To see templates included in the base skeleton, please run 'list.files(system.file('templates','skeleton', package = 'asar'))' in the console.
create_template(
format = "pdf",
type = "SAR",
office = c("AFSC", "PIFSC", "NEFSC", "NWFSC", "SEFSC", "SWFSC"),
region = NULL,
species = "species",
spp_latin = NULL,
year = format(as.POSIXct(Sys.Date(), format = "%YYYY-%mm-%dd"), "%Y"),
authors = NULL,
file_dir = getwd(),
title = "[TITLE]",
model_results = NULL,
tables_dir = getwd(),
figures_dir = getwd(),
spp_image = "",
bib_file = "asar_references.bib",
new_template = TRUE,
rerender_skeleton = FALSE,
custom = FALSE,
custom_sections = NULL,
new_section = NULL,
section_location = NULL,
parameters = TRUE,
param_names = NULL,
param_values = NULL,
...
)Rendering format (pdf, html, or docx).
Type of report to build. Default is SAR (NOAA Fisheries Stock Assessment Report).
Regional Fisheries Science Center producing the report (i.e., AFSC, NEFSC, NWFSC, PIFSC, SEFSC, SWFSC).
Full name of region in which the species is evaluated (if applicable). If the region is not specified for your center or species, do not use this variable.
Full common name for target species. Split naming with a space and capitalize first letter(s). Example: "Dover sole".
Latin name for the target species. Example: "Pomatomus saltatrix".
Year the assessment is being conducted. Default is the year in which the report is rendered.
A character vector of author names with their accompanying
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
is found in a database located in the package: system.file("resources",
"affiliation_info.csv", package = "asar"). Keys to the office addresses
follow the naming convention of the office acronym (ex. NWFSC) with a dash
followed by the first initial of the city then the 2 letter abbreviation for
the state the office is located in. If the city has 2 or more words such as
Panama City, the first initial of each word is used in the key
(ex. Panama City, Florida = PCFL)
Location of stock assessment files produced by this function. Default is the working directory.
A custom title that is an alternative to the default title (composed in asar::create_title()). Example: "Management Track Assessments Spring 2024".
Path to standard output file made from asar::convert_output()
The location of the "tables" folder, which contains tables files. Default is the working directory.
The location of the "figures" folder, which contains figures files. Default is the working directory.
File path to the species' image if not using the image included in the project's repository.
File path to a .bib file used for citing references in the report
TRUE/FALSE; Create a new template? If true, will pull the last saved stock assessment report skeleton. Default is false.
Re-create the "skeleton.qmd" in your outline when changes to the main skeleton need to be made. This reproduces the yaml, output (if changed), preamble quantities, and restructures your sectioning in the skeleton if indicated. All files in your folder will remain as is.
TRUE/FALSE; Build custom sectioning for the template, rather than the default for stock assessments in your region? Default is false.
List of existing sections to include in the custom template. Note: this only includes 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'). If adding a new section, also use parameters 'new_section' and 'section_location'.
Names of section(s) (e.g., introduction, results) 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.
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.
TRUE/FALSE; For parameterization of the script. Default is true.
List of parameter names that will be called in the document. Parameters automatically included: office, region, species (each of which are listed as individual parameters for this function, above).
List of values associated with the order of parameter names. Parameters automatically included: office, region, species (each of which are listed as individual parameters for this function, above).
Additional arguments passed into functions used in create_template
such as create_citation(), format_quarto(), add_chunk(), ect
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.
if (FALSE) { # \dontrun{
create_template(
new_section = "a_new_section",
section_location = "before-introduction"
)
create_template(
new_template = TRUE,
format = "pdf",
office = "NWFSC",
species = "Dover sole",
spp_latin = "Microstomus pacificus",
year = 2010,
authors = c(
"John Snow" = "AFSC",
"Danny Phantom" = "NEFSC",
"Patrick Star" = "SEFSC-ML"
),
model_results = here::here("folder", "std_output.rda"),
figures_dir = here::here(),
tables_dir = here::here("tables_folder_location"),
new_section = "an_additional_section",
section_location = "after-introduction"
)
asar::create_template(
new_template = TRUE,
format = "pdf",
office = "PIFSC",
species = "Striped marlin",
spp_latin = "Kajikia audax",
year = 2018,
authors = c("John Snow" = "AFSC"),
new_section = c("a_new_section", "another_new_section"),
section_location = c("before-introduction", "after-introduction"),
custom = TRUE,
custom_sections = c("executive_summary", "introduction")
)
create_template(
new_template = TRUE,
format = "pdf",
office = "NWFSC",
region = "my_region",
species = "Bluefish",
spp_latin = "Pomatomus saltatrix",
year = 2010,
authors = c("John Snow", "Danny Phantom", "Patrick Star"),
title = "Management Track Assessments Spring 2024",
parameters = TRUE,
param_names = c("region", "year"),
param_values = c("my_region", "2024"),
model_results = here::here("folder", "std_output.rda"),
new_section = "an_additional_section",
section_location = "before-discussion",
type = "SAR",
custom = TRUE,
custom_sections = c("executive_summary", "introduction", "discussion"),
spp_image = "dir/containing/spp_image"
)
} # }