Remove manual and add an FAQs vignette#234
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* Minor updates to readme * Remove manual and add an FAQs vignette (#234) * Scale uncertainty intervals if relative = TRUE for B and SB plots (#230) * [Fix] plot_indices (#221) * initial commit of new obs v pred plot * adjust process data so it converts all indexed data to character to function even when input values are numeric per #212 * update plot indices to use new plot_obsvpred function and adjust based on needs * update documentation for package * adjust plot_indices where nfleet = 1 and update test to remove new file produced * add missing dependency * Address #218 by scaling uncertainty intervals if relative = TRUE for B and SB plots * remove previous calcs of relative and add if statement instead * adjust relative=TRUE cases to extract proportion from model rather than calc in fxn * add era into arg for plot_biomass * reflect changes for plotting relative values from the model for spawning_biomass * add other option to find biomass when relative * remove relative option from reference_line * adjust ref line when ref is unfished becomes point * remove option to be relative in F plot * remove commented out code * move placement of unfished reference point in if statement * update documentation * remove outdated tests for sb plot * remove extra test and fix relative testing * remove relative example from sb plt since it doesnt exist in the example data * update documentation * remove rel F quantities --------- Co-authored-by: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> * Update documentation: move info from 'returns' to 'details' (#246) * Update roxygen 'return' to 'returns'; Start moving some information from roxygen 'returns' to 'details' as per #244 * Finish updating roxygen as per #244 * Add "seealso" section to documentation (#247) * Add "seealso" section to roxygen documentation in utils_rda.R functions * Add "seealso" section to roxygen documentation for all other functions besides figures * Add "seealso" section to roxygen documentation for all figures functions * Update seealso function formatting * Update WORDLIST * update save_all_plots() to export landings table; remove now-deprecated 'relative' arg from plot_fishing_mortality() in save_all_plots() (#249) --------- Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
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* Minor updates to readme * Remove manual and add an FAQs vignette (#234) * Scale uncertainty intervals if relative = TRUE for B and SB plots (#230) * [Fix] plot_indices (#221) * initial commit of new obs v pred plot * adjust process data so it converts all indexed data to character to function even when input values are numeric per #212 * update plot indices to use new plot_obsvpred function and adjust based on needs * update documentation for package * adjust plot_indices where nfleet = 1 and update test to remove new file produced * add missing dependency * Address #218 by scaling uncertainty intervals if relative = TRUE for B and SB plots * remove previous calcs of relative and add if statement instead * adjust relative=TRUE cases to extract proportion from model rather than calc in fxn * add era into arg for plot_biomass * reflect changes for plotting relative values from the model for spawning_biomass * add other option to find biomass when relative * remove relative option from reference_line * adjust ref line when ref is unfished becomes point * remove option to be relative in F plot * remove commented out code * move placement of unfished reference point in if statement * update documentation * remove outdated tests for sb plot * remove extra test and fix relative testing * remove relative example from sb plt since it doesnt exist in the example data * update documentation * remove rel F quantities --------- Co-authored-by: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> * Update documentation: move info from 'returns' to 'details' (#246) * Update roxygen 'return' to 'returns'; Start moving some information from roxygen 'returns' to 'details' as per #244 * Finish updating roxygen as per #244 * Add "seealso" section to documentation (#247) * Add "seealso" section to roxygen documentation in utils_rda.R functions * Add "seealso" section to roxygen documentation for all other functions besides figures * Add "seealso" section to roxygen documentation for all figures functions * Update seealso function formatting * Update WORDLIST * update save_all_plots() to export landings table; remove now-deprecated 'relative' arg from plot_fishing_mortality() in save_all_plots() (#249) --------- Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Schiano-NOAA
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May 8, 2026
* Minor updates to readme * Remove manual and add an FAQs vignette (#234) * Scale uncertainty intervals if relative = TRUE for B and SB plots (#230) * [Fix] plot_indices (#221) * initial commit of new obs v pred plot * adjust process data so it converts all indexed data to character to function even when input values are numeric per #212 * update plot indices to use new plot_obsvpred function and adjust based on needs * update documentation for package * adjust plot_indices where nfleet = 1 and update test to remove new file produced * add missing dependency * Address #218 by scaling uncertainty intervals if relative = TRUE for B and SB plots * remove previous calcs of relative and add if statement instead * adjust relative=TRUE cases to extract proportion from model rather than calc in fxn * add era into arg for plot_biomass * reflect changes for plotting relative values from the model for spawning_biomass * add other option to find biomass when relative * remove relative option from reference_line * adjust ref line when ref is unfished becomes point * remove option to be relative in F plot * remove commented out code * move placement of unfished reference point in if statement * update documentation * remove outdated tests for sb plot * remove extra test and fix relative testing * remove relative example from sb plt since it doesnt exist in the example data * update documentation * remove rel F quantities --------- Co-authored-by: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> * Update documentation: move info from 'returns' to 'details' (#246) * Update roxygen 'return' to 'returns'; Start moving some information from roxygen 'returns' to 'details' as per #244 * Finish updating roxygen as per #244 * Add "seealso" section to documentation (#247) * Add "seealso" section to roxygen documentation in utils_rda.R functions * Add "seealso" section to roxygen documentation for all other functions besides figures * Add "seealso" section to roxygen documentation for all figures functions * Update seealso function formatting * Update WORDLIST * update save_all_plots() to export landings table; remove now-deprecated 'relative' arg from plot_fishing_mortality() in save_all_plots() (#249) --------- Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
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Remove manual and add an FAQs vignette