diff --git a/.Renviron.example b/.Renviron.example new file mode 100644 index 0000000..1502854 --- /dev/null +++ b/.Renviron.example @@ -0,0 +1,31 @@ +################################################################################ +# Benchling Authentication Configuration +################################################################################ +# +# This file is ONLY needed if using Benchling App (OAuth2) authentication +# for long-running workflows. The default JWT approach doesn't need this. +# +# See README.md "Authentication Methods" section for when to use each approach. +# +################################################################################ + +# -------------------------------------------------------------------------- +# Option 1: Analysis Key (JWT) - Default, no configuration needed! +# -------------------------------------------------------------------------- +# The script prompts for your analysis key when you run it. +# +# OPTIONAL: Set this to avoid prompts (useful for automation) +# BENCHLING_ANALYSIS_KEY=ana_XXXXX:eyJhbGc... + +# -------------------------------------------------------------------------- +# Option 2: Benchling App (OAuth2) - For production/long workflows +# -------------------------------------------------------------------------- +# Prerequisites: +# 1. Create Benchling App: https://docs.benchling.com/docs/getting-started-benchling-apps +# 2. Grant permissions: analyses, data-frames, files (read/write) +# 3. Set USE_OAUTH2 <- TRUE in get_dataframe.R (line 12) and app.R (line 17) +# +# Then set these values: +# BENCHLING_CLIENT_ID=your_client_id_here +# BENCHLING_CLIENT_SECRET=your_client_secret_here +# BENCHLING_DOMAIN=your_tenant.benchling.com diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..4b6d2f3 --- /dev/null +++ b/.gitignore @@ -0,0 +1,42 @@ +# Credentials and Environment Variables +.Renviron +.Rprofile + +# Project-specific Claude configuration +CLAUDE.md + +# R Data files +*.RData +*.Rhistory +*.rda +*.rds + +# Output files from examples +examples/local_test_output.html +examples/local_test_summary.csv +examples/*.html +examples/*.csv +# But keep the sample input data +!examples/sample_ic50_data.csv +examples/*_files/ + +# RStudio project files +.Rproj.user/ +*.Rproj + +# Shiny +rsconnect/ +.shiny_app_cache/ + +# macOS +.DS_Store + +# IDE +.vscode/ +.idea/ + +# Temporary files +tmp/ +*.tmp +*.bak +*~ diff --git a/Mortality IC50.csv b/Mortality IC50.csv deleted file mode 100644 index 2257250..0000000 --- a/Mortality IC50.csv +++ /dev/null @@ -1,22 +0,0 @@ -Concentration,Mortality 24h,Mortality 48h -0.3,3.979,2.192 -1,17.07,16.345 -3,18.356,42.458 -10,25.288,57.408 -30,54.813,70.365 -100,76.379,81.727 -300,81.514,85.11 -0.3,4.4929,5.382 -1,9.114,16.141 -3,10.141,41.06 -10,24.261,57.408 -30,51.732,67.774 -100,67.651,83.3189 -300,82.028,84.31 -0.3,8.383,2.280 -1,16.338,14.755 -3,15.5688,38.698 -10,25.577,54.996 -30,57.399,68.879 -100,77.67,80.952 -300,82.0359,83.367 \ No newline at end of file diff --git a/README.md b/README.md index 16b01b5..3ffe873 100644 --- a/README.md +++ b/README.md @@ -1,20 +1,275 @@ # Sample Code - Working with Datasets Using R + A repository containing the sample scripts described in the [Working with Datasets Using R](https://docs.benchling.com/docs/working-with-datasets-using-r) developer guide. Provided for educational purposes only; not for production use. -## Configuration and Setup -1. Create a [Benchling App](https://docs.benchling.com/docs/getting-started-benchling-apps) -2. Create a [Benchling Analysis](https://help.benchling.com/hc/en-us/articles/15298157390861-Creating-an-analysis) -3. Configure the sample script(s) with your tenant-specific variables +## Quick Setup + +1. **Install R 4.5.3+** (if not already installed) +2. **Install dependencies:** `Rscript -e "renv::restore()"` +3. **Create Analysis:** [Create an analysis](https://help.benchling.com/hc/en-us/articles/15298157390861) in Benchling +4. **Upload Sample Data:** Attach `examples/sample_ic50_data.csv` as an input dataset to your analysis + - **Note:** In production usage, this would be an existing dataset or results table from your experiments +5. **Get Analysis Key:** In your analysis, click **"Connect with external tool"** → **"Copy Analysis Key"** +6. **Run the workflow:** The script will prompt for your analysis key - that's it! + +## Authentication Methods + +This repository uses **Analysis Key (JWT) authentication** by default. + +**Analysis Key Structure:** `ana_XXXXX:eyJhbGc...` (analysis_id + JWT token separated by colon) + +### Analysis Key (JWT) - Default ✅ + +**Best for:** Learning, demos, workflows under 10 minutes + +- ✅ **Simple:** Just paste your analysis key +- ✅ **User-attributable:** Actions are tied to the person who generated the key +- ⚠️ **Expires after 10 minutes:** If your workflow takes longer, it will fail +- ⚠️ **Analysis-specific:** Each analysis has its own key + +The JWT token (part after the colon) contains the authentication credentials and is used directly as the bearer token for API requests. + +### Benchling App (OAuth2) - Alternative + +**Best for:** Production systems, long-running workflows, processing multiple analyses + +- ✅ **Permanent credentials:** No expiration +- ✅ **Reusable:** Works across all analyses +- ⚠️ **More setup:** Requires creating a Benchling App +- ⚠️ **App-attributable:** Actions are tied to the app, not a specific user + +**Want to use App credentials?** Set `USE_OAUTH2 <- TRUE` at the top of `get_dataframe.R` (line 12) and/or `app.R` (line 17). See [Benchling Apps Guide](https://docs.benchling.com/docs/getting-started-benchling-apps) for setup. + +📖 **Detailed Setup Instructions** (click to expand) + +### Prerequisites + +- R 4.5.3+ installed +- Access to a Benchling tenant +- Access to Benchling Analyses feature + +### Part 1: Create a Benchling Analysis + +Analyses are where you'll attach input datasets and receive output results. + +1. **Navigate to Analyses:** + - In Benchling, go to your project or notebook + - Click **"Create"** → **"Analysis"** +2. **Configure Analysis:** + - **Name:** e.g., "IC50 Dose-Response Calculation" + - **Description:** Optional, explains what this analysis does +3. **Attach Input Dataset:** + - Click **"Add Input"** → **"Dataset"** + - **For this example:** Upload `examples/sample_ic50_data.csv` from this repository + - **For production use:** Select an existing dataset or results table from your experiments + - **Required columns:** + - `Cell.Mortality.Concentration` - Drug concentration values + - `Cell.Mortality.Mortality.24h` - Mortality percentage at 24 hours + - `Cell.Line.Name` - Cell line identifier + **Example data format:** +4. **Get the Analysis Key:** + - In your analysis, click **"Connect with external tool"** + - In the popup window, click **"Copy Analysis Key"** + - Format looks like: `ana_XXXXXXXX:eyJhbGc...` (`analysis_id`:`JWT token`) + - **Note:** Analysis keys are specific to each analysis run and expire after 10 minutes + +### Part 2: Install Dependencies + +```bash +# Restore the renv environment (installs all packages) +Rscript -e "renv::restore()" + +# Or install packages individually +Rscript -e "renv::install(c('httr', 'jsonlite', 'base64enc', 'drc', 'plotly', 'htmlwidgets', 'pracma'))" +``` + +**Note:** On macOS, you may need CMake first: + +```bash +brew install cmake +``` + +### Part 3: Run the Workflow + +⚠️ **Important:** Scripts must run **sequentially in the same R session** because `results_analysis.R` depends on variables from `get_dataframe.R`. + +**Option A: RStudio (Recommended)** + +```r +source('get_dataframe.R') # Will prompt: "Analysis Key: " + # Paste: ana_XXXXX:eyJhbGc... +ls() # Verify: df, subdomain, analysis_id, access_token, folder_id +head(df) # Check data loaded correctly +source('results_analysis.R') +``` + +**Option B: Script Based Execution in Interactive R Session** + +```r +source('get_dataframe.R') +# Prompts for analysis key, paste it and press Enter +source('results_analysis.R') +``` + +**Option C: Non-Interactive (Command Line)** + +```bash +export BENCHLING_ANALYSIS_KEY="ana_XXXXX:eyJhbGc..." +Rscript -e "source('get_dataframe.R'); source('results_analysis.R')" +``` + +**Option D: Shiny Web App (Easiest) from Interactive R Session** + +```r +shiny::runApp("app.R") +# Enter your analysis key in the web interface +``` + +### Verify Success + +The scripts print status codes as they run: + +``` +[1] "200" # Dataframe upload successful +[1] "200" # File upload successful +[1] "200" # Analysis update successful +``` + +Check your Analysis in Benchling - you should see: + +- **Dataset:** `Mortality_IC50` - CSV with IC50 statistics +- **File:** `mortality_24h.html` - Interactive plot + +### Common Issues + +**Error: "HTTP 401 Unauthorized" or "Failed to authenticate"** + +- Your analysis key JWT may have expired (check the `exp` field in the JWT) +- Generate a new analysis key from your Benchling analysis +- Ensure you copied the complete key (format: `ana_XXXXX:eyJhbGc...