NMFS, PTAGIS, SNKTRP, CJS and SURPH Steven G. Smith Northwest Fisheries Science Center National Marine Fisheries Service 2004 PIT Tag Workshop

Minimum requirements –Statistics and parameter estimates Example: Snake River trap 2003 –PTAGIS data requirements –Generalization from minimum requirements –Tools used in NMFS/UW survival study –SURPH for CJS estimates –SURPH for modeling parameters 2004 PIT Tag Workshop

PIT-Tagged Smolts and Mark-Recapture Statistical Models Minimum requirements: R Dam 1Dam PIT Tag Workshop

Minimum requirements: R Dam 1Dam PIT Tag Workshop **

Minimum requirements: R Dam 1Dam PIT Tag Workshop **

Minimum requirements: R Dam 1Dam PIT Tag Workshop ** P

Minimum requirements: R Dam 1Dam PIT Tag Workshop ** S P

Minimum requirements: R Dam 1Dam PIT Tag Workshop ** S P

Minimum requirements: R Dam 1Dam PIT Tag Workshop ** S P r = number of tagged smolts released

Minimum requirements: R Dam 1Dam PIT Tag Workshop ** S P r = number of tagged smolts released a = number detected at Dam 1

Minimum requirements: R Dam 1Dam PIT Tag Workshop ** S P r = number of tagged smolts released a = number detected at Dam 1 g = number detected at both dams

Minimum requirements: R Dam 1Dam PIT Tag Workshop ** S P r = number of tagged smolts released a = number detected at Dam 1 g = number detected at both dams h = number detected at Dam 2 but not Dam 1

Parameter Estimates R Dam 1Dam 2 ** S P r = number of tagged smolts released a = number detected at Dam 1 g = number detected at both dams h = number detected at Dam 2 but not Dam PIT Tag Workshop

Parameter Estimates R Dam 1Dam 2 ** S P r = number of tagged smolts released a = number detected at Dam 1 g = number detected at both dams h = number detected at Dam 2 but not Dam 1 ^ 2004 PIT Tag Workshop

Parameter Estimates R Dam 1Dam 2 ** S P r = number of tagged smolts released a = number detected at Dam 1 g = number detected at both dams h = number detected at Dam 2 but not Dam 1 ^ ^ 2004 PIT Tag Workshop

Adjustment for transport r = number of tagged smolts released a = number detected at Dam 1 g = number detected at both dams h = number detected at Dam 2 but not Dam PIT Tag Workshop t = number transported at Dam 1 after detection ^ ^

Oregon Idaho Washington Ice Harbor Bonneville The Dalles John Day McNary Lower Monumental Little Goose Lower Granite ** * ** * SNKTRP 2004 PIT Tag Workshop

Data needs from PTAGIS Identify release group –All MY 2003 yearling chinook salmon tagged at Snake River trap 2004 PIT Tag Workshop

Data needs from PTAGIS Identify release group List of all tag codes in release group 2004 PIT Tag Workshop

Tagging Details query 2004 PIT Tag Workshop

Tagging Details CSV list (“tag file”) 2004 PIT Tag Workshop

Data needs from PTAGIS Identify release group List of all tag codes in release group Record of detectors and/or coils on which each fish was seen at each site 2004 PIT Tag Workshop

Interrogation Summary query 2004 PIT Tag Workshop

Interrogation Summary CSV list (“obs file”) 2004 PIT Tag Workshop

Why Get All Coil Records? 2004 PIT Tag Workshop

Why Get All Coil Records?

Data for multiple detection sites Detection (capture) history for each fish in group: –where detected, disposition at each dam: “1” = detected; returned to river “2” = detected; transported “0” = not detected 2004 PIT Tag Workshop

Data for multiple detection sites Detection history for each fish in group: –where detected; disposition “1” = detected; returned to river “2” = detected; transported “0” = not detected e.g. SNK LGR LGO LMO MCN last fish A fish B fish C

Software developed for and used by NMFS/UW survival study CSV list processors CaptHist – PTAGIS reports  detection histories –Windows interactive version “PitPro” cjs – single-release model probability estimates SURPH – suite of analyses of detection history data latest version for Windows SURPH PIT Tag Workshop

Tag File: snktrp03.1.h.tag Obs File: snktrp03.1.h.obs CSV lists processed into text files

CaptHist “chrc” file: parameters to guide processing of input

CaptHist Files: snktrp03.1.h.tag snktrp03.1.h.obs snktrp03.1.w.tag snktrp03.1.h.tag 2004 PIT Tag Workshop

SURPH 2.2 Input File snktrp03.1.srh 2004 PIT Tag Workshop

SURPH 2.2 Base Window before loading data Let’s go SURPHin’ now

2004 PIT Tag Workshop SURPH 2.2 Load Data Everybody’s learnin’ how’

2004 PIT Tag Workshop SURPH 2.2 Base Window after loading data Come on a safari with me

CJS Estimates 2004 PIT Tag Workshop SURPH

2004 PIT Tag Workshop SURPH : Modeling parameters SURPHin’ is the only life

The only way for me 2004 PIT Tag Workshop

Now SURPH, SURPH with me

2004 PIT Tag Workshop SURPH

2004 PIT Tag Workshop SURPH

2004 PIT Tag Workshop SURPH

2004 PIT Tag Workshop SURPH

2004 PIT Tag Workshop Everybody’s gone SURPHin’

2004 PIT Tag Workshop SURPHin’ USA!