kcurti / asap.agepro.pre-post-processing

ASAP.AGEPRO.pre-post-processing

This repository contains R code for post-processing ASAP output, getting the data and ASAP outputs ready for input into AGEPRO, and post-processing AGEPRO output.

The following programs require a specific file structure for the modeling directory.

current.assess.dir

current.assess.dir/RunXXX

current.assess.dir/RunXXX/retro

current.assess.dir/RunXXX/mcmc.2000.it.1000.thin

.... and require that the programs are run in the following order

Run ASAP Model

Complete.ASAP.Plots.R --> Runs ASAPplots package

Summarize.ASAP.model.estimates.R --> Summary.Tables.RDATA Summarizes SSB, B, F, FAA, NAA, selectivity and terminal year estimates

Run MCMC and Retro Analyses

Summarize.Terminal.yr.ests.with.CIs.R --> Summary.Tables.with.CIs.RDATA Takes the MCMC results and summarizes the 90% CIs

Complete.retro.adjs.and.compare.Terminal.yr.ests.R --> Retrospective.Analysis.RDATA Takes terminal year estimates and mohns rho estimates from the restrospective analysis to calculate rho adjusted values Compares the rho adjusted values to the terminal year estimates with CIs to determine if a retro adjustment is needed

Projection.Prep.ASAP.Output.R --> ASAP.Data.For.Projections.RDATA Gets ASAP outputs ready for projections

Run Long-term projections in AGEPRO

Analyze.Long.Term.Projection.Output.R --> Projection.summary.RDATA

Compare.Terminal.yr.ests.to.BRPs.R --> Comparison.with.BRPs.RDATA Creates phase plot with and without CIs

Run Short-term projections in AGEPRO

Analyze.Short.Term.Projection.Output.R --> Projection.summary.RDATA

Plot.Short.Term.Projections.R --> Summary.All.Projections.RDATA

Compile.Summary.Catch.Status.Table.R --> Summary.Catch.Status.Table.RDATA

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Plot.Historical.Retrospective.R --> Historical.retrospective.comparison.RDATA Creates plots comparing outputs with those of previous assessments

Run.Likelihood.Profile.R --> Final.Summary.RDATA Completes likelihood profiling over a specified parameter