Fisheries Management Assessment (FMA) Dashboard

The FMA Dashboard is an R package called { rarefma }

The portal can be accessed through https://portal.rare.org/en/tools-and-data/fma/

The current application sits in shinyapps.io under the ID "12308687" named "FMA_Dash_test"

Installing for Development & Updating the data

It is recommended to use RStudio for development and deployment purposes!

Key steps to follow to update the the existing data and application.

1. Clone the repository to your desired location/folder.
   • You can either use git clone or download the repository from shinyapps.io
   • ! Recommended to download the repository from shinyapps.io !
2. Make sure you have { devtools } installed
3. Load the package using CMD-SHIFT-L or devtools::load_all() (Command specific to RStudio) - this should install rarefma library to the R environment
4. To update the follow the steps mentioned in "Generating Updated data" below.
5. Once the data is updated in the data folder, test the app locally using the run_app() command. The app should launch on a separate window or on localhost (usually on http://127.0.0.1:5765)
   • Note, do not use runApp() use run_app()
   • This is only to test the application in development (local environment)

Generating updated data

There are scripts in the data-raw folder to create the underlying data.

• The main one is prepare-ourfish-data.R

  • Info: The prepare-ourfish-data.R script utilizes the prepare-historical-data.R script.

Data requirements & Update

The current process of updating the data in the Fisheries Management (FMA) Dashboard uses static datasets downloaded from the respective data source.

• The prepare-ourfish-data.R script uses the join_ourfish_footprint.csv dataset (This is the only data that needs to be updated for the FMA dashboard to update the data)

  The dataset join_ourfish_footprint.csv is available on data.world -> https://data.world/rare/ourfish/workspace/file?filename=join_ourfish_footprint

  Key Steps:

  1. Download the join_ourfish_footprint.csv file (referred to as "data file" from here on") from data.world using the above link and save the data file in data-raw folder.
  2. Run the complete prepare-ourfish-data.R script This prepares the data and uploads the updated data to the data folder automatically.

Deploying the Shiny app to shinyapps.io

Prerequisities

Since this is a private repository, the user will need an auth_token from https://github.com/settings/tokens.

Recommended Steps for deploying the app

1. Restart the R session (recommended before deploying the application)

2. Use the command remotes::install_github("Rare-Technology/FMA_Dashboard", auth_token = 'GITHUB_AUTH_TOKEN')

3. if the devtools has been installed then use command devtools::load_all() -> This loads the rarefma library in the environment.

4. Prior to deployment Check the package before sending to production using: devtools::check(), followed by golem::add_shinyappsio_file()

   • The golem::add_shinyappsio_file() command creates the FMA_Dash_test.dcf file in the rsconnect folder (Always check if it is present before deploying the app)
   • Ensure there are no errors in in this step, running the devtools::check() command (warnings are fine, errors are not)

5. Make sure the library or package rfishbase is uninstalled from the environment

   This doesn't let the app deploy to shinyapps.io

6. Open the app.R file and,

   Use the blue button on top of the file in RStudio, enter the name of the app "FMA_Dash_test" (Recommended!)

   OR

   Use command rsconnect::deployApp() in the RStudio console -> Use this only if the rsconnect folder is present in the repository (This throws an error at times)

    In case the `rsconnect` folder is not present in the repository use command golem::add_shinyappsio_file()
   

7. Post deployment the app either launches automatically or can be visited using the relevant link in shinyapps.io

Potential Errors during deployment

1. Connection was reset errors - try deploying the app again (This issue is with the connection to shinyapps.io) and not the script
2. If the library rfishbase is present, the deployment never ends -> The process has to be force stopped in this case and the app needs to be redeployed again after unsinstalling the library.
3. If the rarefma library is not installed prior to deployment, the app doesn't work.