[Bug]: plot_biomass not plotting relative error values when relative = TRUE

[CPerretti]

library(asar)

load("Western_Gulf_of_Maine_cod2024.rda")
wgom <- model_results

stockplotr::plot_biomass(
dat = wgom,
geom = "line",
group = NULL,
facet = NULL,
#ref_line = c("target" = 10),
unit_label = "mt",
scale_amount = 1,
relative = TRUE, # changed from FALSE
#interactive = FALSE,
#module = "TIME_SERIES",
linewidth = 2 # increase width of lines
) +
ggplot2::geom_vline(xintercept = 2005, linetype = "dashed", color = "red")

[Schiano-NOAA]

@sbreitbart-NOAA I assigned you to this issue. This was the bug that @CPerretti showed in the workshop. I believe the only issue is that uncertainty intervals are not scaled when relative = TRUE. This just needs to be adjusted and all should work

[sbreitbart-NOAA]

@Schiano-NOAA Do you know of a sample dataset that will show this issue? I've tried with the stockplotr example data, bsb, hake, sablefish, skate, and vsnap, and haven't produced a plot with uncertainty intervals.

[Schiano-NOAA]

@sbreitbart-NOAA I believe the updated plots in dev will give you access to derived quantities when era = NULL which will then give you error

[sbreitbart-NOAA]

While trying to reproduce that error, I found that these commands produce the same plot:

plot_fishing_mortality(hake,
  group = NULL,
  module = "DERIVED_QUANTITIES", 
  era = NULL, relative = TRUE, 
  ref_line = c("test" = 0.01))

plot_fishing_mortality(hake,
  group = NULL,
  module = "DERIVED_QUANTITIES", 
  era = NULL, relative = TRUE, 
  ref_line = c("test" = 1000))

[sbreitbart-NOAA]

Also @Schiano-NOAA I'm still not able to produce a biomass plot with the ribbon 😬 could you please provide a reprex?

[Schiano-NOAA]

Could you try running a plot and adjusting the error? For example try:

plot_biomass(
dat = sablefish |> dplyr::mutate(uncertainty = 0.5, uncertainty_label = "se"), 
era = NULL)

I think this should brute force it by setting all estimates to an uncertainty of 0.5 and now it's available when plotting.