part1Templates

Report templates for the WCPFC SciData Part 1 report, built on tufman2R.

Installation

devtools::install_github("PacificCommunity/part1Templates")
# or, testing a local copy:
devtools::install("path/to/part1Templates")

After installation, run usethis::edit_r_environ() to make sure TUF_USER / TUF_PASSWORD / TUF_COUNTRY are set up (per tufman2R's own README). If IKASAVEA is used by your CCM to record tuna catches and you want to include those catches in your Artisanal ACE table, set IKA_USER_NAME and IKA_PASSWORD the same way as the TUF_* variables:

IKA_USER_NAME=your_username
IKA_PASSWORD=your_password

You can update your environment variables at any time using usethis::edit_r_environ(). You will have to save and restart R for the new variables to take effect.

Setup

1. (Optional) Create a project called part_1_reports.

Open your project and run all the next steps inside it.

2. Load the library, specify report year (in this example 2025) and your country code (in this example the TUF_COUNTRY specified in the .Renv ).

library(part1Templates)

report_yr = 2025
country_cd = Sys.getenv("TUF_COUNTRY")

3. Create a project folder for the report year and country specified in the step above.

new_scidata_report(report_year = report_yr, country_code = country_cd)

This creates a project folder (e.g. [country_cd]_[report_yr]_scidata) and downloads all the data from required from Tufman 2 reports to your computer. You can check R/scidata_bundle.yaml if you want to know the list of Tufman 2 reports used for Part1.

4. Set your working environment

Set the working environment to the folder you just created.

setwd(paste0(country_cd, "_", report_yr, "_scidata"))

5. Generate your Part1 report

quarto::quarto_render(
  "part1-report.qmd",
  execute_params = list(refresh_data = TRUE)
)

The line above will re-download all Tufman 2 reports fresh to your computer as CSVs under data/scidata__/ before running your report. If after running the first time you want to reuse the CSVs downloaded in previous run, just set refresh_data to FALSE.

Special cases: Niue, Tokelau (and soon Wallis & Futuna)

Niue and Tokelau don't have a licensed foreign-flagged fleet, so their Part 1 report skips the flag-state reporting section entirely, it's a different report structure, not just different data (see R/special_cases.R). new_scidata_report() picks the right skeleton automatically based on country code, so you don't need a separate function:

new_scidata_report(report_year = 2025, country_code = "nu")
new_scidata_report(report_year = 2025, country_code = "tk")

Files to update every report cycle

• inst/extdata/sc_session.yml: SC session number, CCM number, meeting location, session dates — one edit here updates the cover page for every report (standard, NU, TK). |

• sections/*.qmd: The actual yearly narrative content (Abstract, Background, Addendum, etc.) that gets filled in per country once the folder is created.

Marking Addendum CMMs as not applicable

sections/Addendum.qmd walks through a fixed list of CMMs (2009-03, observer coverage, 2009-06, 2011-03, 2018-03, 2006-04, 2015-02, 2019-03, 2023-03, ...). For a given country, some of CMMS won't apply. Which ones are marked not-applicable is controlled per project folder, in R/config.yaml, under addendum.not_applicable_measures:

addendum:
  not_applicable_measures:
    "2009-03": "{{country_code}} flagged vessels do not target SWORDFISH nor fish south of 20°S."
    "2011-03": ""   # blank -> falls back to the generic "This measure does not apply to {country_name}."

• Leave it as the default not_applicable_measures: none to treat every CMM as applicable (nothing suppressed).
• CMM codes must be quoted.
• A blank reason ("") falls back to a generic "This measure does not apply to {country_name}." sentence.
• A CMM code left out of the map entirely is treated as applicable — you only need to list the ones you're suppressing.

This only applies to the standard skeleton. Niue and Tokelau's Addendum.qmd hardcodes a blanket "not applicable, no domestic commercial fishing industry" under every CMM directly in the qmd — there's nothing to configure there.

One caveat: a handful of CMM subsections in the standard skeleton's Addendum.qmd (the shark measures — 2013-08, 2012-04, 2011-04, 2010-07) are currently gated to Vanuatu only (#| eval: !expr tolower(country_code) == "vu") rather than going through config.yaml like the rest of the section — for any other country they don't render at all, not even as "not applicable".

Rendering multiple countries at once (admin only)

render_all_countries(
  path = "vu_2025_scidata",
  countries = c("FJ", "TO", "WS"),
  report_year = 2025,
  refresh_data = FALSE   # TRUE re-downloads every country's data fresh
)

Special-case countries (Niue, Tokelau) can't be included in the same batch as standard countries since their report body is different, so they need their own project folder and their own render_all_countries() call:

render_all_countries(path = "nu_2025_scidata", countries = "nu", report_year = 2025)