Deploy an LLM-powered Shiny for R app to Connect Cloud

Deploy an LLM-powered Shiny for R app to Connect Cloud with an OpenAI API key stored as a secret. Use GitHub, Positron or VS Code, RStudio, or the command line.

You have a Shiny app written in R that calls the OpenAI API.

Your API key works like a password: anyone who has it can use your OpenAI account. So keep it out of your code and your GitHub repository.

Instead, you enter the key in Connect Cloud. Connect Cloud stores it encrypted and passes it to your app when the app runs. The app reads it by name from the OPENAI_API_KEY environment variable. This guide shows how to enter the key for each way of deploying.

The sample app generates a fake dataset from your description, summarizes it, and lets you download it as a CSV file.

A Shiny for R app named AI Dataset Generator with a description box and Generate Dataset button in a sidebar and a data table in the main panel

The sample AI Dataset Generator running locally

The source code is available in the examples-shiny-r-llm repository.

Getting started

Whichever method you choose, you need the following:

  • A Connect Cloud account.
  • An OpenAI API key. See the OpenAI quickstart.
  • A Shiny for R app that reads the key from the OPENAI_API_KEY environment variable. This guide uses the sample app, which has a main file (Connect Cloud calls it the primary file) named app.R.
  • If you publish from GitHub, a renv.lock or manifest.json file that lists the R packages your content uses. Posit Publisher and push-button publishing do this for you.

Save this file as app.R. It reads your key with Sys.getenv("OPENAI_API_KEY").

app.R
library(shiny)
library(httr)
library(jsonlite)
library(DT)
library(stringr)
library(tidyverse)
library(bslib)
library(janitor)
library(shinyjs)
library(shinycssloaders)

# Internal API key (replace with your actual API key)
OPENAI_API_KEY <- Sys.getenv("OPENAI_API_KEY")

ui <- page_fluid(
  theme = bs_theme(version = 5),
  useShinyjs(),  # Add this to use shinyjs
  br(),
  titlePanel("AI Dataset Generator"),
  sidebarLayout(
    sidebarPanel(
      textInput("description", "Describe the dataset you want", 
                placeholder = "e.g., health data for a family of 4"),
      actionButton("generate", "Generate Dataset"),
      hidden(downloadButton("download", "Download CSV")),  # Hide download button initially
      br(), br(),
      uiOutput("summary"),
      hr(),
      tags$small("Note: Generated data may not be accurate or suitable for real-world use. The maximum number of records is limited to 25.")
    ),
    mainPanel(
      navset_tab(
        nav_panel("Data Table", 
                  br(),
                DTOutput("dataset")
        )
      )
    )
  )
)

server <- function(input, output, session) {
  dataset <- reactiveVal(NULL)
  summary_text <- reactiveVal("")
  
  preprocess_csv <- function(csv_string) {
    # Extract only the CSV part
    csv_pattern <- "(?s)(.+?\\n(?:[^,\n]+(?:,[^,\n]+)*\n){2,})"
    csv_match <- str_extract(csv_string, csv_pattern)
    
    if (is.na(csv_match)) {
      stop("No valid CSV data found in the response")
    }
    
    lines <- str_split(csv_match, "\n")[[1]]
    lines <- lines[lines != ""]  # Remove empty lines
    
    # Get the number of columns from the header
    header <- str_split(lines[1], ",")[[1]]
    num_cols <- length(header)
    
    # Ensure all rows have the same number of columns
    processed_lines <- sapply(lines[-1], function(line) {  # Skip header
      cols <- str_split(line, ",")[[1]]
      if (length(cols) < num_cols) {
        cols <- c(cols, rep("", num_cols - length(cols)))
      } else if (length(cols) > num_cols) {
        cols <- cols[1:num_cols]
      }
      cols
    })
    
    # Create a tibble
    tibble(!!!setNames(as.list(as.data.frame(t(processed_lines))), header))
  }
  
  generate_summary <- function(df) {
    prompt <- paste("Summarize the following dataset:\n\n",
                    "Dimensions: ", nrow(df), "rows and", ncol(df), "columns\n\n",
                    "Variables:\n", paste(names(df), collapse=", "), "\n\n",
                    "Please provide a brief summary of the dataset dimensions and variable definitions. Keep it concise, about 3-4 sentences.")
    
