1. Experiences Handling PTAGIS Data in Comparative Survival Study By Tom Berggren Fish Passage Center Portland OR

2. Overview Presentation to address experiences working with PTAGIS data – see CSS Annual Reports at www.fpc.org for report results Downloading PIT tag data from PTAGIS Assigning capture disposition based on route of passage Verifying fish migrating in year of interest Applying 2 approaches of CJS single release model Checking adult returns of “never detected smolts” Planning to investigate hatchery-to-hatchery and wild stock-to-wild stock variations in SARs

3. Downloading PIT tag data from PTAGIS Check release number in PTAGIS Tagging Details Report & UW DART Web page Obtain tag_id list and run thru Registered Tag Id File Report -- lists <50,000 tags best FPC puts TAG, REC, MOR, OBS info into Sequel Database Provide FPC programmers with information on route of passage for determining fish capture histories

4. Determining passage routes of PIT tagged fish at dams Check with SMP crews at each dam with transportation to see if “exceptions” to normal routes of passage during season -- e.g., dumping raceway fish back to river Check capture histories and verify times of “exceptions” and tweak as necessary to insure proper assignment of routing Exceptions list created for programmers

5. LGR disposition “A”in “1Axxxxxx” Last Monitor NameDates in 2001Cap_Disposition Digit Diversion RE; -1; -2All Dates“1” Raceway East5/15 11:59 – 5/16 00:24 5/16 01:58 – 5/16 14:57 5/16 18:54 – 5/16 20:56:59 5/16 20:57 – 5/17 01:59 All other dates Change “2” to “1” Change “2” to “3” Change “2” to “1” “2” Raceway West5/15 08:57 – 5/15 13:58:30 5/17 01:50 – 5/18 05:10 All other dates Change “2” to “3” “2” Sample Tank5/15 06:00 – 5/18 06:00 All other dates Change “2” to “3” “2” Diversion/SbyC Gate or SbyC Gate 4/30 14:59 – 5/06 08:42 5/16 06:23 – 5/16 20:08 All other dates Change “1” to “3” “1” A-; B-SeparatorAll dates“3”

6. Level of capture disposition assignment related to study If only need river survival, determine which tagged fish are returned-to-river, since all others are removals in CJS model If need survival by route of system passage, determine which tagged fish are transported as well as those returned-to-river Use unknown disposition when in doubt

7. Survival estimation software For survival only, we use CSU’s MARK program due to ease with large releases, and presence of Burnham’s Test 2 and Test 3 For survival plus SARs, FPC created a bootstrap program that gives river reach survivals, SARs for transported and in-river migrants, ratios of SARs, and D plus 95% confidence intervals

8. Using aggregate PIT tag groups Hatchery chinook -- we run each hatchery group separately to get survivals and SAR Wild fish -- we run an aggregated set of all wild PIT tagged chinook originating above LGR tagged in 10-mon period 7/25 to 5/20 Exclude fish detected completely in year outside of expected migration year Smolts detected in two years, consider removal after last detection in first year

9. CJS survival estimates from full sample vs LGR subcohorts Aggregates of PIT tagged wild fish – typically use weighted mean of Sj from LGR subcohorts due to wider passage distribution; WM Survival estimates have wider confidence intervals Single hatchery PIT tagged fish – typically use full release sample due to narrower passage distribution; Full Sample Survival estimates have narrower CI

10. Geometric mean reach survival across raph, mcca,dwor,imna Reach CJS 2001 2000 1999 1998 S2*S3Sub-cohorts Full sample 0.80 0.79 0.82 0.85 0.89 0.86 0.89 0.83 VcSub-cohorts Full sample 0.26 0.30 0.36 0.57 0.56 0.66 0.65 0.62

11. Comparison of Full Sample vs LGR sub-cohort CJS survivals Reach LGR tailrace to LMN tailrace S2*S3 tends to have lower estimates with Full Sample CJS, but still close Reach LGR tailrace to BON tailrace Vc tends to have higher estimates with Full Sample CJS, and more variable from LGR sub-cohort Simulation studies to investigate approaches

12. Check PIT tagged adult returns for feasibility of capture history Straightforward for detected smolts Check adults of “never detected” smolts MY 2001 has 5 tagged CSS hatchery adults & 1 tagged wild adult with “10000000” 4 of the 5 hatchery adults from McCall H Suspicious since Category C0 has only 2 more hatchery adults (none from McCall H) and no more wild adults

13. LGR passage timing of McCall H chinook was in May during period of high total fish passage

14. Cont. “10000000” tagged adults PIT tagged adults with history “10000000” may have been undetected but transported at LGR for smolts migrating in 2001 Since undetected PIT tagged fish in bypass channel will go to raceways with untagged fish Since PTAGIS logs a computer malfunction in 2001 for 18 minutes on 5/21 when all PIT tagged fish likely passed to the raceways undetected

15. LGR: 1-hit tagged fish

16. Est. Number Smolts per Category (sum of raph, mcca, dwor, imna) Category 2001 2000 1999 1998 T0 48 K 54 K 38 K 42 K C0 3 K 42 K 29 K 21 K Because of few PIT tagged fish in Category C0 in 2001, greater impact of including a mis-assigned “10000000” PIT tagged adult than in earlier years

17. Final thoughts Hatchery-to-hatchery variation in SARs: highest for MCCA; RAPH& IMNA intermediate; DWOR lowest Possible large sub-basin to sub-basin survival variation for PIT tagged wild smolts in aggregate – PIT tagged Imnaha R wild chinook migrating in 2001 had a 3-fold higher SAR (2-salts only) compared to aggregate of other 3 sub-basins above LGR Plan to investigate sub-basin variation with 1994-2001 data (where feasible due to tag numbers) in next annual report