`) + +**Error: "HTTP 404 Not Found"** + +- `analysis_id` is incorrect +- Check the analysis ID in the Benchling URL +- Ensure the analysis exists and you have access + +**Error: "Variables not found in results_analysis.R"** + +- Must run `get_dataframe.R` first in the same R session +- Don't start a new R session between running the scripts + +**Error: "Package not found"** + +- Run `renv::restore()` to install all dependencies + +**Error: "No input dataframes found"** + +- Ensure you've attached an input dataset to your analysis in Benchling +- Dataset must have the required columns (see data format above) + +### Data Flow + +``` +┌─────────────────────────────────────────┐ +│ Benchling Analysis │ +│ Input Dataset (CSV) │ +└──────────────┬──────────────────────────┘ + │ + ▼ + ┌──────────────────┐ + │ get_dataframe.R │ + │ 1. Authenticate │ + │ 2. Fetch dataset │ + └────────┬─────────┘ + │ + ▼ + Variables: df, subdomain, + analysis_id, access_token + │ + ▼ + ┌──────────────────┐ + │ results_analysis │ + │ 1. Calculate IC50│ + │ 2. Generate plot │ + │ 3. Upload both │ + └────────┬─────────┘ + │ + ▼ +┌─────────────────────────────────────────┐ +│ Benchling Analysis │ +│ Output: Mortality_IC50 (CSV) │ +│ Output: mortality_24h.html (plot) │ +└─────────────────────────────────────────┘ +``` + +### Additional Resources + +- [Benchling API Documentation](https://docs.benchling.com/docs/api-overview) +- [Benchling Apps Guide](https://docs.benchling.com/docs/getting-started-benchling-apps) +- [Benchling Analyses Guide](https://help.benchling.com/hc/en-us/articles/15298157390861) +- [Working with Datasets Using R](https://docs.benchling.com/docs/working-with-datasets-using-r) + +## Local Testing 🧪 + +Want to test IC50 calculations without connecting to Benchling? Use the local test script: + +```r +# From project root: +source("examples/local_test.R") + +# Or from examples directory: +setwd("examples") +source("local_test.R") +``` + +**What it does:** + +- Loads dose-response data from `examples/sample_ic50_data.csv` (21 observations, 7 concentrations × 3 replicates) +- Calculates IC50 using 4-parameter log-logistic model +- Uses utility functions from `utils.R` +- Creates interactive plotly visualization +- Generates results summary + +**Output files:** + +- `examples/local_test_output.html` - Interactive plot (open in browser) +- `examples/local_test_summary.csv` - Results table + +**Prerequisites:** None! Works completely offline with sample data. Perfect for testing during development. + +--- ## Usage -* `get_dataframe.R` pulls the input dataset from a Benchling analysis and converts it into an R dataframe. -* `results_analysis.R` performs an IC50 calculation on a dataframe, creates a plot, and imports both -as outputs to a Benchling analysis. -* `Mortality IC50.csv` contains basic sample data of the form required by `results_analysis.R` - -It's recommended to start by working with `get_dataframe.R` and `results_analysis.R` in order to familiarize -yourself with the principles involved. For best results, these should be run sequentially, since the latter expects -a dataframe to be imported. Once you're confident using the scripts and with the configuration in Benchling, the -techniques involved can be applied to more robust applications using tools like Rshiny. + +### Main Script Files + +- `get_dataframe.R` - Pulls input dataset from Benchling using analysis key +- `results_analysis.R` - Performs IC50 calculation, creates plot, and uploads to Benchling +- `app.R` - Full-featured Shiny web app with UI for IC50 analysis +- `utils.R` - Shared utility functions for IC50 calculation and plotting + +### Full Workflow (Benchling Integration) + +**Option 1: Shiny Web App (Easiest)** + +```r +shiny::runApp("app.R") # Opens web interface +``` + +**Option 2: Command Line Scripts** + +```r +source('get_dataframe.R') # Will prompt for analysis key +source('results_analysis.R') +``` + +⚠️ **Important:** + +- Scripts must run sequentially in the same R session +- The script will prompt you for the analysis key +- Analysis keys contain JWT tokens that may expire - regenerate if needed + +Once you're confident with the workflow, these techniques can be applied to more robust applications using tools like Shiny. \ No newline at end of file diff --git a/app.R b/app.R new file mode 100644 index 0000000..ddc3c7a --- /dev/null +++ b/app.R @@ -0,0 +1,341 @@ +# Load R packages +library(shiny) +library(shinythemes) +library(httr) +library(jsonlite) +library(base64enc) +library(digest) +library(shinycssloaders) +library(dplyr) +library(htmlwidgets) + +# Source utility functions +source("utils.R") + +################################################################################ +# AUTHENTICATION CONFIGURATION - Set your method here +################################################################################ +USE_OAUTH2 <- FALSE # Set to FALSE for JWT (default), TRUE for OAuth2 + +# OAuth2 credentials (only used if USE_OAUTH2 = TRUE) +if (USE_OAUTH2) { + client_id <- Sys.getenv("BENCHLING_CLIENT_ID") + client_secret <- Sys.getenv("BENCHLING_CLIENT_SECRET") + domain_fixed <- Sys.getenv("BENCHLING_DOMAIN") + + if (client_id == "" || client_secret == "" || domain_fixed == "") { + stop("OAuth2 enabled but credentials missing! Set BENCHLING_CLIENT_ID, BENCHLING_CLIENT_SECRET, and BENCHLING_DOMAIN in .Renviron") + } +} +################################################################################ + +# Define UI +ui <- fluidPage(theme = shinytheme("cerulean"), + + navbarPage( + "R Shiny - IC50 Calc", + + tabPanel("Import Dataset", + + sidebarPanel( + tags$h3("Input:"), + textInput("DatasetKey", "Analysis Key:", ""), + actionButton("submitbutton", "Get Dataset", class = "btn btn-primary"), + actionButton("sendresultAnalysis", "Send Analysis", class = "btn btn-primary") + ), + + mainPanel( + tags$label(h4("Tenant Subdomain")), + verbatimTextOutput("subdomain"), + verbatimTextOutput("analysis") %>% withSpinner(color="#0dc5c1"), + tableOutput('tabledata') + ) + ), + + tabPanel("Regression Algorithm", + mainPanel( + tags$h2("4-Parameter Log-Logistic Model (LL.4)"), + tags$p("IC50 calculations use dose-response curve fitting with the drc package.") + ) + ) + ) +) + +# Define server function +server <- function(input, output) { + + # Extract base domain (full domain including suffix) + base_domain <- reactive({ + if (USE_OAUTH2) { + # OAuth2: use domain from credentials + domain_fixed + } else { + # JWT: extract from analysis key + split_key <- strsplit(input$DatasetKey, ".", fixed = TRUE) + payload <- jsonlite::fromJSON(rawToChar(base64decode(split_key[[1]][2]))) + domain_raw <- payload$aud + + # Determine if this is a full domain or just a subdomain + if (grepl("\\.", domain_raw)) { + # Contains a dot - it's a full domain, use as-is + domain_raw + } else { + # No dot - it's just a subdomain, append .benchling.com + paste0(domain_raw, ".benchling.com") + } + } + }) + + # Extract subdomain (first part only, for display) + subdomain <- reactive({ + sub("\\..