SSMSE
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ALK tolerance mismatch between OM and EM can cause a large bias in SSB
Thanks to the sardine team for pointing this out! In the OM, the ALK tolerance setting is reset to 0, as Rick Methot has recommended turning off tail compression in an OM. However, nothing is done for EM's, so in a sardine model with ALK tolerance of 0.001 in the EM, there was a large bias in SSB between OM and EM (and the EM had estimation issues). Setting the ALK tolerance to 0 as well for the EM seems to solve the issue.
A potential solution would be to reset ALK tolerance to 0 in EMs as well or at least warning users to consider doing this.