multiMSE/dev_notes.rmd at master · DLMtool/multiMSE · GitHub

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# multiMSE

## Assumptions:
1. Two-sex stocks have identical fleet structure (taken from Stock 1)
2.


## Known issues:
  1. maxage is the same across species so computationally inefficient
  2. initdist is no yet working as a cpars value (indeed I'm not sure where this comes into the OM specification at all!)
  3. NO custom MP check whether already in DLMtool
  4. No parallel processing option at present
  5. plus-group not accounted for yet
  6. bio-economics not included
  7. cpars$mov not dealt with yet
  8. Blow calcs aren't included
  9. initial depletion isn't included
  10. conditioning with real data not yet implemented
  11. Hist option not included
  12. Discard mortality will have to be stock-fleet specific
  13. Changing MOM@nsim doesn't seem to work - because of CatchFrac I think
  14. curE doesn't result in MMSE@Effort = 1
  15. add a check that MPs is correct structure - correct documentation for MPs in multiMSE
  16. Fleet, Obs, and Imp parameters are copied over for 2-sex stocks (ie both sexes have identical fleet, obs and imp parameters)

## Priority list
  1. Multi-fleet popdynCPP needed to properly account for fleet-specific MPAs, spatial targetting etc.
  2. How should same fleets by handled? Use identical parameters simulation-by-simulation for each stock?

## Known issues
  1) SSN[SPAYR] <- Nfrac[SA] * StockPars[[p]]$R0[S] * StockPars[[p]]$initdist[SAR]  this is Pinitdist[SR] in runMSE but I have no idea where Pinitdist comes from
  2) currently assume unfished vulnerability is equally weighted among fleets (first V calculation)
  3) MICE mode: MSY calcs are fully dynamic and by year - we do not solve the long-term equilibrium MSY for MICE models
  4) No check for MOM correct object formatting yet
  5) MICE mode: SSB0 is constant (does not change with M for example) and based on long-term ecosystem average as specified in StockPars[[p]]$SSB0
  6) For MSY calculations, vulnerability is calculated by fishing mortality rate summed over both areas (not weighted by total catches for example)
  7) Blow calculations are currently not coded!
  8) RefY reference yield is currently MSY!
  9) No control$Cbias_yr functionality!
  10) MGT calculation not currently coded!
  11) No annual MSY calculation currently (need updating inside MP loop because it now responds to MICE modelled relationships)
  12) Currently there is no MMP checking
  13) SelectChanged, the switch that only does MSY calcs if selectivity has changed, is currently set permanently to TRUE (around line 1392)
  14) Historical vulnerability is calculated across fleets according to todays catch fraction
  15) Pstar quantiles of TACs not available nreps fixed to 1


## Needs checking
  1) The vulnerability in the fleets does not max to 1
  2) When calculating aggregate retention in the multi_q_estimation function, how should max retention at age be calculated (what is the max value)?
  3) Single simulation run nsim=1
  4) get rid of any DLMtool::: triple colons