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Create string for yml header in quarto file

Source: R/create_yaml.R
create_yaml.Rd

Create string for yml header in quarto file

Usage

create_yaml(
  format = "pdf",
  office = NULL,
  region = NULL,
  species = "species",
  spp_latin = NULL,
  spp_image = NULL,
  year = NULL,
  bib_name = NULL,
  bib_file = NULL,
  author_list = NULL,
  title = "[TITLE]",
  rerender_skeleton = FALSE,
  prev_skeleton = NULL,
  prev_format = NULL,
  parameters = TRUE,
  custom_params = NULL,
  type = "SAR"
)

Arguments

format

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

Default: "pdf"

Options: "pdf", "html"

office

Regional Fisheries Science Center producing the report.

Default: NULL

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

region

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

species

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

Default: "species"

spp_latin

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

Default: NULL

spp_image

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

year

Year the assessment is conducted.

Default: the year in which the report is rendered.

bib_name

Name of a bib file being added into the yaml. For example, "asar.bib".

bib_file

File path to an existing additional bibliography file (.bib) used for citing references in the report. By default, all bibliography files are sourced from the journals package and references for all NMFS stock assessment reports are provided. To see a full list of journals included in these files, please visit the journals README or see the description at the top of each bib file. It is recommended to open these files in a text editor rather than R.

Default: NULL

author_list

A list of strings containing pre-formatted author names and affiliations that would be found in the format in a yaml of a quarto file when using base R function cat().

title

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.

rerender_skeleton

TRUE/FALSE; Update the skeleton YAML and structure (R parameters, preamble, and skeleton sectioning) if relevant or indicated. All files in your folder, such as the .qmd child docs, will remain as is.

Default: FALSE

prev_skeleton

Vector of strings containing all the lines of the previous skeleton file. File is read in using the function readLines from base R.

prev_format

The format that the previous skeleton was directed to render to. Parameter is inherited from create_template.

parameters

Logical indicating whether to include parameters in the yaml. Default is TRUE.

custom_params

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

type

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)

Value

Create a string indicating the important formatting pieces for a quarto file for a stock assessment report.

Examples

if (FALSE) { # \dontrun{
my_author_list <- paste(
  "  - name: 'Patrick Star'",
  "    affiliations:",
  "      - name: 'NOAA Fisheries Southeast Fisheries Science Center'",
  "        address: '75 Virginia Beach Drive'",
  "        city: 'Miami'",
  "        state: 'FL'",
  "        postal-code: '33149'",
  sep = "\n"
)
create_yaml(
  rerender_skeleton = FALSE,
  prev_skeleton = NULL,
  title = "My title",
  author_list = my_author_list,
  author = c("Patrick Star" = "SEFSC"),
  office = "SEFSC",
  add_author = NULL,
  spp_image = NULL,
  species = "",
  spp_latin = NULL,
  region = NULL,
  format = "pdf",
  parameters = TRUE,
  custom_params = NULL,
  bib_file = "path/asar_references.bib",
  bib_name = "asar_references.bib",
  year = 2025
)
} # }