Create Stock Assessment Report Template. To see templates included in the base skeleton, please run 'list.files(system.file('templates','skeleton', package = 'asar'))' in the console.

Usage

create_template(
  new_template = TRUE,
  format = c("pdf", "docx", "html", NULL),
  office = c("AFSC", "PIFSC", "NEFSC", "NWFSC", "SEFSC", "SWFSC"),
  region = NULL,
  complex = "NO",
  species = NULL,
  spp_latin = NULL,
  year = NULL,
  author = "",
  add_author = NULL,
  include_affiliation = FALSE,
  simple_affiliation = TRUE,
  alt_title = FALSE,
  title = NULL,
  parameters = TRUE,
  param_names = NULL,
  param_values = NULL,
  resdir = NULL,
  model_results = NULL,
  model = NULL,
  new_section = NULL,
  section_location = NULL,
  type = "SAR",
  prev_year = NULL,
  custom = FALSE,
  custom_sections = NULL,
  include_figures = TRUE,
  include_tables = TRUE,
  add_image = FALSE,
  spp_image = NULL
)

Arguments

new_template: TRUE/FALSE; default is false otherwise if true, will pull the last saved stock assessment report skeleton
format: File type for the render (i.e. pdf, docx, html)
office: Regional fisheries science center producing the report (AFSC, NEFSC, NWFSC, PIFSC, SEFSC, SWFSC)
region: Full name of region in which the species is evaluated if applicable; Note: if this is not specified for your center or for the species, do not use this variable.
complex: Is this a species complex? "YES" or "NO"
species: Full common name for target species, split naming by a space and capitalize first letter(s)
spp_latin: Latin name for the target species of this assessment
year: Year the assessment is being conducted, default is current year report is being rendered
author: List of authors to include in the assessment; keep authorship order
add_author: temporarily add an author that is not currently in the database. Follow the format of "First MI Last". Please leave a comment on the github issues page to be added.
include_affiliation: TRUE/FALSE; does the analyst want to include affiliations of the authors in the document?
simple_affiliation: If including affiliation, adding just office name rather than full address; TRUE/FALSE, default is TRUE
alt_title: TRUE/FALSE create an alternative title than the default
title: Name of new title if default is not appropriate; Example, "Management Track Assessments Spring 2024"
parameters: TRUE/FALSE; default TRUE - for parameterization of the script
param_names: List of parameter names that will be called in the document; parameters automatically included are office, region, and species listed in function parameters
param_values: List of values associated with the order of parameter names; parameters automatically included are office, region, and species listed in function parameters
resdir: Directory where the model results file(s) are located
model_results: Name of the model results file
model: Type of assessment model that was used to assess the stock (i.e. "BAM", "SS3", "AMAK", "ASAP", ect)
new_section: File name of the new section
section_location: Location where the section should be added relative to the base skeleton document
type: Type of report to build - default is SAR
prev_year: Year that previous assessment report was conducted in - for pulling previous assessment template
custom: TRUE/FALSE Build custom sectioning for the template rather than the default for stock assessments in your region
custom_sections: List of the sections you want to include in the custom template. Note: this only includes sections within 'templates' > 'skeleton'. The section name can be used such as 'abstract' rather than the entire name '00_abstract.qmd'. If a new section is to be added, please also use parameters 'new_section', and 'section_location'
include_figures: Determine if figures are included into the report
include_tables: Indicate if tables are included into the report
add_image: add outside image of species to the template
spp_image: full directory and species image name to direct the program where to find and extract the image

Value

Create template and pull skeleton for a stock assessment report. Function builds a YAML specific to the region and utilizes current resources and workflows from different U.S. Fishery Science Centers. General sections are called as child documents in this skeleton and each of the child documents should be edited separately.

Examples

create_template()
#> Warning: Results file or model name not defined.
#> Warning: Results file or model name not defined.
#> [1] "__________Built YAML Header______________"
#> Authorship is not defined.
#> [1] "_______Add Report Citation________"
#> [1] "___Created report template______"
#> Saved report template in directory: ~/stock_assessment_reports/report
#> To proceeed, please edit sections within the report template in order to produce a completed stock assessment report.