget.fit calls Gadget and compiles fit statistics, relevant biomass trajectories and consumption. It returns an object of class 'gadget.fit' which is essentially a list containing the following objects:

sidat: data.frame containing the model fit to the surveyindices
resTable: Table of likelihood component scores from the different stages of the iterative reweighting run
nesTable: Same as resTable but normalised with the minimum score for each component
suitability: The model estimated fleet predator suitability
stock.recruitment: Recruitment by stock
res.by.year: Results by year
stomachconten: Fit combined with data from the stomachcontent likelihood
likelihoodsummary: Likelihood component scores by year and step
catchdist.fleets: Data compared with model output for the catchdistribution components
stockdist: Data compared with model output for the stockdistribution components
SS: The likelihood output from the model
stock.full: Modeled abundance and mean weight by year,step, length and stock
stock.std: Modeled abundance, mean weight, number consumed by age, stock and year
stock.prey: Consumption of prey (or fleet catches) by prey, length, year and step
fleet.info: Information on catches, harvest rate and harvestable biomass by fleet, year and step
predator.prey: consumption of preys by predators, length, year and step
params: parameter values used for the fit
catchstatistics: Data compared with model output for the catchdstatistics components

bind.gadget.fit combines two (or more) gadget.fit objects into a single list. Each object in the list will have an extra column indicating the model, if the list is named those names will be used to identify the model.

Usage

gadget.fit(
  wgts = "WGTS",
  main.file = NULL,
  fleet.predict = NULL,
  mat.par = NULL,
  params.file = NULL,
  f.age.range = NULL,
  fit.folder = "FIT",
  printatstart = 1,
  steps = 1,
  recruitment_step_age = NULL,
  gd = NULL
)

bind.gadget.fit(...)

Arguments

`wgts`	Location of the iterative reweighting folder, if null gadget.fit requires a parameter file
`main.file`	if the main file is different from the 'main' or 'wgts/main.final'
`fleet.predict`	data.frame containing the basis fleets used to calculate the harvestable biomass. Fleet names should be specified in the fleet column.
`mat.par`	parameters for the maturity ogive
`params.file`	parameter file used in the fit (defaults to "WGTS/params.final")
`f.age.range`	data.frame describing the desired age range where the F's are calculated, if null this defaults to the apical F fro all stocks. Input columns should include stock, age.min and age.max
`fit.folder`	location of the output
`printatstart`	should the stock standard output be printed at the beginning or the end of the timestep
`steps`	what steps should be printed
`recruitment_step_age`	data frame defining the recruitment age by stock and time step. Default is the minimum age at step 1. Expects columns stock, age and step
`gd`	gadget_directory object to optionally set the location of the gadget directory
`...`	any number of gadget.fit objects