*", "", base_domain()) + }) + + # Get dataset from Benchling + datasetInput <- reactive({ + + # Extract analysis ID from key + key_parts <- strsplit(input$DatasetKey, ":", fixed = TRUE)[[1]] + analysis_id <- key_parts[1] + + # Get access token based on auth method + if (USE_OAUTH2) { + # OAuth2: Generate token from app credentials + token_url <- paste0("https://", domain_fixed, "/api/v2/token") + token_request <- httr::POST( + url = token_url, + body = paste0("client_id=", client_id, + "&client_secret=", client_secret, + "&grant_type=client_credentials"), + httr::accept('application/json'), + httr::content_type('application/x-www-form-urlencoded') + ) + + if (token_request$status_code != 200) { + stop("OAuth2 authentication failed!") + } + + request_body <- jsonlite::fromJSON(rawToChar(token_request$content)) + access_token <- request_body$access_token + } else { + # JWT: Use token from analysis key + access_token <- key_parts[2] + } + + # Get analysis + endpoint <- "/api/v2-beta/analyses/" + URL <- paste("https://", isolate(base_domain()), endpoint, analysis_id, sep = "") + + analysis_req <- GET(URL, add_headers( + Accept = 'application/json', + Authorization = paste("Bearer", access_token) + )) + dat <- jsonlite::fromJSON(rawToChar(analysis_req$content)) + + datasetId <- c(dat$dataFrameIds)[1] + folder_id <- c(dat$folderId) + + # Store for later use + assign("access_token", access_token, envir = .GlobalEnv) + assign("folder_id", folder_id, envir = .GlobalEnv) + assign("analysis_id", analysis_id, envir = .GlobalEnv) + + # Get dataset + endpoint <- "/api/v2-beta/data-frames/" + URL <- paste("https://", isolate(base_domain()), endpoint, datasetId, sep = "") + + Dataset_req <- GET(URL, add_headers( + Accept = 'application/json', + Authorization = paste("Bearer", access_token) + )) + dat <- jsonlite::fromJSON(rawToChar(Dataset_req$content)) + + DatasetUrl <- c(dat$manifest$url) + df <- read.csv(DatasetUrl) + + df + }) + + # Process analysis and upload results + analysis <- reactive({ + + df <- datasetInput() + + # Find concentration column + conc_col <- grep("^Concentration$|Cell\\.Mortality\\.Concentration", + names(df), ignore.case = TRUE, value = TRUE)[1] + + # Find mortality columns (matches "Mortality.24h" or "Cell.Mortality.Mortality.24h") + mort_24h_col <- grep("Mortality\\.24h", + names(df), ignore.case = TRUE, value = TRUE)[1] + mort_48h_col <- grep("Mortality\\.48h", + names(df), ignore.case = TRUE, value = TRUE)[1] + + # Calculate IC50 for 24h using utility function + result_24 <- calculate_ic50(df, conc_col, mort_24h_col) + IC50_24 <- result_24$ic50 + slope_24 <- result_24$slope + + # Calculate IC50 for 48h using utility function + result_48 <- calculate_ic50(df, conc_col, mort_48h_col) + IC50_48 <- result_48$ic50 + slope_48 <- result_48$slope + + # Create plotly graphs using utility function + imageName_24 <- "mortality_24h.html" + File_24 <- tempfile(fileext = ".html") + + plot_24 <- create_ic50_plot(df, conc_col, mort_24h_col, IC50_24, slope_24, + title = "IC50 24h Dose-Response") + saveWidget(widget = plot_24, file = File_24, selfcontained = TRUE) + + imageName_48 <- "mortality_48h.html" + File_48 <- tempfile(fileext = ".html") + + plot_48 <- create_ic50_plot(df, conc_col, mort_48h_col, IC50_48, slope_48, + title = "IC50 48h Dose-Response") + saveWidget(widget = plot_48, file = File_48, selfcontained = TRUE) + + # Upload files to Benchling + upload_file <- function(filepath, filename, folder_id, access_token, base_domain) { + endpoint <- "/api/v2-beta/files" + URL <- paste("https://", base_domain, endpoint, sep = "") + + my_data <- readBin(filepath, "raw", 10e6) + + filePostBody <- list(name = filename, folderId = folder_id, filename = filename) + filePostResponse <- httr::POST( + url = URL, + body = toJSON(filePostBody, pretty = TRUE, auto_unbox = TRUE), + httr::accept('application/json'), + httr::add_headers('Authorization' = paste("Bearer", access_token)), + httr::content_type('application/json') + ) + + dat <- jsonlite::fromJSON(rawToChar(filePostResponse$content)) + fileID <- dat$id + s3_Put_Url <- filePostResponse$headers$`content-location` + + s3FileUpload <- httr::PUT( + url = s3_Put_Url, + body = my_data, + httr::add_headers('x-amz-server-side-encryption' = 'AES256') + ) + + if (s3FileUpload$status_code == 200) { + endpoint <- "/api/v2-beta/files/" + URL <- paste("https://", base_domain, endpoint, fileID, sep = "") + + s3FileUploadStatus <- list(uploadStatus = 'SUCCEEDED') + + PatchFile <- httr::PATCH( + url = URL, + body = toJSON(s3FileUploadStatus, pretty = TRUE, auto_unbox = TRUE), + httr::accept('application/json'), + httr::add_headers('Authorization' = paste("Bearer", access_token)), + httr::content_type('application/json') + ) + } + + fileID + } + + fileID_24 <- upload_file(File_24, imageName_24, folder_id, access_token, isolate(base_domain())) + fileID_48 <- upload_file(File_48, imageName_48, folder_id, access_token, isolate(base_domain())) + + # Create and upload CSV results + cell_name <- unique(df$Cell.Name)[1] + Cell <- rep(cell_name, 2) + Hours <- c(24, 48) + Function <- c('LL.4', 'LL.4') + IC50 <- c(IC50_24, IC50_48) + + Csv_df <- data.frame(Cell, Hours, Function, IC50) + + Csv_file <- tempfile(fileext = ".csv") + write.csv(Csv_df, Csv_file, row.names = FALSE) + + # Upload CSV as dataframe + endpoint <- "/api/v2-beta/data-frames" + URL <- paste("https://", isolate(base_domain()), endpoint, sep = "") + + my_data <- readBin(Csv_file, "raw", 10e6) + + DatasetBody <- list(manifest = list(list(fileName = "mortality.csv")), name = 'MortalityIC50') + + DatasetPostResponse <- httr::POST( + url = URL, + body = toJSON(DatasetBody, pretty = TRUE, auto_unbox = TRUE), + httr::accept('application/json'), + httr::add_headers('Authorization' = paste("Bearer", access_token)), + httr::content_type('application/json') + ) + + dat <- jsonlite::fromJSON(rawToChar(DatasetPostResponse$content)) + DatasetID_Result <- dat$id + s3_Put_Url <- dat$manifest$url + + s3FileUpload <- httr::PUT( + url = s3_Put_Url, + body = my_data, + httr::add_headers('x-amz-server-side-encryption' = 'AES256') + ) + + if (s3FileUpload$status_code == 200) { + endpoint <- "/api/v2-beta/data-frames/" + URL <- paste("https://", isolate(base_domain()), endpoint, DatasetID_Result, sep = "") + + DatasetStatusBody <- list(uploadStatus = "IN_PROGRESS") + + PatchFile <- httr::PATCH( + url = URL, + body = toJSON(DatasetStatusBody, pretty = TRUE, auto_unbox = TRUE), + httr::accept('application/json'), + httr::add_headers('Authorization' = paste("Bearer", access_token)), + httr::content_type('application/json') + ) + } + + # Patch analysis with outputs + endpoint <- "/api/v2-beta/analyses/" + URL <- paste("https://", isolate(base_domain()), endpoint, analysis_id, sep = "") + + Analysisfiles <- list(fileIds = list(fileID_24, fileID_48), dataFrameIds = list(DatasetID_Result)) + + PatchAnalysis <- httr::PATCH( + url = URL, + body = toJSON(Analysisfiles, pretty = TRUE, auto_unbox = TRUE), + httr::accept('application/json'), + httr::add_headers('Authorization' = paste("Bearer", access_token)), + httr::content_type('application/json') + ) + + dat <- jsonlite::fromJSON(rawToChar(PatchAnalysis$content)) + paste("Analysis complete! Status:", dat$status) + }) + + # Outputs + output$subdomain <- renderText({ + if (input$submitbutton > 0) { + isolate(subdomain()) + } else { + "Enter Analysis Key" + } + }) + + output$tabledata <- renderTable({ + if (input$submitbutton > 0) { + datasetInput() + } + }) + + output$analysis <- renderText({ + if (input$sendresultAnalysis > 0) { + isolate(analysis()) + } else { + "Click 'Send Analysis' to process" + } + }) +} + +shinyApp(ui = ui, server = server) diff --git a/examples/local_test.R b/examples/local_test.R new file mode 100644 index 0000000..2650452 --- /dev/null +++ b/examples/local_test.R @@ -0,0 +1,219 @@ +########################################################################################## +# Local IC50 Calculation (No Benchling Required) +# +# LEARNING OBJECTIVES: +# 1. Understand IC50 calculation using dose-response curves +# 2. Use utility functions for reproducible analysis +# 3. Create interactive plots with plotly +# 4. Work with concentration-response data +# +# NO PREREQUISITES: This example works with local data only - no Benchling account needed! +########################################################################################## + +library(htmlwidgets) + +# Source utility functions from parent directory +# Handle both running from examples/ and from project root +if (file.exists("../utils.R")) { + source("../utils.R") +} else if (file.exists("utils.R")) { + source("utils.R") +} else { + stop("Cannot find utils.R - please run from project root or examples/ directory") +} + +cat("\n") +cat("=====================================\n") +cat("Local IC50 Calculation\n") +cat("=====================================\n\n") + +################################################################################ +# STEP 1: Load Sample Data +################################################################################ + +cat("STEP 1: Loading sample data from CSV...\n") + +# Load the sample IC50 data +# Handle both running from examples/ and from project root +if (file.exists("sample_ic50_data.csv")) { + df <- read.csv("sample_ic50_data.csv") +} else if (file.exists("examples/sample_ic50_data.csv")) { + df <- read.csv("examples/sample_ic50_data.csv") +} else { + stop("Cannot find 'sample_ic50_data.csv' - please run from project root or examples/ directory") +} + +cat("✓ Data loaded successfully\n") +cat(" Cell line:", unique(df$Cell.Name)[1], "\n") +cat(" Observations:", nrow(df), "\n") +cat(" Concentration range:", min(df$Concentration), "-", max(df$Concentration), "µg/ml\n") +cat(" Columns:", paste(names(df), collapse = ", "), "\n\n") + +# Display first few rows to understand the data structure +cat("First few rows of data:\n") +print(head(df)) +cat("\n") + +################################################################################ +# STEP 2: Calculate IC50 Using Utility Function +################################################################################ + +cat("STEP 2: Calculating IC50...