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Opakapaka SS3 OM/EM truth and EM output (extracted)

opaka_truth.Rd

A small list containing Stock Synthesis (SS3) output extracted from an operating model (OM) and an estimation model (EM) pair using r4ss::SS_output(). Intended as a truth / comparison object for simulation-experiment workflows and diagnostics.

Usage

opaka_truth

Format

A list with three named elements, om, em, and em_no_platoon, each containing the SS3 sprseries and cpue outputs as data.frames suitable for plotting and comparison of true vs estimated indices and spawning biomass trajectories.

Source

Produced by calling r4ss::SS_output() on OM and EM model directories and collecting the sprseries and cpue components.

Details

The object is a list with three elements: om, em, and em_no_platoon. Each element is a sub-list that contains sprseries (spawning biomass time series) and cpue (standardized index output). The contained data frames have the following structures:

om$sprseries

A data.frame with 100 rows and 2 columns:

Yr

Integer year (e.g., 1949...)

SSB

Numeric spawning stock biomass

om$cpue

A data.frame with 107 rows and 7 columns:

Yr

Integer year

Fleet

Integer fleet id

Fleet_name

Character fleet label

Vuln_bio

Numeric vulnerable biomass predicted by SS3

Obs

Observed CPUE (integer in OM)

Exp

Expected CPUE (numeric)

SE

Standard error (numeric)

em$sprseries

A data.frame with 100 rows and 2 columns: same format as om$sprseries.

em$cpue

A data.frame with 107 rows and 7 columns: same column names as om$cpue, with Obs shown as numeric in the EM output shown here.

em_no_platoon$sprseries

A data.frame with 100 rows and 2 columns: same format as om$sprseries.

em_no_platoon$cpue

A data.frame with 107 rows and 7 columns: same column names as om$cpue, with Obs shown as numeric in the EM output shown here.

Examples

if (FALSE) { # \dontrun{
  data(opaka_truth)
  str(opaka_truth)
  plot(opaka_truth$om$sprseries$Yr, opaka_truth$om$sprseries$SSB, type = "l")
  lines(opaka_truth$em$sprseries$Yr, opaka_truth$em$sprseries$SSB, col = "red")
  lines(opaka_truth$em_no_platoon$sprseries$Yr,
        opaka_truth$em_no_platoon$sprseries$SSB, col = "blue")
  # Compare CPUE
  head(opaka_truth$om$cpue)
  head(opaka_truth$em$cpue)
} # }