    response <- POST(
      url = "https://api.openai.com/v1/chat/completions",
      add_headers(Authorization = paste("Bearer", OPENAI_API_KEY)),
      content_type_json(),
      body = toJSON(list(
        model = "gpt-3.5-turbo-0125",
        messages = list(
          list(role = "system", content = "You are a helpful assistant that summarizes datasets."),
          list(role = "user", content = prompt)
        )
      ), auto_unbox = TRUE),
      encode = "json"
    )
    
    if (status_code(response) == 200) {
      content <- content(response)
      summary <- content$choices[[1]]$message$content
      return(summary)
    } else {
      return("Error generating summary. Please try again later.")
    }
  }
  
  observeEvent(input$generate, {
    req(input$description)
    showPageSpinner()
    
    prompt <- paste("Generate a fake dataset with at least two variables as a CSV string based on this description:",
                    input$description, "Include a header row. Limit to 25 rows of data. Ensure all rows have the same number of columns. Do not include any additional text or explanations.")
    
    response <- POST(
      url = "https://api.openai.com/v1/chat/completions",
      add_headers(Authorization = paste("Bearer", OPENAI_API_KEY)),
      content_type_json(),
      body = toJSON(list(
        model = "gpt-3.5-turbo-0125",
        messages = list(
          list(role = "system", content = "You are a helpful assistant that generates fake datasets."),
          list(role = "user", content = prompt)
        )
      ), auto_unbox = TRUE),
      encode = "json"
    )
    
    if (status_code(response) == 200) {
      content <- content(response)
      csv_string <- content$choices[[1]]$message$content
      
      tryCatch({
        # Preprocess the CSV string and create a tibble
        df <- preprocess_csv(csv_string) %>% clean_names() %>% 
          mutate(across(everything(), ~ ifelse(suppressWarnings(!is.na(as.numeric(.))), as.numeric(.), as.character(.))))
        dataset(df)
        updateSelectInput(session, "variable", choices = names(df))
        
        # Generate and set summary
        summary <- generate_summary(df)
        summary_text(summary)
        
        # Show download button
        hidePageSpinner()
        shinyjs::show("download")
        
        
        
      }, error = function(e) {
        showNotification(paste("Error parsing CSV:", e$message), type = "error")
      })
    } else {
      showNotification("Error generating dataset. Please try again later.", type = "error")
    }
    
    # Hide loading spinner
    shinyjs::hide("loading-spinner")
  })
  
  output$dataset <- renderDT({
    req(dataset())
    datatable(dataset(), rownames = FALSE, options = list(pageLength = 10))
  })
  
  
  output$download <- downloadHandler(
    filename = function() {
      "generated_dataset.csv"
    },
    content = function(file) {
      req(dataset())
      write.csv(dataset(), file, row.names = FALSE)
    }
  )
  
  output$summary <- renderUI({
    req(summary_text())
    div(
      h4("Dataset Summary"),
      p(summary_text()),
      style = "background-color: #f0f0f0; padding: 10px; border-radius: 5px;"
    )
  })
}

shinyApp(ui, server)

To preview the app before you deploy, store your key in a file named .Renviron in your project, restart R, and then click Run App in RStudio.

.Renviron
OPENAI_API_KEY='your-api-key-here'

Add .Renviron to your .gitignore file so you do not commit your key:

.gitignore
.Renviron

Choose a deployment method

Method When to use it Jump to
GitHub Your code is on GitHub and you want it to update when you push (public repositories only on free accounts) Deploy from GitHub
Posit Publisher You work in Positron or VS Code and do not use GitHub Deploy from Positron or VS Code
Push-button publishing You work in RStudio and do not use GitHub Deploy from RStudio
rsconnect You want to deploy from the R console or automate deployments Deploy from the command line

For more on how these methods differ, see Publishing.

Deploy from GitHub

Use this method when your app’s code is in a GitHub repository and you want changes you push to publish automatically. On a free account, your repository must be public, so anyone can see your code.

  1. Create a manifest.json file by running this in the R console from the folder that contains app.R:

    rsconnect::writeManifest()

  2. List .Renviron in .gitignore so you do not commit your API key. Then commit app.R and manifest.json and push your app to a GitHub repository.

  3. Sign in to Connect Cloud.

  4. Click Publish at the top of your Home page. If this is your first time publishing, Connect Cloud prompts you to install the GitHub App, which lets Connect Cloud read your repository.

  5. Select Shiny.

  6. Select your repository.

  7. Check that Branch is the branch that has your content, usually main.

  8. Select app.R as the Primary file.

  9. Leave Automatically publish on push on if you want Connect Cloud to update what you published each time you push to this branch. Turn it off to update only when you choose.

  10. Click Advanced settings.

  11. Click Add variable under Configure variables.

  12. In the Name field, enter OPENAI_API_KEY.

  13. In the Value field, enter your OpenAI API key.

  14. Click Publish.

  • Result: Connect Cloud shows a log of the install steps while it deploys. When it finishes, your app is live at an address like https://[content-id].share.connect.posit.cloud, where [content-id] is a unique identifier that Connect Cloud picks. You can set a custom name to change the URL.
  • Update or redeploy: Commit and push to the connected branch and Connect Cloud republishes automatically. If you turned off automatic publishing, click Republish on the content’s card on your Home page. See Republishing.

