85403: Rev 1: WE H: Work Element Summary

Work Element Summary PDF

Select a work element:

Basics

Contract Number:

85403

Contract Title:

2019-006-00 EXP BIOMARK SNAKE RIVER FISH AND HABITAT

Contract Start Date:

6/1/2020

Contract End Date:

5/31/2021

WE ID:

156. Develop RM&E Methods and Designs

Work Element Usage Report

Title:

H: 156 - Improve flexibility and end-user support for the Dam Branch Occupancy Model (DABOM).

Description:

DABOM was developed as a proof-of-concept model to generate age and sex structured escapement above Lower Granite Dam and Priest Rapids Dam using PIT tag interrogation data. In recent years the use of DABOM has become commonplace, and requests to extend DABOM and support end-users (i.e., co-managers) has become commonplace. This work element will support recoding of DABOM to enable end-users to more easily add/remove interrogation sites, new watersheds, and new tag groups (e.g., hatchery-origin adults). When approriate work on the PITCleanR and STADEM tools where interoperable should be conducted .

WE Agreement Type:

Contracted

Deliverable Specification:

This Work Element will be considered complete when a new protocol and method have been created in monitoringresources.org. Outcomes will be summarized for the contract annual report (Work Element I).

WSE Effective Budget:

$139,899

% of Total WSE Effective Budget:

51.89%

WSE Start:

06/01/2020

WSE End:

05/28/2021

WSE Completion:

WSE Progress:

Other

WSE ID Continued From:

[Unassigned]

WSE ID Continued To:

[Unassigned]

Finite or Recurring:

Finite

Budget History

SOWRevision	Planned	Updated	Contractor Comments (optional)	BPA Comments (optional)
Work Element Budget (Current Performance Period)	$139,899	$139,899
	$139,899	$139,899

Milestones

4 Milestones

Sort	Type	Title	Start	End	Status	Modified By	Modified Date
A	EC	Environmental compliance requirements complete	6/1/2020	6/30/2020	Canceled	Jody Lando	5/12/2020 8:52:11 AM
		Description: On-the-ground work associated with this work element cannot proceed until this milestone is complete. Milestone is complete when final documentation is received from BPA environmental compliance staff.
B		Recode DABOM.	6/1/2020	3/31/2021	Active	Jody Lando	5/15/2020 10:25:45 AM
		Description: Specific modifications to DABOM include: • Development of a function to take generic node order from PITCleanR and automatically generate the appropriate DaBOM model in JAGS. • Incorporate ability to include hatchery and natural origin fish, as currently implemented at Priest Rapids Dam. • Development of a standard naming convention for detection and transition probabilities based on PTAGIS site codes. • A generic function to appropriately name multinomial transition probabilities based on site codes. • A generic function to combine transition probabilities appropriately (currently hard-wired for 3 starting points with specific parameter names). • A generic function to generate initial values for JAGS. • Improve the ability to combine outputs of StaDEM (or other estimate of total escapement) with transition probabilities to estimate escapement. • Development of functions to summarize escapement to larger spatial scales (e.g. MPG, ESU / DPS): o Include MPG / ESU boundaries as shapefiles in package and utilize a function to group estimates appropriately to estimate escapement at these scales. o Generic function that utilizes polygons, with the ability to use MPG, ESU, or user-defined polygons. • Development of a function to support user-defined priors on detection probabilities for particular sites (e.g., when additional information supports improved efficiency estimation). • Develop a detailed user-manual.
C	PUBPROTOCOL	Review, revise, and publish Study Design and Methods in monitoringmethods.org	1/1/2021	5/28/2021	Active	Jody Lando	5/12/2020 8:52:11 AM
		Description: The Study Design (including temporal and spatial design) and Methods for this work element are stored at monitoringresources.org and need to be finalized (i.e., "Published" through monitoringresources.org), preferably prior to data collection. Preparations for contract renewals must include reviewing any previously published Study Design/Methods to ensure that they are consistent with how work will be done in any subsequent contract.
D	DELIV	New method and protocol.		5/28/2021	Active	Jody Lando	5/12/2020 8:52:11 AM
		Description: This Work Element will be considered complete when a new protocol and method have been created in monitoringresources.org. Outcomes will be summarized for the contract annual report (Work Element I).

Metrics

Implementation Metrics

None

Study Plan Name	Study Plan Owner	Protocol State	Sample Design Name
Operation Monitor Salmon ISEMP Snake River Adult Salmon Steelhead Tributary Escapement Estimation Protocol v1.0 v1.0	Carol Volk	Draft

Methods:

ID	Name	Type	Optional	Customized Based On	Status
303	Carcass tissue sampling - fin tissue for genetic analysis v1.0	Data Collection	No	N/A	Finalized

Metrics:

Title	Category	Subcategory	Subcategory focus 1	Subcategory focus 2
Abundance by Age of Adult Returning Salmonids at PIT Arrays	Fish	Abundance of Fish (ID: 46)	Fish Life Stage: Adult - Returner	Fish Origin: Both
Adult Salmonid PIT tag abundance detected at PIT Array	Fish	Abundance of Fish (ID: 46)	Fish Life Stage: Adult - Returner	Fish Origin: Both
Age of Adult Salmonids Detected at PIT Array	Fish	Age Structure: Fish (ID: 49)	Fish Life Stage: Adult - Returner	NA
Tributary Adult to Juvenile Tributary Productivity	Fish	Progeny-per-Parent Ratio (P:P) (Productivity) (ID: 86)	Fish Life Stage: RANGE: Juvenile to Adult	NA

Please correct the errors noted below.

Basics

Budget History

Milestones

Metrics

Implementation Metrics

Location

Focal Species

Environmental Compliance

RM&E Metadata