ecodata maintenance

NOAA-EDAB

2024-04-23

The purpose of the ecodata package is to hold and facilitate the use of ecosystem indicator datasets used in the annual State of the Ecosystem reports developed for the New England and Mid-Atlantic Fisheries Management Councils. Since these reports are iterative, the indicators used to develop the reports are added to or changed regularly. To ensure continuity between years and package authors, the following protocols have been established.

Workflow Overview

Update existing indicator

From year to year most datasets will be delivered in the same format using the same name. In this case, ensure delivered .csv/.xls/.Rdata file is in the data-raw folder and run the get_example.R script.

In some cases the data will not arrive in the same format or naming convention. In this case, ensure the delivered .csv/.xls/.Rdata file is in the data-raw folder and edit the get_example.R script to ensure that the output data frame is structured correctly (i.e. 5 columns (Time, Var, Value, Units, EPU)).

Add new indicator

To add a new indicator dataset to the ecodata package, first ensure the delivered .csv/.xls/.Rdata file is in the data-raw folder. Write a get_example.R function which wrangles the raw data set into the desired format. Be sure to include a get_example(save_clean = T) line after closing the function. This will store the data frame in the data folder which is used to lazy load the data when the package is installed.

The data-raw folder should hold contributor datasets, functions for wrangling data into SOE format (get_example.R scripts) and any supplimental functions used to create those datasets.

The data folder should hold only wrangled .rda files.

Document indicator

  1. For each new indicator add a .R file to the R folder. This file should include the name of the dataset, a short description of the dataset, a “@format” section describing the dataframe structure, an itemized list of all of the columns in the dataframe and a “@details” section which links to the relevant tech doc chapter and any other important information.

  2. When the package is built, the files in the R folder will be used to populate the man folder.

  3. Ecodata uses pkgdown so once the manual documentation is complete run pkgdown::build_site(). This will populate the website with is updated indicator dataset information.

Website link - https://noaa-edab.github.io/ecodata/landing_page