TBEP_Habitat_Restoration

This dataset contains a comprehensive list of habitat restoration projects conducted in Tampa Bay and its watershed from 1971 to the present. Records prior to 2006 were compiled during the Tampa Bay Estuary Program's Habitat Master Plan Update (HMP, 2020). Since 2006, habitat restoration data are reported to the Tampa Bay Estuary Program by regional partners and submitted each year to the US Environmental Protection Agency (EPA) through the National Estuary Program Online Reporting Tool (NEPORT) to conform to the Government Performance and Results Act (GPRA). The dataset includes information on each project including name, date, location, restoration activity, habitat type, partner responsible for the project, and approximate coverage. The dataset is updated annually.

The archived dataset is available on KNB at: https://doi.org/10.5063/F1J101NP

Please see the sas branch for the original SAS code used to clean and merge the two data sources.

The workflow for updating data in this repository that then updates multiple downstream products is shown below.

Loading

flowchart TD
    A[TBEP Partners] -->|Annual Data Entry| B[Smartsheet]
    B --> C[USEPA NEPORT]
    B --> D[GitHub: TBEP_Habitat_Restoration - see additional steps below]
    D -->|Update| E[restoration.csv]
    E -->|Import| F[GitHub: habitat-report-card]
    F -->|Generate| G[Quarto HTML]
    G -->|Push| F
    G -->|Manual Extract| H[Habitat Report Card PDF]
    C -->|Approval| I[Final Data]
    E -->|"Email (After Final)"| J[USF Water Atlas]
    E -->|"Run Scripts (After Final)"| K[Data Package with Metadata]
    K -->|Submit| L[KNB Data Archive - see additional steps below]
    I -->|Final Corrections| B
    
    classDef repo fill:#427355,stroke:#333,stroke-width:2px,color:#ffffff
    classDef system fill:#004F7E,stroke:#333,stroke-width:2px,color:#ffffff
    classDef file fill:#958984,stroke:#333,stroke-width:2px,color:#333333
    classDef output fill:#5C4A42,stroke:#333,stroke-width:2px,color:#ffffff
    classDef default fill:#00806E,stroke:#333,stroke-width:2px,color:#ffffff
    
    class D,F repo
    class B,C,J,L system
    class E,K file
    class G,H output

Updating restoration.csv

Once USEPA approval is given and final approvals are made, the data is updated in the restoration.csv file in this repository. The steps to update the restoration.csv file are as follows:

1. Pull the most recent version of this repository to the local version.
2. All of the contents of R/00_smartsheetimport.R must be run. This file retrieves the updated data from the Smartsheet and appends it to the existing data in restoration.csv. Ensure the following before running the script.
   • Running this file requires an installation of the R package rsmartsheet. Uncomment and run line 1 to install the package if it is not already installed.
   • An authentication token from Smartsheet is also needed and saved as an environmental variable. A token can be retrieved in Smartsheet by going to your account, then Apps and Integrations, then API Access. Generate the new access token and copy it to your local computer as it cannot be retrieved again after it is created. This token must be stored in the .Renviron file, which can be edited by running usethis::edit_r_environ(). Add a line to the file that looks like smartsheets_key=your_token_here. Save the file and restart R. The token will be available as Sys.getenv("smartsheets_key").
   • Change line 5 to the current year.
   • Do not run the script more than once. Running the script multiple times will append the data multiple times.
3. Once the files are updated, commit the changes to the repository and push the changes to GitHub.
4. Follow the instructions below to update the KNB archive and the instructions on the README for the habitat-report-card repository to update figures used in the two-pager.

Updating KNB repository

The "official" dataset that needs to be updated each year is archived on KNB. This should only be done after the data are approved by USEPA and the file restoration.csv is updated as above. The steps to update the KNB repository are as follows:

1. Open the script R/03_update.R.
2. Before the script is run, a token for DataONE must be available in the .Renviron file. Get the token from Marcus and add it to the .Renviron file as dataone_token=your_token_here using usethis::edit_r_environ(). Save the file and restart R. The token will be available as Sys.getenv("dataone_token").
3. Change line 17 to the current version ID. This should be available at the of the page for the repository.
4. Change line 62 to December 31st for the year in which the data were updated, e.g., 2024-12-31.
5. Run the script, verify the console output (dimensions of new and old data should be different, new and old dates should be different) and that the data package has been successfully uploaded to KNB by visiting the URL.
6. Commit the changes in R/03_update.R and push the changes to GitHub (only line 62 should be changed).