In marinebon/nms4r: Office of National Marine Sanctuaries functions for dataset-specific wrangling and plotting in R

knitr::opts_chunk$set(echo = TRUE)

Data Source

ERDDAP (Environmental Research Division Data Access Portal) data is sourced from the ERDDAP server using the rerddap R library.

Data Preparation

As data on the ERDDAP server is updated regularly this provides the opportunity for interactive figures using ERDDAP data to be updated regularly as well. The first step in this process is to update the relevant tables, which for the Channel Islands Marine Sanctuary (CINMS) are located at: https://github.com/marinebon/cinms/tree/master/data/oceano. These tables, saved in csv format, are updated monthly via GitHub Actions using the update_oceano.yml workflow. This workflow in turn calls the R script update_oceano-data.R, which uses the calculate_statistics() and calculate_SST_anomaly functions from the onmsR package to update the relevant csv files.

Figure Preparation

Once the data tables have been updated, the next step is to update the figures that draw upon those tables. This is done by rerendering the modal windows (which are R Markdown files) that contain those figures. This also occurs on a monthly basis via GitHub Actions using the update_oceano.yml workflow. The workflow calls the R script render_oceano-modals.R, which calls the onmsR function render_all_rmd() to update the relevant modal windows.

marinebon/nms4r documentation built on April 23, 2023, 6:09 p.m.