\n") +cat(" Model: 4-parameter log-logistic (LL.4)\n") +cat(" Fixed parameters: Lower=0, Upper=100\n") +cat(" Estimating: IC50 and Slope\n\n") + +# The calculate_ic50() function does all the heavy lifting: +# - Fits a dose-response curve to the data +# - Estimates IC50 (concentration at 50% mortality) +# - Calculates slope (steepness of the curve) +# - Provides statistical measures (p-value, std error, etc.) + +cat("Calculating 24h IC50...\n") +result_24h <- calculate_ic50( + df, + concentration_col = "Concentration", + mortality_col = "Mortality.24h" +) + +cat("✓ 24h IC50 calculation complete!\n\n") + +cat("Calculating 48h IC50...\n") +result_48h <- calculate_ic50( + df, + concentration_col = "Concentration", + mortality_col = "Mortality.48h" +) + +cat("✓ 48h IC50 calculation complete!\n\n") + +cat("RESULTS:\n") +cat("24h Results:\n") +cat(" IC50 Value:", result_24h$ic50, "µg/ml\n") +cat(" Slope:", result_24h$slope, "\n") +cat(" Standard Error:", result_24h$std_error, "\n") +cat(" t-value:", result_24h$t_value, "\n") +cat(" p-value:", result_24h$p_value, "\n") +if (result_24h$p_value < 0.05) { + cat(" ✓ Statistically significant (p < 0.05)\n\n") +} else { + cat(" ⚠ May not be statistically significant (p >= 0.05)\n\n") +} + +cat("48h Results:\n") +cat(" IC50 Value:", result_48h$ic50, "µg/ml\n") +cat(" Slope:", result_48h$slope, "\n") +cat(" Standard Error:", result_48h$std_error, "\n") +cat(" t-value:", result_48h$t_value, "\n") +cat(" p-value:", result_48h$p_value, "\n") +if (result_48h$p_value < 0.05) { + cat(" ✓ Statistically significant (p < 0.05)\n\n") +} else { + cat(" ⚠ May not be statistically significant (p >= 0.05)\n\n") +} + +# Understanding the results: +# - IC50: The concentration that kills 50% of cells +# - Slope: How steep the dose-response curve is (more negative = steeper) +# - p-value: Statistical significance (< 0.05 means significant) +# - Note: 48h IC50 is typically lower (more potent) as cells have more time to respond + +################################################################################ +# STEP 3: Create Interactive Visualizations +################################################################################ + +cat("STEP 3: Creating interactive plots...\n") + +# The create_ic50_plot() function generates a publication-quality plot: +# - Scatter points show your actual data +# - Smooth curve shows the fitted model +# - Log scale on x-axis (standard for pharmacology) +# - Interactive hover tooltips for data exploration + +# Determine if we're in examples/ or project root +if (basename(getwd()) == "examples") { + output_file_24h <- "local_test_output_24h.html" + output_file_48h <- "local_test_output_48h.html" +} else { + output_file_24h <- file.path("examples", "local_test_output_24h.html") + output_file_48h <- file.path("examples", "local_test_output_48h.html") +} + +# Create and save 24h plot +cat(" Creating 24h plot...\n") +plot_24h <- create_ic50_plot( + df, + concentration_col = "Concentration", + mortality_col = "Mortality.24h", + ic50_value = result_24h$ic50, + slope = result_24h$slope, + title = paste0("IC50 Dose-Response Curve - 24h (", unique(df$Cell.Name)[1], ")") +) +saveWidget(plot_24h, output_file_24h, selfcontained = TRUE) +cat(" ✓ 24h plot saved to:", output_file_24h, "\n") + +# Create and save 48h plot +cat(" Creating 48h plot...\n") +plot_48h <- create_ic50_plot( + df, + concentration_col = "Concentration", + mortality_col = "Mortality.48h", + ic50_value = result_48h$ic50, + slope = result_48h$slope, + title = paste0("IC50 Dose-Response Curve - 48h (", unique(df$Cell.Name)[1], ")") +) +saveWidget(plot_48h, output_file_48h, selfcontained = TRUE) +cat(" ✓ 48h plot saved to:", output_file_48h, "\n\n") + +################################################################################ +# STEP 4: Create Results Summary +################################################################################ + +cat("STEP 4: Creating results summary...\n") + +# Create a dataframe with the key results from both timepoints +# This format is useful for reporting or further analysis +cell_name <- unique(df$Cell.Name)[1] +summary_df <- data.frame( + Cell.Name = rep(cell_name, 10), + Timepoint = c("24h", "24h", "24h", "24h", "24h", "48h", "48h", "48h", "48h", "48h"), + Parameter = rep(c("IC50", "Slope", "Std Error", "t-value", "p-value"), 2), + Value = c(result_24h$ic50, result_24h$slope, result_24h$std_error, result_24h$t_value, result_24h$p_value, + result_48h$ic50, result_48h$slope, result_48h$std_error, result_48h$t_value, result_48h$p_value), + Unit = rep(c("µg/ml", "(unitless)", "µg/ml", "(unitless)", "(unitless)"), 2) +) + +print(summary_df) + +# Save summary to CSV in the examples directory +if (basename(getwd()) == "examples") { + summary_file <- "local_test_summary.csv" +} else { + summary_file <- file.path("examples", "local_test_summary.csv") +} +write.csv(summary_df, summary_file, row.names = FALSE) +cat("\n✓ Summary saved to:", summary_file, "\n") + +################################################################################ +# Success Message +################################################################################ + +cat("\n") +cat("=====================================\n") +cat("SUCCESS!\n") +cat("=====================================\n") +cat("You've successfully calculated IC50 from dose-response data for both timepoints.\n\n") +cat("What you learned:\n") +cat(" ✓ How to load and prepare concentration-response data\n") +cat(" ✓ How to calculate IC50 using the LL.4 model\n") +cat(" ✓ How to interpret IC50 statistics\n") +cat(" ✓ How to create interactive visualizations\n") +cat(" ✓ How to compare IC50 values across different timepoints\n\n") +cat("Files created:\n") +cat(" - ", output_file_24h, " (24h plot - open in browser)\n", sep = "") +cat(" - ", output_file_48h, " (48h plot - open in browser)\n", sep = "") +cat(" - ", summary_file, " (results table for both timepoints)\n\n", sep = "") +cat("NEXT STEPS:\n") +cat(" → Open the HTML files in your web browser to see the interactive plots\n") +cat(" → Compare the 24h vs 48h IC50 values - typically 48h shows lower IC50 (more potent)\n") +cat(" → For full Benchling integration, see the main scripts in the parent directory\n\n") diff --git a/examples/sample_ic50_data.csv b/examples/sample_ic50_data.csv new file mode 100644 index 0000000..bdaf5a4 --- /dev/null +++ b/examples/sample_ic50_data.csv @@ -0,0 +1,22 @@ +Cell Name,Concentration,Mortality 24h,Mortality 48h +CHO-B-002,0.3,3.979,2.192 +CHO-B-002,1,17.07,16.345 +CHO-B-002,3,18.356,42.458 +CHO-B-002,10,25.288,57.408 +CHO-B-002,30,54.813,70.365 +CHO-B-002,100,76.379,81.727 +CHO-B-002,300,81.514,85.11 +CHO-B-002,0.3,4.4929,5.382 +CHO-B-002,1,9.114,16.141 +CHO-B-002,3,10.141,41.06 +CHO-B-002,10,24.261,57.408 +CHO-B-002,30,51.732,67.774 +CHO-B-002,100,67.651,83.3189 +CHO-B-002,300,82.028,84.31 +CHO-B-002,0.3,8.383,2.280 +CHO-B-002,1,16.338,14.755 +CHO-B-002,3,15.5688,38.698 +CHO-B-002,10,25.577,54.996 +CHO-B-002,30,57.399,68.879 +CHO-B-002,100,77.67,80.952 +CHO-B-002,300,82.0359,83.367 \ No newline at end of file diff --git a/get_dataframe.R b/get_dataframe.R index dedf417..7771be7 100644 --- a/get_dataframe.R +++ b/get_dataframe.R @@ -6,62 +6,163 @@ library(httr) library(jsonlite) library(base64enc) -# Get Analysis Key from Benchling tenant -# INPUT -#Please uncomment analysis_key client Id and client secret -#analysis_key <- "" +################################################################################ +# AUTHENTICATION CONFIGURATION - Set your method here +################################################################################ +USE_OAUTH2 <- FALSE # Set to FALSE for JWT (default), TRUE for OAuth2 +# OAuth2 credentials (only used if USE_OAUTH2 = TRUE) +if (USE_OAUTH2) { + client_id <- Sys.getenv("BENCHLING_CLIENT_ID") + client_secret <- Sys.getenv("BENCHLING_CLIENT_SECRET") + domain_fixed <- Sys.getenv("BENCHLING_DOMAIN") -# Get the analysis ID by extracting string prior to : in analysis_key -analysis_id <- gsub(":.