For all options, see Publish from GitHub.

Deploy from Positron or VS Code

Use this method when you work in Positron or VS Code and want to deploy your app directly. Positron includes the Posit Publisher extension. In VS Code, install it from the marketplace first.

  1. Open your project folder in Positron, or in VS Code with Posit Publisher installed.
  2. Click the Posit Publisher icon in the Activity Bar.
  3. Next to CREDENTIALS, click + and select Posit Connect Cloud. A credential is a saved connection to your Connect Cloud account. Your browser opens.
  4. In your browser, check that the Authorize Access code matches the code in Positron or VS Code. Then click Continue and Authorize.
  5. Return to Positron or VS Code and accept or change the name for this credential. Do this once.
  6. Click the + next to Deployments. If Posit Publisher asks which file to publish, select app.R.
  7. Enter a title for your content, then select the credential you just added.
  8. Under PROJECT FILES, check that the list includes app.R but not .Renviron. Connect Cloud uploads only the files in this list.
  9. Under Secrets, add a secret named OPENAI_API_KEY with your API key as the value.
  10. Click Deploy Your Project.
  • Result: A success message appears in the lower right of Positron or VS Code. Click View Content in the extension to open the app on Connect Cloud. Its address has the form https://[content-id].share.connect.posit.cloud, where [content-id] is unique to your app.
  • Update or redeploy: Save your changes, open Posit Publisher, select the previous deployment, and click Deploy Your Project again. Keep the .posit folder in your project. It remembers which Connect Cloud content this project publishes to, so the next deploy updates the same content instead of creating a new one.

For the configuration file, multiple deployments per project, and troubleshooting, see Publish from your IDE.

Deploy from RStudio

Use this method when you work in RStudio and want to publish your app directly with push-button publishing.

  1. Open app.R in RStudio.
  2. Click Publish in the editor toolbar.
  3. Follow the prompts to connect your Connect Cloud account and publish. Do not include .Renviron in the files you publish.
  4. Add your API key as a variable. Open the content’s content settings, click Add variable, enter OPENAI_API_KEY as the name, and enter your API key as the value. Then republish the app so it picks up the key. Until then, the app shows an error.
  • Result: RStudio opens your app on Connect Cloud.
  • Update or redeploy: Save your changes and click Publish again.

For setup instructions and supported content types, see Publish from your IDE and the RStudio IDE publishing documentation.

Deploy from the command line

Use this method to script deployments from the R console with the rsconnect package. You do not need a manifest.json or renv.lock file for this method.

  1. Install the package.

    install.packages("rsconnect")

  2. Add your Connect Cloud account. Your browser opens for you to authorize access.

    rsconnect::connectCloudUser()

  3. Deploy the folder that contains app.R. Do not include .Renviron.

    rsconnect::deployApp()

  4. Add your API key as a variable. Open the content’s content settings, click Add variable, enter OPENAI_API_KEY as the name, and enter your API key as the value. Then republish the app so it picks up the key. Until then, the app shows an error.

If your app is in a subdirectory, pass it with appDir, for example rsconnect::deployApp(appDir = "Dashboard"). If you have several accounts configured, rsconnect asks which one to use.

  • Result: A successful deployment opens your browser to your content’s page on Connect Cloud.
  • Update or redeploy: Run rsconnect::deployApp() again.

For noninteractive credentials and other options, see Publish from your console or terminal.

After you deploy

Common things to set up next. They work the same however you deployed your app:

  • Passwords and API keys: Change or add secret variables under Variables in content settings. The app reads the key with Sys.getenv("OPENAI_API_KEY").
  • Access and sharing: Control who can view your app in Sharing.
  • Scheduling: On paid plans, schedule your app to republish at set times.
  • Custom name and domain: Change the app’s URL with a custom name or a custom domain.
  • Upload size limit: The upload size limit applies when you upload your project files from your editor or the R console.

Troubleshooting

  • Error generating dataset or summary: The app shows these messages when OpenAI returns an error, for example when the key is missing or invalid. Check that the variable is named exactly OPENAI_API_KEY and that its value is a valid key.
  • Missing package error: Re-run rsconnect::writeManifest() so manifest.json lists every package your app loads, then commit it and republish.
  • API key committed by mistake: Revoke the key in your OpenAI account, create a new one, and store the new key as a variable on Connect Cloud.
  • Repository not listed: Confirm that the GitHub App has access to it.

If your deployment still fails, read the log that Connect Cloud shows while it deploys and look for the first error. You can also try Error Assist, which gives guidance based on your log output.

Next steps