add "Total without prior" line to profile plots #822
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- also make verbose work better
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## main #822 +/- ##
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Coverage 51.97% 51.98%
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Files 111 111
Lines 26170 26260 +90
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+ Hits 13602 13651 +49
- Misses 12568 12609 +41
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chantelwetzel-noaa
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Jun 14, 2023
Deprecate the use_prior_like function input for parameter profiles (issue #6) since r4ss is now dynamically showing this in profiles if a prior likelihood is used r4ss/r4ss#822
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For profiles over parameters which have a prior, this adds a line to the profile plot showing the total likelihood without the contribution of the prior (fixes #750 and eventually can resolve pfmc-assessments/nwfscDiag#6).
For parameters with no prior or with the prior for fixed parameters excluded via starter file settings, it should have no impact.
Changes include
SSsummarize()now includes apar_prior_likestable in the list it returnsSSplotProfile()uses that information to add a line when it sees non-zero/non-NA values for the parameter being profiledSSplotProfile(..., add_no_prior_line = FALSE)but the default is TRUE.PinerPlot()because it is focused on the fleet-specific likelihood contributions to a single data type and that data type will never be the priors (because they are not generally fleet-specific).Example result shown in figure below (showing that for an in-process Petrale Sole model, all sources except the prior point to higher steepness).
