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Rerender skeleton quarto document

Source: R/rerender_skeleton.R
rerender_skeleton.Rd

Rerender skeleton quarto document

Usage

rerender_skeleton(
  file_dir,
  species = "species",
  spp_latin = NULL,
  office = NULL,
  region = NULL,
  year = format(as.POSIXct(Sys.Date(), format = "%YYYY-%mm-%dd"), "%Y"),
  custom_sections = NULL,
  new_section = NULL,
  section_location = NULL,
  custom_params = NULL,
  title = "[TITLE]",
  model_results = NULL,
  bib_file = NULL,
  type = "sar",
  spp_image = NULL,
  format = "pdf",
  authors = NULL
)

Arguments

file_dir

Required. Directory where the skeleton file is located. Can include or leave out the report folder in the path.

species

String. Common name of target species. Split multi-word names with space and capitalize first letter(s). Example: "Dover sole".

Default: "species"

spp_latin

String. Latin name of target species. Example: "Pomatomus saltatrix".

Default: NULL

office

String. Regional Fisheries Science Center producing the report.

Default: NULL

Options: "AFSC", "NEFSC", "NWFSC", "PIFSC", "SEFSC", "SWFSC"

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

year

Number. Year the assessment is conducted.

Default: the year in which the report is rendered.

custom_sections

List of existing sections to include in a custom template (rather than the default for stock assessments in your region). If adding a new section, also use arguments 'new_section' and 'section_location'.

Default: NULL

Options: sections within list.files(system.file("templates", "skeleton", package = "asar")). The name of the section, rather than the name of the file, can be used (e.g., 'abstract' rather than '00_abstract.qmd').

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

custom_params

List. Character vector of additional custom parameter names and values to include in the skeleton YAML. For example, a parameter "year2" and its value "2026" would have an entry of c("year2" = "2026"). Parameters automatically included: office, region, species (each of which are listed as individual parameters for this function, above).

Default: NULL

title

String. Custom report title superceding the default composed in asar::create_title(). Example: "Management Track Assessments Spring 2024".

Default: [TITLE]. If species and region are provided, a title will be generated based on the report type, species, and region.

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

bib_file

A character string of the path to a custom .bib file, or a logical. If a path is provided, the custom file is added to the skeleton and copied into the bibliography files folder.

Default: NULL

type

String. Report template type.

Default: "sar" (a NOAA standard "Stock Assessment Report")

Options: "sar" (Stock Assessment Report), "nemt" (Northeast Management Track), "pfmc" (Pacific Fishery Management Council), "safe" (Stock Assessment and Fishery Evaluation)

spp_image

Path. Filepath to a custom species image to be used on the report cover. Supported file extension is .png. If empty, searches asar resources for a matching species name.

Default: NULL

format

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

Default: "pdf"

Options: "pdf", "html"

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.

Value

Update the "skeleton" file produce after running create_template. Prevents the loss of data in child documents and make easy updates without prior knowledge of quarto.

Examples

if (FALSE) { # \dontrun{
rerender_skeleton(
file_dir = getwd(),
species = "Red Snapper",
office = "SEFSC",
region = "Gulf of America",
year = 2027,
authors = c("Jane Doe" = "SEFSC")
)
} # }