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.

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

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

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)

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

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

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

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”

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

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)

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

Testing procedure for source code developments

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

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

Recent developments since SC6 cont.: 4. Versionning Increased version number to 1.1.0.0 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

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

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

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

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

Swordfish sex-specific growth

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…

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

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

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

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

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

Current MFCL release details New version ready for release; vsn 1.1.1.0 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