Rebuilder year values #2
brianlangseth-NOAA
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I want to be clear on the values for Yinit, Ydecl, and Yinit^0
Per old emails with Owen (send Sept 8, 2021), the 2021 quillback values for Yinit, Ydecl, and Yinit^0 were
Yinit = 2021
Yinit^0 = 2021
Ydecl = 2023
These align with the 2009 petrale rebuilder files.
From the rebuilder manual, the definitions of these are as follows:
5) Yinit: “First year of the projection (Yinit)”:
6) Ydecl: “First year the OY could have been zero”:
19) Age-structure at the start of year Yinit^0”: For each sex (females then males), enter the ‘best estimates’ of the numbers of animals of each age at the start of the year in which the rebuilding plan first could have had an impact on the ACL, yinit^0. In general, this year should be the year in which the species / stock was declared overfished. However, it will be a year before ydecl if an assessment has not taken place since ydecl.
20) “Year Yinit^0”: Enter the year to which the previous input relates, yinit^0. This input should either be ydecl or yinit depending on whether an assessment has occurred since ydecl or not.
The tricky thing is with the definition of Yinit^0, for which the user must enter in the age structure. SS3 defaults this value to Ydecl, but it could be Yinit. For 2021 quillback I used 2021, so for setting up rebuilding, I had to overwrite the SS3 generated output by copying over the 2021 (Yinit) age structure for this entry (and also for each state of nature run for having uncertainty with starting conditions). Although the rebuild.dat file defaults this entry to be from Ydecl, the echo.dat file generated after running the rebuilder exe calls this entry "Age-structure at the start of the year Yinit" which suggests Yinit is to be used.
Use of Yinit for Yinit^0 is also supported in section 1.1.2 of the manual, which suggests the age-structure should be from Yinit for the 2021 quillback case (because Yinit < Ydecl). This section is copied below, with the pertinent parts highlighted.
All this to say, for 2023 quillback, I plan to use the following, which also means I need to overwrite SS3 output for the second age-structure values when running rebuilder, and when setting up the alternative states of nature.
Yinit = 2021
Yinit^0 = 2021
Ydecl = 2025
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