[Bug:] cannot estimate log_sd in a distribution

[kellijohnson-NOAA]

Describe the bug

I am trying to estimate the log_sd parameter in a normal distribution for recruitment deviations. I changed the estimation type to be "fixed effects" and yet get_fixed() does not add log_sd to the parameter list.

Describe how to reproduce the bug

This is in the Pacific Hake case study or a test in testthat using power user way can do this by changing

recruitment_distribution$log_sd[1]$estimation_type$set("fixed_effects")

Screenshots

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Which OS are you seeing the problem on?

No response

Which browser are you seeing the problem on?

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Which version of FIMS are you seeing the problem on?

v0.8.0

Additional context

No response

[Andrea-Havron-NOAA]

@kellijohnson-NOAA, this may be an error in your implementation.

By default, methods::new(DnormDistribution) sets up an initial log_sd vector of size one, so you do not need to call the following line:

recruitment_distribution$log_sd <- methods::new(ParameterVector, 1)

I think you are changing the estimation type setting of a copy that never gets passed into the model. If you removed the above line, you can just set the value of log_sd and its estimation type directly and this should carry through to the model.

[nathanvaughan-NOAA]

Well hopefully @Andrea-Havron-NOAA found the actual solution. I was going to say that log_sd is also setup as a fixed effect in the test-projections-looped.R code and is being added to the get_fixed() output if that helps to have as an example. In the projections scenario it is probably what has caused some of the problems so I'll be trying with it constant at some point.

[kellijohnson-NOAA]

You are spot on @Andrea-Havron-NOAA. Now we need to

• get the parameter in the json output
• get the parameter in the estimates tibble
• fix the advanced case study that I copied this from to not do it

[Andrea-Havron-NOAA]

@kellijohnson-NOAA, the PR NOAA-FIMS/FIMS#1125 adds log_sd to the json output

[kellijohnson-NOAA]

Great @Andrea-Havron-NOAA. I am going to move this issue to the case-study repository now.