*$", "", analysis_key) + if (client_id == "" || client_secret == "" || domain_fixed == "") { + stop("OAuth2 enabled but credentials missing! Set BENCHLING_CLIENT_ID, BENCHLING_CLIENT_SECRET, and BENCHLING_DOMAIN in .Renviron") + } +} +################################################################################ -# Get the JWT Token and decode it to extract the subdomain of the tenant -split_key <- strsplit(analysis_key, ".", fixed = TRUE) -token <- - jsonlite::fromJSON(rawToChar(base64decode(split_key[[1]][2]))) -subdomain <- token$aud +################################################################################ +# Get Analysis Key +################################################################################ -###### Generate Bearer Token ###### +# Check if analysis key is in environment (optional) +analysis_key <- Sys.getenv("BENCHLING_ANALYSIS_KEY") -# Construct url -# The resulting URL should look like: https://.benchling.com/api/v2/token -api_path <- '/api/v2/token' -url <- paste("https://", subdomain, api_path, sep = "") +if (analysis_key == "") { + cat("\n") + cat("========================================\n") + cat("Enter your Benchling Analysis Key\n") + cat("========================================\n") + cat("The analysis key format is: ana_XXXXX:eyJhbGc...\n") + cat("You can find this in your Benchling analysis.\n") + if (USE_OAUTH2) { + cat("Note: Using OAuth2 - only analysis ID portion will be used.\n\n") + } else { + cat("Note: JWT tokens expire after 10 minutes.\n\n") + } + + # Prompt for analysis key + analysis_key <- readline(prompt = "Analysis Key: ") + + # Trim whitespace + analysis_key <- trimws(analysis_key) + + if (analysis_key == "") { + stop("Analysis key is required. Please run the script again and provide the key.") + } + + cat("\n✓ Analysis key provided\n\n") +} + +################################################################################ +# Parse Analysis Key and Authenticate +################################################################################ + +cat("Parsing analysis key...\n") + +tryCatch({ + # Split the analysis key: ana_XXXXX:JWT_TOKEN + key_parts <- strsplit(analysis_key, ":", fixed = TRUE)[[1]] + + if (length(key_parts) != 2) { + stop("Invalid analysis key format. Expected format: ana_XXXXX:eyJhbGc...") + } + + analysis_id <- key_parts[1] -# Provide Client ID and Secret -# INPUT -client_id <- "" -# INPUT -client_secret <- "" + if (USE_OAUTH2) { + # OAuth2: Use domain from credentials, generate new token + base_domain <- domain_fixed + subdomain <- sub("\\..*", "", domain_fixed) # Extract first part for display -request_payload <- - paste("client_id=",client_id,"&client_secret=",client_secret,"&grant_type=client_credentials", sep = "") + cat("✓ Analysis key parsed successfully\n") + cat(" Analysis ID:", analysis_id, "\n") + cat(" Domain:", base_domain, "(from credentials)\n\n") -# Perform a post request and get the token -token_request <- httr::POST( - url = url, - body = request_payload, - httr::accept('application/json'), - httr::content_type('application/x-www-form-urlencoded') -) + # Generate OAuth2 bearer token + cat("Authenticating with Benchling App credentials...\n") + token_url <- paste0("https://", base_domain, "/api/v2/token") + token_request <- httr::POST( + url = token_url, + body = paste0("client_id=", client_id, + "&client_secret=", client_secret, + "&grant_type=client_credentials"), + httr::accept('application/json'), + httr::content_type('application/x-www-form-urlencoded') + ) -# Use the jsonLite library to read the Json body -request_body <- jsonlite::fromJSON(rawToChar(token_request$content)) + if (token_request$status_code != 200) { + stop("OAuth2 authentication failed! Check your client_id and client_secret.") + } -# Bearer Token needs to be regenerated every 900 seconds -access_token <- request_body$access_token + request_body <- jsonlite::fromJSON(rawToChar(token_request$content)) + access_token <- request_body$access_token + + cat("✓ OAuth2 authentication successful (app-attributable)\n") + cat(" Token expires in:", request_body$expires_in, "seconds\n\n") + + } else { + # JWT: Extract subdomain from JWT, use JWT as bearer token + jwt_token <- key_parts[2] + + # Decode JWT to extract subdomain + jwt_parts <- strsplit(jwt_token, ".", fixed = TRUE)[[1]] + payload_json <- rawToChar(base64decode(jwt_parts[2])) + payload <- jsonlite::fromJSON(payload_json) + + # Extract domain from aud or iss field + domain_raw <- payload$aud + if (is.null(domain_raw) || domain_raw == "") { + domain_raw <- payload$iss + } + + # Determine if this is a full domain or just a subdomain + # Full domain examples: "tenant.benchling.com", "tenant.bnchdev.org" + # Subdomain example: "tenant" + if (grepl("\\.", domain_raw)) { + # Contains a dot - it's a full domain, use as-is + base_domain <- domain_raw + subdomain <- sub("\\..*", "", domain_raw) # Extract first part for display + } else { + # No dot - it's just a subdomain, append .benchling.com + subdomain <- domain_raw + base_domain <- paste0(domain_raw, ".benchling.com") + } + + # The JWT token IS our bearer token + access_token <- jwt_token + + cat("✓ Analysis key parsed successfully\n") + cat(" Domain:", base_domain, "\n") + cat(" Analysis ID:", analysis_id, "\n") + cat(" Authentication: Using JWT from analysis key (user-attributable)\n") + cat(" Token expires: ~10 minutes from generation\n\n") + } + +}, error = function(e) { + stop(paste( + "Failed to parse analysis key!", + "Please check that you've entered the complete key in format: ana_XXXXX:eyJhbGc...", + "\nError:", e$message, + sep = "\n" + )) +}) ############################################################### -# Use the Get analysis endpoint and retrieve the dataframe id # +# Use the Get analysis endpoint and retrieve the dataframe id ############################################################### +cat("Fetching analysis metadata...\n") + # Construct url -# The resulting URL should look like: https://.benchling.com/api/v2-beta/analyses/ana_ABCD1234 +# The resulting URL should look like: https:///api/v2-beta/analyses/ana_ABCD1234 api_path <- "/api/v2-beta/analyses/" url <- - paste("https://", subdomain, api_path, analysis_id, sep = "") + paste("https://", base_domain, api_path, analysis_id, sep = "") -# Perform a get request +# Perform a get request using JWT as bearer token analysis_response <- httr::GET(url, add_headers( @@ -69,6 +170,15 @@ analysis_response <- Authorization = paste("Bearer", access_token, sep = " ") )) +# Check for errors +if (analysis_response$status_code != 200) { + stop(paste( + "Failed to fetch analysis! Status code:", analysis_response$status_code, + "\nPlease check your analysis key is valid and not expired", + sep = "" + )) +} + # Use the jsonlite library to read the JSON body analysis_body <- jsonlite::fromJSON(rawToChar(analysis_response$content)) @@ -77,17 +187,31 @@ analysis_body <- # Note: This assumes there is a single input dataframe dataframe_id <- c(analysis_body$dataFrameIds) +if (length(dataframe_id) == 0) { + stop(paste( + "No input dataframes found in analysis!", + "Please attach a dataset to your analysis in Benchling", + sep = "\n" + )) +} + # Get the folder ID folder_id <- c(analysis_body$folderId) +cat("✓ Analysis metadata retrieved\n") +cat(" Dataframe ID:", dataframe_id, "\n") +cat(" Folder ID:", folder_id, "\n\n") + ################################################################ -# Use the Get dataframe endpoint and retrieve the dataframe id # +# Use the Get dataframe endpoint and retrieve the dataframe ################################################################ +cat("Downloading dataset...\n") + # Construct url -# The resulting URL should look like: https://.benchling.com/api/v2-beta/data-frames/dset_bHbGo1FP79Kl) +# The resulting URL should look like: https:///api/v2-beta/data-frames/dset_bHbGo1FP79Kl) api_path <- "/api/v2-beta/data-frames/" -url <- paste("https://", subdomain, api_path, dataframe_id, sep = "") +url <- paste("https://", base_domain, api_path, dataframe_id, sep = "") # Perform a get request dataframe_response <- @@ -97,6 +221,14 @@ dataframe_response <- Authorization = paste("Bearer", access_token, sep = " ") )) +# Check for errors +if (dataframe_response$status_code != 200) { + stop(paste( + "Failed to fetch dataframe! Status code:", dataframe_response$status_code, + sep = "" + )) +} + # Use the jsonlite library to read the JSON body dataframe_body <- jsonlite::fromJSON(rawToChar(dataframe_response$content)) @@ -104,5 +236,26 @@ dataframe_body <- # Retrieve the url to retrieve the dataframe in CSV format dataframe_url <- c(dataframe_body$manifest$url) -# Read the dataframe csv, save it as an R dataframe and let the R magic begin +# Read the dataframe csv and save it as an R dataframe df <- read.csv(dataframe_url) + +cat("✓ Dataset loaded successfully\n") +cat(" Rows:", nrow(df), "\n") +cat(" Columns:", ncol(df), "\n") +cat(" Column names:", paste(names(df), collapse = ", "), "\n\n") + +cat("==========================================\n") +cat("SUCCESS! Dataset ready for analysis\n") +cat("==========================================\n") +cat("Available variables:\n") +cat(" df - Dataset as R dataframe\n") +cat(" base_domain - Benchling domain (e.g., tenant.benchling.com or tenant.bnchdev.org)\n") +cat(" subdomain - Tenant subdomain (first part of domain)\n") +cat(" analysis_id - Analysis ID\n") +if (USE_OAUTH2) { + cat(" access_token - OAuth2 bearer token (15 min expiration)\n") +} else { + cat(" access_token - JWT bearer token (10 min expiration)\n") +} +cat(" folder_id - Folder ID for uploads\n") +cat("\nNext step: Run results_analysis.R\n") diff --git a/renv.lock b/renv.lock new file mode 100644 index 0000000..cbb3c39 --- /dev/null +++ b/renv.lock @@ -0,0 +1,4483 @@ +{ + "R": { + "Version": "4.5.3", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + } + ] + }, + "Packages": { + "Deriv": { + "Package": "Deriv", + "Version": "4.2.0", + "Source": "Repository", + "Type": "Package", + "Title": "Symbolic Differentiation", + "Date": "2025-06-20", + "Authors@R": "c(person(given=\"Andrew\", family=\"Clausen\", role=\"aut\"), person(given=\"Serguei\", family=\"Sokol\", role=c(\"aut\", \"cre\"), email=\"sokol@insa-toulouse.fr\", comment = c(ORCID = \"0000-0002-5674-3327\")), person(given=\"Andreas\", family=\"Rappold\", role=\"ctb\", email=\"arappold@gmx.at\"))", + "Description": "R-based solution for symbolic differentiation. It admits user-defined function as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.", + "License": "GPL (>= 3)", + "Suggests": [ + "testthat (>= 0.11.0)" + ], + "BugReports": "https://github.com/sgsokol/Deriv/issues", + "RoxygenNote": "7.3.1", + "Imports": [ + "methods" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Andrew Clausen [aut], Serguei Sokol [aut, cre] (ORCID: ), Andreas Rappold [ctb]", + "Maintainer": "Serguei Sokol ", + "Repository": "CRAN" + }, + "Formula": { + "Package": "Formula", + "Version": "1.2-5", + "Source": "Repository", + "Date": "2023-02-23", + "Title": "Extended Model Formulas", + "Description": "Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side (see ).", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Yves\", family = \"Croissant\", role = \"aut\", email = \"Yves.Croissant@univ-reunion.fr\"))", + "Depends": [ + "R (>= 2.0.0)", + "stats" + ], + "License": "GPL-2 | GPL-3", + "NeedsCompilation": "no", + "Author": "Achim Zeileis [aut, cre] (), Yves Croissant [aut]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" + }, + "MASS": { + "Package": "MASS", + "Version": "7.3-65", + "Source": "Repository", + "Priority": "recommended", + "Date": "2025-02-19", + "Revision": "$Rev: 3681 $", + "Depends": [ + "R (>= 4.4.0)", + "grDevices", + "graphics", + "stats", + "utils" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "lattice", + "nlme", + "nnet", + "survival" + ], + "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Brian.Ripley@R-project.org\"), person(\"Bill\", \"Venables\", role = c(\"aut\", \"cph\")), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\", comment = \"support functions for polr\"))", + "Description": "Functions and datasets to support Venables and Ripley, \"Modern Applied Statistics with S\" (4th edition, 2002).", + "Title": "Support Functions and Datasets for Venables and Ripley's MASS", + "LazyData": "yes", + "ByteCompile": "yes", + "License": "GPL-2 | GPL-3", + "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", + "Contact": "", + "NeedsCompilation": "yes", + "Author": "Brian Ripley [aut, cre, cph], Bill Venables [aut, cph], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb] (support functions for polr)", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" + }, + "Matrix": { + "Package": "Matrix", + "Version": "1.7-5", + "Source": "Repository", + "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", + "Date": "2026-03-20", + "Priority": "recommended", + "Title": "Sparse and Dense Matrix Classes and Methods", + "Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.", + "License": "GPL (>= 2) | file LICENCE", + "URL": "https://Matrix.R-forge.R-project.org", + "BugReports": "https://R-forge.R-project.org/tracker/?atid=294&group_id=61", + "Contact": "Matrix-authors@R-project.org", + "Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Mikael\", \"Jagan\", role = \"aut\", comment = c(ORCID = \"0000-0002-3542-2938\")), person(\"Timothy A.\", \"Davis\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7614-6899\", \"SuiteSparse libraries\", \"collaborators listed in dir(system.file(\\\"doc\\\", \\\"SuiteSparse\\\", package=\\\"Matrix\\\"), pattern=\\\"License\\\", full.names=TRUE, recursive=TRUE)\")), person(\"George\", \"Karypis\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2753-1437\", \"METIS library\", \"Copyright: Regents of the University of Minnesota\")), person(\"Jason\", \"Riedy\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4345-4200\", \"GNU Octave's condest() and onenormest()\", \"Copyright: Regents of the University of California\")), person(\"Jens\", \"Oehlschlägel\", role = \"ctb\", comment = \"initial nearPD()\"), person(\"R Core Team\", role = \"ctb\", comment = c(ROR = \"02zz1nj61\", \"base R's matrix implementation\")))", + "Depends": [ + "R (>= 4.4)", + "methods" + ], + "Imports": [ + "grDevices", + "graphics", + "grid", + "lattice", + "stats", + "utils" + ], + "Suggests": [ + "MASS", + "datasets", + "sfsmisc", + "tools" + ], + "Enhances": [ + "SparseM", + "graph" + ], + "LazyData": "no", + "LazyDataNote": "not possible, since we use data/*.R and our S4 classes", + "BuildResaveData": "no", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Douglas Bates [aut] (ORCID: ), Martin Maechler [aut, cre] (ORCID: ), Mikael Jagan [aut] (ORCID: ), Timothy A. Davis [ctb] (ORCID: , SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (ORCID: , METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (ORCID: , GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (ROR: , base R's matrix implementation)", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" + }, + "MatrixModels": { + "Package": "MatrixModels", + "Version": "0.5-4", + "Source": "Repository", + "VersionNote": "Released 0.5-3 on 2023-11-06", + "Date": "2025-03-25", + "Title": "Modelling with Sparse and Dense Matrices", + "Contact": "Matrix-authors@R-project.org", + "Authors@R": "c( person(\"Douglas\", \"Bates\", role = \"aut\", email = \"bates@stat.wisc.edu\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", comment = c(ORCID = \"0000-0002-8685-9910\")))", + "Description": "Generalized Linear Modelling with sparse and dense 'Matrix' matrices, using modular prediction and response module classes.", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "stats", + "methods", + "Matrix (>= 1.6-0)", + "Matrix(< 1.8-0)" + ], + "ImportsNote": "_not_yet_stats4", + "Encoding": "UTF-8", + "LazyLoad": "yes", + "License": "GPL (>= 2)", + "URL": "https://Matrix.R-forge.R-project.org/, https://r-forge.r-project.org/R/?group_id=61", + "BugReports": "https://R-forge.R-project.org/tracker/?func=add&atid=294&group_id=61", + "NeedsCompilation": "no", + "Author": "Douglas Bates [aut] (), Martin Maechler [aut, cre] ()", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" + }, + "R6": { + "Package": "R6", + "Version": "2.6.1", + "Source": "Repository", + "Title": "Encapsulated Classes with Reference Semantics", + "Authors@R": "c( person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.", + "License": "MIT + file LICENSE", + "URL": "https://r6.r-lib.org, https://github.com/r-lib/R6", + "BugReports": "https://github.com/r-lib/R6/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Suggests": [ + "lobstr", + "testthat (>= 3.0.0)" + ], + "Config/Needs/website": "tidyverse/tidytemplate, ggplot2, microbenchmark, scales", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Winston Chang [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Winston Chang ", + "Repository": "CRAN" + }, + "RColorBrewer": { + "Package": "RColorBrewer", + "Version": "1.1-3", + "Source": "Repository", + "Date": "2022-04-03", + "Title": "ColorBrewer Palettes", + "Authors@R": "c(person(given = \"Erich\", family = \"Neuwirth\", role = c(\"aut\", \"cre\"), email = \"erich.neuwirth@univie.ac.at\"))", + "Author": "Erich Neuwirth [aut, cre]", + "Maintainer": "Erich Neuwirth ", + "Depends": [ + "R (>= 2.0.0)" + ], + "Description": "Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org.", + "License": "Apache License 2.0", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "Rcpp": { + "Package": "Rcpp", + "Version": "1.1.1", + "Source": "Repository", + "Title": "Seamless