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PIFSCstockassessments / ss3diags

R package with advanced diagnostics to evaluate a Stock Synthesis model. Diagnostics include residual analyses, hindcasting and cross-validation techniques, and retrospective analyses.
http://pifscstockassessments.github.io/ss3diags/
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Remove this argument #95

Open MOshima-PIFSC opened 1 year ago

MOshima-PIFSC commented 1 year ago

There is an 'uncertainty' argument but it does not seem to be used in the code and when I tested it, there was no obvious impact on the plot. The 'indexUncertainty' argument turns the uncertainty interval on and off but I think this argument can be removed.

https://github.com/PIFSCstockassessments/ss3diags/blob/80ba04ab6e3bb88186923582b53bf349b6395885/R/SSplotHCxval.R#L99

MOshima-PIFSC commented 1 year ago

To resolve this issue, @efletcherPIFSC and I decided to remove the #' @inheritParams SSplotGenericUncertainty argument, and include `#' @param mcmcVec

' Logical vector of TRUE/FALSE values (or single value) indicating

' whether input values are from MCMC or to use normal distribution around

' MLE.

'

' @param models Optional subset of the models of summaryoutput (or a similar

' field with a different name): a list created by the function

' [r4ss::SSsummarize]. Either "all" or a vector of numbers indicating

' columns in summary tables.manually in the function documentation. Theuncertaintyparameter was added automatically from using theinheritParamsfunction. We discussed keepinguncertainty` and removing indexUncertainty (and renaming to uncertainty in the code) however, Eric made a good point that for compatibility reasons, we should keep indexUncertainty and remove uncertainty.