perfect.oem: A perfect observation of catch and abundances-at-age.

In iagomosqueira/mse: Tools for Running Management Strategy Evaluations using FLR

A perfect observation of catch and abundances-at-age.

Description

This observation error model function generates a set of perfect observations on catches, biology and abundance. Direct observations are made of the stock, while a single age-structured index of abundance, in numbers, is created with a fixed catchability of 0.01. deviances on either stk$catch.n or idx$index, if given, are applied.

Usage

perfect.oem(stk, deviances, observations, args, tracking, biomass = FALSE, ...)

Arguments

deviances	A named list of observation deviances, class list.
observations	A list of past observations, extended to the end of om, class list.
args	The mp dimensions arguments, as generated by mp, class list.
tracking	Object to track module decisions and outputs, class FLQuant.
om	An operating model, class FLom or FLombf.

Details

This oem function generates a full observation time series every time step, and does not append them to existing objects in observations.

Value

A named list with elements stk (FLStock), idx (FLIndices), deviances, observations and tracking.

Examples

# On FLom
data(sol274)
obs <- perfect.oem(stock(om), deviances=NULL, observations=NULL,
  args=list(y0=1957, dy=2021), tracking=FLQuant())

iagomosqueira/mse documentation built on April 24, 2024, 4:35 a.m.