1. UPDATE OF RECENT DEVELOPMENTS IN MULTIFAN-CL AND RELATED SOFTWARE FOR STOCK ASSESSMENT
The MULTIFAN-CL project team:
Dave Fournier1, John Hampton2, Pierre Kleiber3, Nick Davies2, Simon Hoyle2, Fabrice Bouyé2, and Shelton Harley2
1Otter Research Ltd, Sidney, British Columbia, Canada
2Oceanic Fisheries Programme, Secretariat of the Pacific Community, Noumea, New Caledonia.
3Islands Fisheries Science Center, National Marine Fisheries Service, Honolulu, Hawaii, USA.

2. MULTIFAN-CL (MFCL)
Population modelling software - age-structured and length-based; fitted to catch, length-frequency, CPUE, tagging data.
Used for tuna stock assessments - WCPFC and elsewhere
Developments are ongoing
SPC-OFP manages the software project
Progress report given to each SC

3. This presentation Current status (at SC6)
Recent and Future developments
Website status
Current MFCL release details

4. CURRENT STATUS Main points of the last update presented to SC6:
New feature added - stochastic recruitments
Incorporating natural variability is necessary for estimating risk
recruitment is a dominant source of natural variability in fish populations and largely determines temporal fluctuations in biomass for some tuna species
Management is increasingly using risk-based reference points, e.g. 10% probability of the stock size being less than that which supports BMSY ; known as a Biological Limit Reference Point (BLRP)

5. Stochastic future recruitments: - Randomly resample with replacement from historical recruitments

6. Total biomass – projection under stochastic recruitments - example for 20 simulation projections

7. Total biomass – projection under stochastic recruitments - example BET, 200 simulations, alternative BLRPs …more details provided in a later agenda item.

8. CURRENT STATUS cont. Main points of the last update presented to SC6:
2. New feature added – tag reporting rates are specific to tag release group
Reporting of tag recaptures is usually voluntary, and the motivation is specific to a release programme (rewards, tag visibility, publicity, goodwill, etc.)
advantageous to the analysis of tag-recapture data to estimate the probability of a recaptured tagged fish being reported, specific to each tag release group
“tag release group-specific reporting rate”

9. Tag release group-specific reporting rates - Example from a developmental SKJ model (S.Hoyle)

10. Tag release group-specific reporting rates
Example of impact of new feature from a developmental SKJ model
black - recapture reporting rates assumed constant red, green – tag release group-specific reporting rates estimated
(taken from Hoyle et al. 2010)

11. CURRENT STATUS cont. Main points of the last update presented to SC6:
3. Project source code management – source code testing and repository updates
Formal testing procedure has been developed for managing source code developments
Repository development branches created for Linux and windows code
A test model data set of reduced size (cutbet) was created to facilitate rapid testing of new features
Testing of stochastic recruitments completed

12. Testing procedure for source code developments

13. Recent and Future developments
Recent developments since SC6:
1. Beverton-Holt stock-recruitment relationship
(SRR) calculatation
Time period for calculation is now flexible and user-defined
Previously assumed the entire model calculation period in deriving the SRR as used in for equilibrium yield estimation; this is now the default option
flags may be set to define a part of the model period to be used for the SRR
explore the effects of selecting a period considered to be more reliable or representative

14. Recent developments since SC6 cont.:
2. Increased number of estimable parameters
some complex models were exceeding the limit, e.g. ALB
number of estimable parameters has been increased from 7000 to 8000
3. Fixes
Projection catch equations made more robust
variance calculation of dependent variables

15. Recent developments since SC6 cont.: 4. Versionning
Increased version number to
Acknowledges revisions and fixes made
5. MFCL posting – August 2010
Version used for 2010 assessments
Posted on website
Some issues with windows executable (required a dll to run) which have since been resolved

16. Recent developments since SC6 cont.: 6. MFCL workshop – January 2011
Dave Fournier and Nick Davies
Project management – compilations and repository
Code reconciliation – merged Linux and Windows source
Stochastic projection functionality – recruitments, numbers-at-age in 1st projection year, effort deviates
Multi-species/stock/sex structure – developments for separate growth and length-weight functions

17. Recent and Future developments
Current developments in progress:
1. Deterministic projections
Testing of alternative recruitment options completed:
SRR_full_period: use SRR to define projected recruitment, distributed among regions according to the average for the full model estimation period
av_recr_T1:T2: use average absolute annual recruitments over a specified historical period
SRR_T1:T2: use SRR to define the total (sum across regions) projected recruitment, distributed among regions according to the average for a defined period

18. Current developments in progress (cont.):
1. Deterministic projections cont.
Fixed projections under zero fishing mortality
Under recruitment option av_recr_T1:T2 and zero fishing mortality, zero recruitments were produced
new code has been developed and tested
Fix projections under catch strategies for all fisheries
problem with particular future catch strategies producing large catch deviates

19. Current developments in progress (cont.):
2. Multi-species/stock/sex structure
development and implementation of a ‘multi-stock (species, sex)’ version
A substantial development
Benefits:
Accommodate sex/spp/stock-specific parameters
Sharing of parameters among sex/spp/stocks
Test model data sets of reduced size have been created BET/YFT for 5 and 6 regions, new frq format to integrate multiples sex/spp/stock data
Separate dimensions created – preliminary fits done
Separate growth parameters applied

20. Swordfish sex-specific growth

21. Current developments in progress (cont.): 3. Stochastic projections
Testing of stochasticity in the three variables: recruitments, numbers-at-age in 1st projection year, effort deviates
Stochasticity in all three variables is operating
Variation in recruitment and effort deviates are as specified
Numbers-at-age in 1st projection year is being tested
More detail on this in a later agenda item…

22. Recent and Future developments
1. Enhancements
Allow region-specific environmental correlates of recruitment
Scheme to estimate seasonal variability in selectivity coefficients
time-series variation in selectivity correlated with a metric for gear configuration or other variable hypothesized to affect selectivity
scheme to allow time-series variation in movement coefficients correlated with an environmental index

23. Future developments: 2. Testing and Fixes
Development of testing framework, complete testing:
Catch-conditioned model
Length-based selectivities; constant over time
Tag release group-specific reporting rates
Statically linked runtime dll files for *.exe releases
Check for log-normal bias in MSY calculation
Tasks to rationalise runtime screen output
Output of tagging likelihood and diagnostics
Output of total likelihood components

24. Tools for MFCL Future developments:
MFCL used increasingly within other applications (BLRPeval, uncertainty analyses)
R scripts are being continually developed and maintained for these applications
Future developments planned:
routine MFCL testing
running stochastic projections
MFCL viewer to include tag release group-specific reporting rate diagnostics
Condor version has been updated, now 58 units

25. WEBSITE STATUS
Current status
Latest posting Aug’08
Summary of users

26. WEBSITE STATUS Current status cont.
Experiencing problems with new registrations
Software used for the site is old, requires upgrade
A temporary arrangement is being used to manage enquiries
New website is being constructed with improved features, and including a forum page

27. Current MFCL release details
New version ready for release; vsn
Changes:
Integrated source code for Linux and Windows compilations
number of estimable parameters increased from 7000 to 8000
Flexibility of Beverton-Holt stock-recruitment relationship calculation time period
Various fixes
User’s guide has been updated to include various changes since 2010