Initialisation Appendix Data layer example

The following example illustrates the data-layer inputs used to reconstruct the population-level initial state for species 0 (anchoveta). These parameters do not constitute the initial condition itself. Rather, they provide the information used to generate the population.initialization.* block.

population.initialization.relativebiomass.enabled = TRUE

# species 0 (anchoveta) ------------------------

# used for calculation of natural mortality
species.egg.stage.duration.sp0 = 2 # in days

observed.biomass.file.sp0 = biomass.acousticSurvey-index_month.csv
observed.biomass.ndtPerYear.sp0 = 12
observed.biomass.cutoff.size.sp0 = 5

fisheries.catchatlength.file.sp0 = catchatlength-anchoveta_month.csv
fisheries.catchatlength.ndtPerYear.sp0 = 12

fisheries.yield.file.sp0 = yield_month.csv
fisheries.yield.ndtPerYear.sp0 = 12

This example corresponds to the original data-rich design of reconstructed population-level initialisation, in which biomass, yield, and catch-at-length are all available. In more data-poor situations, the biomass file may be replaced by an approximate biomass guess:

observed.biomass.guess.sp0 = 1.2e8

When such reduced-input configurations are used, the resulting initial state should be inspected carefully, because the reconstruction is then more strongly constrained by assumed biological and selectivity settings.