Alaska ESP templates

The purpose of this package

This package was created to facilitate the development and maintenance of the Alaska Fisheries Science Center’s Ecosystem and Socioeconomic Profiles.

Create figures

This package can quickly generate styled figures based on indicator input data.

Create ESP templates and reports

  1. This package can create templates for ESP report cards. Up-to-date data is pulled from AKFIN and processed into figures and tables. The text is populated with default information and placeholders. The report is knit to Word, where it can be edited.

  2. This package can create templates for partial and full ESP reports. After the user fills out these templates, this package can knit a final Word report, including pulling in figures and tables.

Repo organization

This schematic shows the relationship between the several functions and files that are used to produce the ESP outputs.

Files

R folder

All functions have their own documentation files that can be accessed with the notation ?function_name. Functions are grouped into different .R files based on what they do.

  • R/data.R Documentation for data stored in the R package
  • R/data_functions.R Functions that get and manipulate data
  • R/figure_functions.R Functions that create figures
  • R/functions.R Functions to produce .Rmds and associated outputs
  • R/one-pager.R Function that creates the “one-pager” ESP summary (shorter than a report card)
  • R/render_AKesp_book.R Function that renders an ESP Standard Operating Procedure bookdown document (possibly outdated, not maintained)
  • R/table_functions.R Function to create ESP “traffic light” table
  • R/use_google_files.R Function to use files from google drive to build ESP report (possibly outdated, not maintained)
  • R/utils.R Helper functions used behind the scenes

data folder

  • data/indicator_order.rda Hardcoded indicator order key
  • data/metric_panel.rda Metric panel data

data-raw folder

  • data-raw/create_data.R Created R package data objects from spreadsheets
  • data-raw/create_data_documentation.R Created skeleton data.R file for documentation
  • data-raw/edges.csv Documents connections between functions, data, and files used in this R package
  • data-raw/ESP_Indicators_2020.xlsx Spreadsheet of indicator time series. Not needed if getting data from AKFIN.
  • data-raw/esp_lookup.R Created indicator_order R data object
  • data-raw/ESP_Lookup_Order.csv Hardcoded indicator order spreadsheet
  • data-raw/nodes.csv Documents functions, data, and files used in this R package data-raw/panel5.csv Metric panel data
  • data-raw/visualization.R Creates visual of connections between functions, data, and files used in this R package

inst folder

  • inst/esp-report-card-child.Rmd Child Rmarkdown document that inserts ESP report card information
  • inst/esp-template.Rmd Rmarkdown document that assembles the ESP report (do not edit)
  • inst/figure-child.Rmd Child Rmarkdown document that inserts figures into the ESP report (do not edit)
  • inst/figure_spreadsheet.csv Example figure identifier spreadsheet; used in report creation if no unique figures spreadsheet is provided.
  • inst/full-esp-text-template.docx Text template for full ESP report
  • inst/images/bayes.png Default image of Bayesian Adaptive Sampling results
  • inst/images/header.png Default header for report card
  • inst/images/noaa.jpg Placeholder image for documents
  • inst/partial-esp-text-template.docx Text template for partial ESP report
  • inst/references.bib Example references .bib; used in report creation if no unique references spreadsheet is provided. - inst/references_spreadsheet.csv Example references spreadsheet; used in report creation if no unique references spreadsheet is provided. - inst/table-child.Rmd Child Rmarkdown document that inserts tables into the ESP report (do not edit)
  • inst/table_spreadsheet.csv Example table identifier spreadsheet; used in report creation if no unique tables spreadsheet is provided. - inst/tables/example.csv Example of how to include a spreadsheet that will be turned into a table in the ESP report
  • inst/template.docx Template for Word document formatting (do not edit)

docs folder

Contains the files that create the github pages website. Automatically created by pkgdown; do not edit.

man folder

Automatically created by roxygen2; do not edit.

vignettes folder

old folder

Various old files for reference only.

book folder

Standard Operating Procedure document for this R package. Not recently maintained; likely redundant with the vignettes and pkgdown website.

shiny folder

Shiny app to produce “traffic light” table and figures for the stock of choice. Not recently maintained.

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.