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KFM Shiny Application

Photo: Laurie Montgomery

Data Visualization and Modeling of the Kelp Forest Monitoring Data collected by Channel Islands National Park

This is my second attempt at designing a shiny web application for the KFMP at Channel Islands National Park (CINP). This tool is designed to do exploratory data analysis through interactive data visualization and statistical modeling.

A working example of this app can be found at Cloud Run App or GKE Cluster. I am currently working on finding the best/fastest/cheapest solution to hosting this in the cloud and these are my first two attempts. The Cloud Run service is updated regularly (whenever commits are pushed to github) while the GKE Cluster is not so there will be differences between the two.

File Organization of Repository

This repository is organized with two sub-folders App/ and Raw_Data/ located in the root.

root Folder

The root of this directory contains a dockerfile used for building the app container image as well as several .R files for working with raw data. The .R files produce the necessary tidy data used by the app, satellite maps from google with transect information overlaid, and text summaries of the annual reports. These files take data from the Raw_Data/ folder and produce outputs that get stored in the App/ folder.

Raw_Data/ Folder

This contains the raw data exported from the KFM database and a single subfolder Shapefiles/ with the raw geospatial data. Everything in here is cleaned up and saved within the App/ folder. None of these files are included with the final app.

App/ Folder

This folder houses the application files, data, images, and PDFs used to build it.

The four most important files are located directly in the App/ folder

  • global.R

    • This is the primary file for loading in stored data objects vectors used in the app

  • ui.R

    • This builds the Shiny user interface of the app

  • server.R

    • This serves the app the data and produces the graphics

  • modules.R

    • This stores the modules used to build the app

There are several folders, and some have sub-folders

  • GIS_Data/

    • This houses the .gpkg files used in the maps

  • Meta_Data/

    • This holds the .csv files used for creating tables and cross referencing data in the app

  • Models/

    • This holds the .rds files from our Random Forest models

  • Text/

    • This holds all of the .md files used to create the text chunks in the app

  • Tidy_Data/

    • This holds the .feather files that hold the various data frames used for the bulk of the plots

  • www/

    • This holds most of the .jpg, .png, and .pdf files embedded in the app itself including

    • This includes Annual_Reports/, Graphics/, Handbook/, Maps/, and Photos/

    • Kind of a catch all for extra things