Create Quarto Document of Figures

Create Quarto Document of Figures

create_figures_doc(
  resdir = NULL,
  model_results = NULL,
  model = c("SS3", "BAM", "ASAP", "AMAK", "WHAM"),
  year = NULL,
  subdir = NULL,
  include_all = TRUE
)

Arguments

resdir

Filepath of the directory storing the model results file(s). Examples where dover_sole_2024 is the project root for absolute and relative filepaths, respectively: "C:/Users/patrick.star/Documents/dover_sole_2024/models", "here::here("models")".

model_results

The model results file. Before the stock assessment output file has been converted to a standardized format with the function convert_output.R, the model results file may be a .sso or .rdata file. After conversion, this file will be a .csv file.

model

Type of assessment model that was used to assess the stock (e.g., "BAM", "SS3", "AMAK", "ASAP", etc.).

year

End year for assessment, for inclusion in plotting

subdir

Location of subdirectory storing the assessment report template

include_all

TRUE/FALSE; Option to include all default figures for a stock assessment report. Default is true.

Value

A quarto document with pre-loaded R chunk that adds the stock assessment tables from the nmfs-ost/satf R package. The quarto document will become part of the stock assessment outline.