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Add Rceattle as compatible model in convert_output(...)#209

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conout-rceattle
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Add Rceattle as compatible model in convert_output(...)#209
Schiano-NOAA wants to merge 22 commits intodevfrom
conout-rceattle

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Allow users to standardize Rceattle output and standardize naming conventions from elements in the model output object.

@Schiano-NOAA Schiano-NOAA linked an issue Mar 16, 2026 that may be closed by this pull request
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New version checklist

  • Package version in DESCRIPTION has been updated
  • Release notes have been drafted/published
  • Cheatsheet content has been updated (if applicable)
  • Cheatsheet version has been updated

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Code Metrics Report

Coverage Code to Test Ratio Test Execution Time
68.3% 1:0.1 4m42s

Code coverage of files in pull request scope (52.8%)

Files Coverage
R/convert_output.R 53.7%
R/utils.R 42.1%

Reported by octocov

@Schiano-NOAA Schiano-NOAA changed the base branch from main to dev April 9, 2026 20:36
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Schiano-NOAA commented Apr 10, 2026

Edits:

  • Change name from total+mortality to total_mortality
  • Add indices into converter (data.list$index_data)
  • Align catch_h and log_index_hat with indexing from data.list$catch_data
  • Align indexing for quantities$age_hat with data.list$comp_data

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@GrantAdams I noticed in Rceattle::plot_index(), you rewrite the log_sd in the index_data, but that column is already present. Is the sd value in that column of the data not correct or is there another reason you do this in the function? Thanks!

Srv_list[[i]] <- Rceattle[[i]]$data_list$index_data

Also, the "Observation" column in index_data are the observed index values in log scale?

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Add functionality in convert_output for Rceattle

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