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Update a simulated Hist object with new catch and CPUE data

Source: R/UpdateData.R
UpdateData.Rd

Replaces the historical landings and CPUE index data in a Hist object (from MSEtool::Simulate()) with the updated observations returned by ProcessNewData().

Usage

UpdateData(Hist, plot = FALSE)

Arguments

Hist

A Hist object returned by MSEtool::Simulate().

plot

Logical. If TRUE, plots comparing the conditioned and updated data are saved to figures/data/:

catch_seasonal_fleet.png

Seasonal catch by fleet.

catch_annual_fleet.png

Annual catch by fleet.

catch_annual_overall.png

Annual total catch.

index_seasonal.png

Seasonal CPUE index by fleet, standardized to the mean over the conditioned years.

index_annual_mean.png

Annual mean of the standardized CPUE index by fleet.

Value

The Hist object with updated landings and CPUE data.

Details

This must be called after the observation model (Obs) has been populated in MSEtool::Simulate() using the catch and index data that were used in conditioning. Otherwise the differences between the conditioned and updated data would be interpreted as observation error in the observed catches.

The data are replaced in both the OM data (Hist@OM@Data) and the simulated data (Hist@Data) for the combined stock.

If the fleets of the OM have been combined with MSEtool::CombineFleets(), the new landings are summed over fleets, and the CPUE indices, which MSEtool::CombineFleets() moves to the Survey slot, are replaced there.