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

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.

Value

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

Details

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

Examples

# On FLom
data(plesim)
obs <- perfect.oem(stock(om), deviances=NULL, observations=NULL,
  args=list(y0=1960, dy=2021), tracking=FLQuant())