Draft Summary of Data Used in JPE • SRJPEdata

Overview

The spring run juvenile production estimate (SR JPE) contains a suite of submodels that rely on different datasets. This document is currently focused on Chinook monitoring data that will be used to fit the stock recruit model.

Additional sections will be added to highlight survival, genetics, and covariate data.

Stock Recruit Modeling Data Selection

Gathering and identifying spring run Chinook monitoring data to use in the spring run juvenile production estimate (SR JPE) was an iterative, multistep process. We acquired, processed and described monitoring data, hosted workshops to define a ruleset for evaluating years to exclude based on missing data (see years to include vignette for an in depth overview of this process), selected data where there was both adult and juvenile data, and finally selected a single adult dataset to use for each year and stream. The diagram below visualizes this process and shows the total number of datasets we retained along the way.

Distinct annual datasets are identified by looking at distinct year, stream, and monitoring types

Monitoring Data Overview

Extensive spring run Chinook monitoring is conducted throughout the Central Valley. Monitoring programs have been collecting data since the 1990s and monitoring has increased through time to expand monitoring types and data collection coverage across the seven tributaries and mainstem Sacramento River (identified as the geographic scope for the SR JPE).

The plot below shows all monitoring coverage of rotary screw trap, adult upstream passage, adult holding, adult redd, and adult carcass survey data.

Plot does not include Sacramento River mainstem monitoring. This data may also be utilized in the SR JPE but will not be included in the stock recruit models. For some monitoring types data is collected annually or monthly communicated through gaps in the colored lines.

Filtering data to years that contain both juvinile and adult monitoring

In order to utilize data for the stock recruit models, we need both juvenile data inputs (RST data) and adult data inputs (adults) for each year. The plot below shows the time windows where there is overlapping juvenile and adult monitoring on each tributary. While this limits the amount of data, it still provides a few large windows for most monitoring programs.

Gray boxes indicate that monitoring occurred but data is not being utilized for the stock recruit since a year does not have both adult and juvenile data

Excluding Incomplete Years

Although the SR JPE aims to utilize all available data, there are some years where data is sparse and is excluded from analysis. This decision process is documented in the Years to Include Analysis.

After filtering the RST and adult data to remove incomplete or inconsistent years, we are left with the following windows for the SR JPE. Gray boxes indicate that monitoring occurred but data is not being utilized for modeling. See years to exclude tables for additional information on why a year might be excluded.

Gray boxes indicate that monitoring occurred but data is not being utilized for the stock recruit. Data may be excluded because there is not adult and juvenile annual overlap or because the data was considered incomplete for a given monitoring type and year.

Summary Table of Years to Use for Stock Recruit

The summary table below describes which years have overlapping RST and adult data. This table accounts for years excluded based on data quality and completeness considerations.

Stream	Years to Include in Model	Total Number of Years
battle creek	2005 - 2006, 2009 - 2014, 2016, 2020 - ongoing	11
butte creek	2001 - 2004, 2007 - 2008, 2013 - 2014, 2016 - 2018, 2020 - ongoing	14
clear creek	2003 - 2010, 2012 - 2015, 2021 - ongoing	13
deer creek	1992, 1995 - 1996, 2000 - 2003, 2005, 2007, 2009 - 2010, 2022 - ongoing	11
feather river	2010 - 2012, 2018 - 2020, 2022 - ongoing	7
mill creek	2000 - 2003, 2005 - 2008, 2010	9
yuba river	2004 - 2008	5

This table shows us that there are a total of 70 stream years to use for developing the SR JPE stock recruit model.

Selecting Adult Data Type to Use

There are 35 stream year combinations where there are multiple adult data types to pick from. These occur for: “butte creek”, “battle creek”, “clear creek”, and “feather river.”

The process of determining the appropriate adult data to use in stock recruit modeling for the SR JPE is currently ongoing. This information will be updated as the Modeling Team evaluates the tradeoffs associated with various data types in more detail.

We used the following logic to select data to use in these cases:

if stream = "butte creek" we used carcass estimate data (carcass estimate methods include mark recapture)
if stream = "battle creek" we used…TODO
if stream = "clear creek" we used…TODO
if stream = "feather river" we used…TODO

Year	Stream	Sampling Type	Selected Adult Data Type
2001	butte creek	rst , carcass, holding	carcass estimate
2002	butte creek	rst , carcass, holding	carcass estimate
2003	butte creek	rst , carcass, holding	carcass estimate
2004	battle creek	rst , holding , upstream passage	TBD
2004	butte creek	rst , carcass, holding	carcass estimate
2005	battle creek	rst , redd , holding , upstream passage	TBD
2006	battle creek	rst , redd , holding , upstream passage	TBD
2007	butte creek	rst , carcass, holding	carcass estimate
2008	battle creek	rst , redd , holding , upstream passage	TBD
2008	butte creek	rst , carcass, holding	carcass estimate

… with 28 more rows

Proposed Data to Use in SR JPE

The table below compiles all the filtering above to provide a summary of the data utilized for the stock recruit models for each stream and year.

Year	Stream	Juvenile Data Type	Adult Data Type
1992	deer creek	rst	holding
1995	deer creek	rst	holding
1996	deer creek	rst	holding
2000	deer creek	rst	holding
2000	mill creek	rst	redd
2001	butte creek	rst	TBD
2001	deer creek	rst	holding
2001	mill creek	rst	redd
2002	butte creek	rst	TBD
2002	deer creek	rst	holding

… with 77 more rows