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Call previous assessment report and update

Source: R/update_report.R
update_report.Rd

Call previous assessment report and update

Usage

update_report(
  file_dir = getwd(),
  previous_file_dir,
  authors = NULL,
  model_results = NULL,
  year = format(as.POSIXct(Sys.Date(), format = "%YYYY-%mm-%dd"), "%Y"),
  format = "pdf",
  region = NULL,
  custom_sections = TRUE,
  new_section = NULL,
  section_location = NULL,
  figures_dir = getwd(),
  tables_dir = getwd(),
  reset_tables_and_figures = FALSE,
  reset_authors = FALSE
)

Arguments

file_dir

String of the path where the new report folder and files should be located. Required.

Default: The working directory (getwd())

previous_file_dir

String of the path where the previous report files are located. Required.

authors

String. A character vector of author names and affiliations. For example, a Jane Doe at the NWFSC Seattle, Washington office would have an entry of c("Jane Doe"="NWFSC-SWA"). Information on NOAA offices can be found with: asar::affiliation_info. Keys to the office addresses follow the naming convention of: office acronym (ex. NWFSC), a hyphen (-), the first initial of the city, and then the two-letter abbreviation for the state the office is located in. If the city has two or more words (e.g., Panama City), the first initial of each word is used in the key (ex. Panama City, Florida = PCFL).

Default: NULL

Options: See asar::affiliation_info.

model_results

Path. Filepath to the standardized, converted model output .rda file generated with stockplotr::convert_output(), relative to the skeleton .qmd file that will be created within the 'report' folder.

Default: NULL

year

Number. Year the assessment is conducted.

Default: the year in which the report is rendered.

format

String. Report rendering format. Note: "docx" is currently unsupported and will default to "pdf".

Default: "pdf"

Options: "pdf", "html"

region

String. Full name of the stock's sub-region, if applicable. If the region is not specified for your center or species, leave default. Example: "US West Coast".

Default: NULL

custom_sections

Logical. Indicate whether the previous report had a customized sectioning. If TRUE, the report outline will mimic the previous report. If FALSE, the report will include the full standard guidelines outline along with any custom sectioning from the previous report.

Default: FALSE

new_section

String. Names of section(s) (e.g., "Special Section") or subsection(s) (e.g., a section within the introduction) that will be added to the document. Please make a short list if >1 section/subsection will be added. The template will be created as a quarto document, added into the skeleton, and saved for reference.

Default: NULL

section_location

String. Where new section(s)/subsection(s) will be added to the skeleton template. Please use the notation of 'placement-section'. For example, 'in-introduction' signifies that the new content would be created as a child document and added into the 02_introduction.qmd. To add >1 (sub)section, make the location a list corresponding to the order of (sub)section names listed in the 'new_section' parameter.

Default: NULL

figures_dir

Path. The location of the "figures" folder, which contains figures files

Default: the working directory

tables_dir

Path. The location of the "tables" folder, which contains tables files

Default: the working directory

reset_tables_and_figures

Logical indicating whether to reset tables and figures Quarto documents.

Default: FALSE

reset_authors

Logical indicating whether to reset authorship for the report. Only will work if authors argument is also used.

Default: FALSE

Value

Creates a new folder of pre-filled assessment report files for the next assessment cycle.

Details

This function is designed so a report made from asar::create_template() can be called and updated with the following:

  • year (year)

  • model results (model_results)

  • authorship (authors)

  • region (region)

  • custom sections (custom_sections )

  • new sections (new_section and section_location)

  • figure and table folder locations (figures_dir and tables_dir)

  • format (format)

  • check standard structure against current structure (performed automatically)

This function performs three major tasks: (1) copies all files from the old directory to the new one, (2) updates the skeleton according the the input arguments using the rerender_skeleton() function, and (3) if desired, resets your figures and tables documents.

Examples

if (FALSE) { # \dontrun{
update_report(
  previous_file_dir = "~/testing/goa_2023/report",
  file_dir = "~/testing/goa_2025",
  model_results = "../new_std_res.rda")
  
update_report(
  previous_file_dir = "report_a",
  file_dir = "report_b",
  year = 2027,
  authors = c("John Doe" = "NEFSC"),
  reset_authors = TRUE
)
} # }