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.
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(sol274)
#> Warning: namespace ‘patchwork’ is not available and has been replaced
#> by .GlobalEnv when processing object ‘om’
#> Warning: namespace ‘dplyr’ is not available and has been replaced
#> by .GlobalEnv when processing object ‘om’
#> Warning: namespace ‘TMB’ is not available and has been replaced
#> by .GlobalEnv when processing object ‘om’
#> Warning: namespace ‘remotes’ is not available and has been replaced
#> by .GlobalEnv when processing object ‘om’
#> Warning: namespace ‘shiny’ is not available and has been replaced
#> by .GlobalEnv when processing object ‘om’
#> Warning: namespace ‘htmlwidgets’ is not available and has been replaced
#> by .GlobalEnv when processing object ‘om’
#> Warning: namespace ‘xtable’ is not available and has been replaced
#> by .GlobalEnv when processing object ‘om’
#> Warning: namespace ‘FLAssess’ is not available and has been replaced
#> by .GlobalEnv when processing object ‘om’
#> Warning: namespace ‘FLSRTMB’ is not available and has been replaced
#> by .GlobalEnv when processing object ‘om’
obs <- perfect.oem(stock(om), deviances=NULL, observations=NULL,
args=list(y0=1957, dy=2021), tracking=FLQuant())