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[feat]: Adds index intervals, follows PR #465 - #468
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Schiano-NOAA merged 10 commits intoNov 13, 2026
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convert_output() passed FIMS output through unchanged, so `estimate` and `year` were empty and no stockplotr plot could use it. The new conout_fims() reshapes `FIMS::get_estimates()` output (or a FIMSFit object, or an .rds file with either): - Each data point (index, landings, age and length compositions) is split into "*_observed" and "*_predicted" rows, with the observation error and negative log-likelihood on the observed row, as for SS - `estimated` becomes `estimate`, and the new `start_year` argument converts FIMS year indices to years; `era` is "time", or "fore" after the last year of data. - fims_var_names.csv maps current FIMS labels (e.g., expected_recruitment, numbers_at_age, log_devs) to the standard labels. Also fixes: - convert_output() ignored a user-supplied `model` when `file` is an object. - plot_index() matched every label containing "index" (e.g., index_log_q in Rceattle output or index numbers at age in FIMS output); it now plots only index_observed and index_predicted. - plot_index() failed for a single index fleet, because the fleet facet was added back after process_data() dropped the column.
plot_index() adds `interval`, which draws intervals around the observed index from its observation error, and `log`, which plots the index on a log scale. Intervals assume lognormal errors, as in Stock Synthesis, FIMS, BAM, and Rceattle: uncertainty labeled "se", "sd", or "log_sd" is used as the log-scale standard error, and a CV is converted with sqrt(log(1 + CV^2)). Both default to the current behavior (no intervals, linear scale).
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Make default interval 0.95 per @iantaylor-NOAA
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@sbreitbart-NOAA @Schiano-NOAA This is ready for review |
This was referenced Nov 8, 2026
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This looks good. Just one question to address and I will merge.
Fixed and better documented 3 logic pathways
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@Schiano-NOAA Thanks for the suggestions, all incorporated here: ac9b513 |
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A1! Thanks so much |
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* [feat]: convert FIMS output to the standard format in `convert_output()` convert_output() passed FIMS output through unchanged, so `estimate` and `year` were empty and no stockplotr plot could use it. The new conout_fims() reshapes `FIMS::get_estimates()` output (or a FIMSFit object, or an .rds file with either): - Each data point (index, landings, age and length compositions) is split into "*_observed" and "*_predicted" rows, with the observation error and negative log-likelihood on the observed row, as for SS - `estimated` becomes `estimate`, and the new `start_year` argument converts FIMS year indices to years; `era` is "time", or "fore" after the last year of data. - fims_var_names.csv maps current FIMS labels (e.g., expected_recruitment, numbers_at_age, log_devs) to the standard labels. Also fixes: - convert_output() ignored a user-supplied `model` when `file` is an object. - plot_index() matched every label containing "index" (e.g., index_log_q in Rceattle output or index numbers at age in FIMS output); it now plots only index_observed and index_predicted. - plot_index() failed for a single index fleet, because the fleet facet was added back after process_data() dropped the column. * Update WORDLIST * [feat]: observation-error intervals and log scale in `plot_index()` plot_index() adds `interval`, which draws intervals around the observed index from its observation error, and `log`, which plots the index on a log scale. Intervals assume lognormal errors, as in Stock Synthesis, FIMS, BAM, and Rceattle: uncertainty labeled "se", "sd", or "log_sd" is used as the log-scale standard error, and a CV is converted with sqrt(log(1 + CV^2)). Both default to the current behavior (no intervals, linear scale). * [feat]: plot all indices relative to their means with `plot_index(relative = TRUE)` `relative = TRUE` divides each fleet's observed and predicted index (and intervals) by the mean of its observed index and plots all fleets on one panel, colored by fleet, so that trends can be compared among indices (r4ss SSplotIndices subplot 9). Facet variables with one value for each fleet (e.g., the month of each survey) do not split the panel. `relative = TRUE` divides each fleet's observed and predicted index (and intervals) by the mean of its observed index and plots all fleets on one panel, colored by fleet, so that trends can be compared among indices (r4ss SSplotIndices subplot 9). Facet variables with one value for each fleet (e.g., the month of each survey) do not split the panel. * Update plot_index.R make sure this is consistent with other outstanding PR * Update plot_index.Rd redoc * Bring same files over to update per commit # 467 * update per changing defaults * Update R/plot_index.R Co-authored-by: Sam (Schiano) Bredeck <125507018+Schiano-NOAA@users.noreply.github.com> * devtools::doc --------- Co-authored-by: Sam (Schiano) Bredeck <125507018+Schiano-NOAA@users.noreply.github.com>
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What is the feature?
Adding
intervalargument to plot_index#' plot_index(
#' dat = stockplotr::example_data,
#' interval = 0.95,
#' log = TRUE,
#' interactive = FALSE
#' )
Follows #465
How have you implemented the solution?
Does the PR impact any other area of the project, maybe another repo?
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