Rceattle output in the NOAA standardized assessment format

Relabels report_tables() output into the standardized assessment output that the stockplotr and asar packages consume, so Rceattle results can be plotted and written into a report by the same tools used for SS3, BAM, WHAM and FIMS.

Usage

standard_output(x, species = NULL, model = NULL)

Arguments

x: An "rceattle_report" from report_tables(), or an Rceattle fit, which is passed through report_tables() first.
species: Which stock to emit: a species name, or an index into the species this report holds, required when it holds more than one.
model: Which model to emit when x holds several, defaulting to the first.

Value

A data frame with the standardized columns, in the standard's own order, plus species and model.

Details

Quantity names are translated through the standard_label column of quantity_dictionary(), so ssb becomes spawning_biomass, R becomes recruitment, F_spp becomes fishing_mortality, and so on. A quantity the standard has no name for keeps its Rceattle name, so nothing is silently dropped.

The standard has no species dimension. It describes one stock, so a multispecies CEATTLE fit cannot be represented in it as a whole. A species column is held alongside the standard columns and species selects one stock; with several species in the fit and no selection, this errors rather than returning a frame in which two stocks' biomass share a year.

era follows the standard's own vocabulary: "time" for the hindcast the model was fit to, "fore" for the projection.

Examples

if (FALSE) { # \dontrun{
fit <- fit_mod(data_list = BS2017SS, estimateMode = 1)
std <- standard_output(fit, species = 1)
# ...then, with the stockplotr package installed:
# stockplotr::plot_spawning_biomass(std)
} # }