Confused by the use of rickerSurvModel in the LRP branch

[catarinawor]

I need help understandidng the generation of the survival covariates in the priming loop, when y>3 here.

I am having trouble understanding how the delays relate to the age structure. if either @krHolt or @carrieholt could go over it, that would be fantastic.

[krHolt]

I just added some documentation to the code around this issue, but we should still go over it together to discuss.

[catarinawor]

@krHolt did you push it? I am not seeing it!

[catarinawor]

Thank you for the explanations, Kendra. Super helpful. Just a reminder to follow up on the sources of the variable coVarInit, used to calculate Sgen and Smsy when the RickerSurv model is used.

[krHolt]

At present:

• mu_logCoVar1 is specified as the mean of the logged marine survival rate time series, and is used to specify the distribution that annual marine survival rates come from. E.g., mu_logCoVar1 = mean (log(mSurvs))
• coVarInit is the marine survival rate that gets used to calculate Sgen within samSim. It gets input on the raw scale, and then logged within samSim to calculate the alpha-prime for the Sgen calculations.

I parameterize coVarInit as exp(mu_logCoVar1), which means that these two are retrievable from each other. I think it makes sense to remove coVarInit as an input parameter, and just use exp(mu_logCovar1) to calculate alpha_prime.

[krHolt]

I have now removed coVarInit as a model parameter, and now use exp(mu_logCovar1) to calculate alpha_prime.