R and C++ Integration", + "Date": "2026-01-07", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"JJ\", \"Allaire\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Kevin\", \"Ushey\", role = \"aut\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Qiang\", \"Kou\", role = \"aut\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Nathan\", \"Russell\", role = \"aut\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"John\", \"Chambers\", role = \"aut\"))", + "Description": "The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at , the paper by Eddelbuettel and Francois (2011, ), the book by Eddelbuettel (2013, ) and the paper by Eddelbuettel and Balamuta (2018, ); see 'citation(\"Rcpp\")' for details.", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "methods", + "utils" + ], + "Suggests": [ + "tinytest", + "inline", + "rbenchmark", + "pkgKitten (>= 0.1.2)" + ], + "URL": "https://www.rcpp.org, https://dirk.eddelbuettel.com/code/rcpp.html, https://github.com/RcppCore/Rcpp", + "License": "GPL (>= 2)", + "BugReports": "https://github.com/RcppCore/Rcpp/issues", + "MailingList": "rcpp-devel@lists.r-forge.r-project.org", + "RoxygenNote": "6.1.1", + "Encoding": "UTF-8", + "VignetteBuilder": "Rcpp", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Romain Francois [aut] (ORCID: ), JJ Allaire [aut] (ORCID: ), Kevin Ushey [aut] (ORCID: ), Qiang Kou [aut] (ORCID: ), Nathan Russell [aut], Iñaki Ucar [aut] (ORCID: ), Doug Bates [aut] (ORCID: ), John Chambers [aut]", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "RcppArmadillo": { + "Package": "RcppArmadillo", + "Version": "15.2.4-1", + "Source": "Repository", + "Type": "Package", + "Title": "'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library", + "Date": "2026-03-17", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Binxiang\", \"Ni\", role = \"aut\"), person(\"Conrad\", \"Sanderson\", role = \"aut\", comment = c(ORCID = \"0000-0002-0049-4501\")))", + "Description": "'Armadillo' is a templated C++ linear algebra library aiming towards a good balance between speed and ease of use. It provides high-level syntax and functionality deliberately similar to Matlab. It is useful for algorithm development directly in C++, or quick conversion of research code into production environments. It provides efficient classes for vectors, matrices and cubes where dense and sparse matrices are supported. Integer, floating point and complex numbers are supported. A sophisticated expression evaluator (based on template meta-programming) automatically combines several operations to increase speed and efficiency. Dynamic evaluation automatically chooses optimal code paths based on detected matrix structures. Matrix decompositions are provided through integration with LAPACK, or one of its high performance drop-in replacements (such as 'MKL' or 'OpenBLAS'). It can automatically use 'OpenMP' multi-threading (parallelisation) to speed up computationally expensive operations. . The 'RcppArmadillo' package includes the header files from the 'Armadillo' library; users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. Starting from release 15.0.0, the minimum compilation standard is C++14 so 'Armadillo' version 14.6.3 is included as a fallback when an R package forces the C++11 standard. Package authors should set a '#define' to select the 'current' version, or select the 'legacy' version (also chosen as default) if they must. See 'GitHub issue #475' for details. . Since release 7.800.0, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", + "License": "GPL (>= 2)", + "LazyLoad": "yes", + "Depends": [ + "R (>= 3.3.0)" + ], + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "Rcpp (>= 1.0.12)", + "stats", + "utils", + "methods" + ], + "Suggests": [ + "tinytest", + "Matrix (>= 1.3.0)", + "pkgKitten", + "reticulate", + "slam" + ], + "URL": "https://github.com/RcppCore/RcppArmadillo, https://dirk.eddelbuettel.com/code/rcpp.armadillo.html", + "BugReports": "https://github.com/RcppCore/RcppArmadillo/issues", + "RoxygenNote": "6.0.1", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Romain Francois [aut] (ORCID: ), Doug Bates [aut] (ORCID: ), Binxiang Ni [aut], Conrad Sanderson [aut] (ORCID: )", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "RcppEigen": { + "Package": "RcppEigen", + "Version": "0.3.4.0.2", + "Source": "Repository", + "Type": "Package", + "Title": "'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library", + "Date": "2024-08-23", + "Authors@R": "c(person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Yixuan\", \"Qiu\", role = \"aut\", comment = c(ORCID = \"0000-0003-0109-6692\")), person(\"Authors of\", \"Eigen\", role = \"cph\", comment = \"Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS\"))", + "Copyright": "See the file COPYRIGHTS for various Eigen copyright details", + "Description": "R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library. Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", + "License": "GPL (>= 2) | file LICENSE", + "LazyLoad": "yes", + "Depends": [ + "R (>= 3.6.0)" + ], + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "Rcpp (>= 0.11.0)", + "stats", + "utils" + ], + "Suggests": [ + "Matrix", + "inline", + "tinytest", + "pkgKitten", + "microbenchmark" + ], + "URL": "https://github.com/RcppCore/RcppEigen, https://dirk.eddelbuettel.com/code/rcpp.eigen.html", + "BugReports": "https://github.com/RcppCore/RcppEigen/issues", + "NeedsCompilation": "yes", + "Author": "Doug Bates [aut] (), Dirk Eddelbuettel [aut, cre] (), Romain Francois [aut] (), Yixuan Qiu [aut] (), Authors of Eigen [cph] (Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS)", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "Rdpack": { + "Package": "Rdpack", + "Version": "2.6.6", + "Source": "Repository", + "Type": "Package", + "Title": "Update and Manipulate Rd Documentation Objects", + "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), email = \"georgi.boshnakov@manchester.ac.uk\", comment = c(ORCID = \"0000-0003-2839-346X\")), person(given = \"Duncan\", family = \"Murdoch\", role = \"ctb\", email = \"murdoch.duncan@gmail.com\") )", + "Description": "Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.", + "URL": "https://geobosh.github.io/Rdpack/ (doc), https://CRAN.R-project.org/package=Rdpack", + "BugReports": "https://github.com/GeoBosh/Rdpack/issues", + "Depends": [ + "R (>= 2.15.0)", + "methods" + ], + "Imports": [ + "tools", + "utils", + "rbibutils (> 2.4)" + ], + "Suggests": [ + "grDevices", + "testthat", + "rstudioapi", + "rprojroot", + "gbRd" + ], + "License": "GPL (>= 2)", + "LazyLoad": "yes", + "Encoding": "UTF-8", + "RoxygenNote": "7.1.1", + "NeedsCompilation": "no", + "Author": "Georgi N. Boshnakov [aut, cre] (ORCID: ), Duncan Murdoch [ctb]", + "Maintainer": "Georgi N. Boshnakov ", + "Repository": "CRAN" + }, + "S7": { + "Package": "S7", + "Version": "0.2.1", + "Source": "Repository", + "Title": "An Object Oriented System Meant to Become a Successor to S3 and S4", + "Authors@R": "c( person(\"Object-Oriented Programming Working Group\", role = \"cph\"), person(\"Davis\", \"Vaughan\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Tomasz\", \"Kalinowski\", role = \"aut\"), person(\"Will\", \"Landau\", role = \"aut\"), person(\"Michael\", \"Lawrence\", role = \"aut\"), person(\"Martin\", \"Maechler\", role = \"aut\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Luke\", \"Tierney\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")) )", + "Description": "A new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, 'Bioconductor', 'Posit'/'tidyverse', and the wider R community.", + "License": "MIT + file LICENSE", + "URL": "https://rconsortium.github.io/S7/, https://github.com/RConsortium/S7", + "BugReports": "https://github.com/RConsortium/S7/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "bench", + "callr", + "covr", + "knitr", + "methods", + "rmarkdown", + "testthat (>= 3.2.0)", + "tibble" + ], + "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/Needs/website": "sloop", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Config/testthat/start-first": "external-generic", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "yes", + "Author": "Object-Oriented Programming Working Group [cph], Davis Vaughan [aut], Jim Hester [aut] (ORCID: ), Tomasz Kalinowski [aut], Will Landau [aut], Michael Lawrence [aut], Martin Maechler [aut] (ORCID: ), Luke Tierney [aut], Hadley Wickham [aut, cre] (ORCID: )", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "SparseM": { + "Package": "SparseM", + "Version": "1.84-2", + "Source": "Repository", + "Authors@R": "c( person(\"Roger\", \"Koenker\", role = c(\"cre\",\"aut\"), email = \"rkoenker@uiuc.edu\"), person(c(\"Pin\", \"Tian\"), \"Ng\", role = c(\"ctb\"), comment = \"Contributions to Sparse QR code\", email = \"pin.ng@nau.edu\") , person(\"Yousef\", \"Saad\", role = c(\"ctb\"), comment = \"author of sparskit2\") , person(\"Ben\", \"Shaby\", role = c(\"ctb\"), comment = \"author of chol2csr\") , person(\"Martin\", \"Maechler\", role = \"ctb\", comment = c(\"chol() tweaks; S4\", ORCID = \"0000-0002-8685-9910\")) )", + "Maintainer": "Roger Koenker ", + "Depends": [ + "R (>= 2.15)", + "methods" + ], + "Imports": [ + "graphics", + "stats", + "utils" + ], + "VignetteBuilder": "knitr", + "Suggests": [ + "knitr" + ], + "Description": "Some basic linear algebra functionality for sparse matrices is provided: including Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.", + "License": "GPL (>= 2)", + "Title": "Sparse Linear Algebra", + "URL": "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html", + "NeedsCompilation": "yes", + "Author": "Roger Koenker [cre, aut], Pin Tian Ng [ctb] (Contributions to Sparse QR code), Yousef Saad [ctb] (author of sparskit2), Ben Shaby [ctb] (author of chol2csr), Martin Maechler [ctb] (chol() tweaks; S4, )", + "Repository": "CRAN" + }, + "TH.data": { + "Package": "TH.data", + "Version": "1.1-5", + "Source": "Repository", + "Title": "TH's Data Archive", + "Date": "2025-11-17", + "Authors@R": "c(person(\"Torsten\", \"Hothorn\", role = c(\"aut\", \"cre\"), email = \"Torsten.Hothorn@R-project.org\"))", + "Description": "Contains data sets used in other packages Torsten Hothorn maintains.", + "Depends": [ + "R (>= 3.5.0)", + "survival", + "MASS" + ], + "Suggests": [ + "trtf", + "tram", + "rms", + "coin", + "ATR", + "multcomp", + "gridExtra", + "vcd", + "colorspace", + "lattice", + "knitr", + "dplyr", + "openxlsx", + "plyr" + ], + "LazyData": "yes", + "VignetteBuilder": "knitr", + "License": "GPL-3", + "NeedsCompilation": "no", + "Author": "Torsten Hothorn [aut, cre]", + "Maintainer": "Torsten Hothorn ", + "Repository": "CRAN" + }, + "abind": { + "Package": "abind", + "Version": "1.4-8", + "Source": "Repository", + "Date": "2024-09-08", + "Title": "Combine Multidimensional Arrays", + "Authors@R": "c(person(\"Tony\", \"Plate\", email = \"tplate@acm.org\", role = c(\"aut\", \"cre\")), person(\"Richard\", \"Heiberger\", role = c(\"aut\")))", + "Maintainer": "Tony Plate ", + "Description": "Combine multidimensional arrays into a single array. This is a generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and higher-dimensional arrays (aka tensors). Also provides functions 'adrop', 'asub', and 'afill' for manipulating, extracting and replacing data in arrays.", + "Depends": [ + "R (>= 1.5.0)" + ], + "Imports": [ + "methods", + "utils" + ], + "License": "MIT + file LICENSE", + "NeedsCompilation": "no", + "Author": "Tony Plate [aut, cre], Richard Heiberger [aut]", + "Repository": "CRAN" + }, + "askpass": { + "Package": "askpass", + "Version": "1.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "Password Entry Utilities for R, Git, and SSH", + "Authors@R": "person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\"))", + "Description": "Cross-platform utilities for prompting the user for credentials or a passphrase, for example to authenticate with a server or read a protected key. Includes native programs for MacOS and Windows, hence no 'tcltk' is required. Password entry can be invoked in two different ways: directly from R via the askpass() function, or indirectly as password-entry back-end for 'ssh-agent' or 'git-credential' via the SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can be prompted for credentials or a passphrase if needed when R calls out to git or ssh.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.r-universe.dev/askpass", + "BugReports": "https://github.com/r-lib/askpass/issues", + "Encoding": "UTF-8", + "Imports": [ + "sys (>= 2.1)" + ], + "RoxygenNote": "7.2.3", + "Suggests": [ + "testthat" + ], + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] ()", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "backports": { + "Package": "backports", + "Version": "1.5.0", + "Source": "Repository", + "Type": "Package", + "Title": "Reimplementations of Functions Introduced Since R-3.0.0", + "Authors@R": "c( person(\"Michel\", \"Lang\", NULL, \"michellang@gmail.com\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Duncan\", \"Murdoch\", NULL, \"murdoch.duncan@gmail.com\", role = c(\"aut\")), person(\"R Core Team\", role = \"aut\"))", + "Maintainer": "Michel Lang ", + "Description": "Functions introduced or changed since R v3.0.0 are re-implemented in this package. The backports are conditionally exported in order to let R resolve the function name to either the implemented backport, or the respective base version, if available. Package developers can make use of new functions or arguments by selectively importing specific backports to support older installations.", + "URL": "https://github.com/r-lib/backports", + "BugReports": "https://github.com/r-lib/backports/issues", + "License": "GPL-2 | GPL-3", + "NeedsCompilation": "yes", + "ByteCompile": "yes", + "Depends": [ + "R (>= 3.0.0)" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Author": "Michel Lang [cre, aut] (), Duncan Murdoch [aut], R Core Team [aut]", + "Repository": "CRAN" + }, + "base64enc": { + "Package": "base64enc", + "Version": "0.1-6", + "Source": "Repository", + "Title": "Tools for 'base64' Encoding", + "Author": "Simon Urbanek [aut, cre, cph] (https://urbanek.nz, ORCID: )", + "Authors@R": "person(\"Simon\", \"Urbanek\", role=c(\"aut\",\"cre\",\"cph\"), email=\"Simon.Urbanek@r-project.org\", comment=c(\"https://urbanek.nz\", ORCID=\"0000-0003-2297-1732\"))", + "Maintainer": "Simon Urbanek ", + "Depends": [ + "R (>= 2.9.0)" + ], + "Enhances": [ + "png" + ], + "Description": "Tools for handling 'base64' encoding. It is more flexible than the orphaned 'base64' package.", + "License": "GPL-2 | GPL-3", + "URL": "https://www.rforge.net/base64enc", + "BugReports": "https://github.com/s-u/base64enc/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "boot": { + "Package": "boot", + "Version": "1.3-32", + "Source": "Repository", + "Priority": "recommended", + "Date": "2025-08-29", + "Authors@R": "c(person(\"Angelo\", \"Canty\", role = \"aut\", email = \"cantya@mcmaster.ca\", comment = \"author of original code for S\"), person(\"Brian\", \"Ripley\", role = c(\"aut\", \"trl\"), email = \"Brian.Ripley@R-project.org\", comment = \"conversion to R, maintainer 1999--2022, author of parallel support\"), person(\"Alessandra R.\", \"Brazzale\", role = c(\"ctb\", \"cre\"), email = \"brazzale@stat.unipd.it\", comment = \"minor bug fixes\"))", + "Maintainer": "Alessandra R. Brazzale ", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Description": "Functions and datasets for bootstrapping from the book \"Bootstrap Methods and Their Application\" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.", + "Title": "Bootstrap Functions", + "Depends": [ + "R (>= 3.0.0)", + "graphics", + "stats" + ], + "Suggests": [ + "MASS", + "survival" + ], + "LazyData": "yes", + "ByteCompile": "yes", + "License": "Unlimited", + "NeedsCompilation": "no", + "Author": "Angelo Canty [aut] (author of original code for S), Brian Ripley [aut, trl] (conversion to R, maintainer 1999--2022, author of parallel support), Alessandra R. Brazzale [ctb, cre] (minor bug fixes)", + "Repository": "CRAN" + }, + "broom": { + "Package": "broom", + "Version": "1.0.12", + "Source": "Repository", + "Type": "Package", + "Title": "Convert Statistical Objects into Tidy Tibbles", + "Authors@R": "c( person(\"David\", \"Robinson\", , \"admiral.david@gmail.com\", role = \"aut\"), person(\"Alex\", \"Hayes\", , \"alexpghayes@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(\"Simon\", \"Couch\", , \"simon.couch@posit.co\", role = c(\"aut\"), comment = c(ORCID = \"0000-0001-5676-5107\")), person(\"Emil\", \"Hvitfeldt\", , \"emil.hvitfeldt@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0679-1945\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")), person(\"Indrajeet\", \"Patil\", , \"patilindrajeet.science@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(\"Derek\", \"Chiu\", , \"dchiu@bccrc.ca\", role = 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role = \"ctb\"), person(\"Hong\", \"Ooi\", , \"hongooi@microsoft.com\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", , \"henrikb@braju.com\", role = \"ctb\"), person(\"Eduard\", \"Szocs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", , \"davidhughjones@gmail.com\", role = \"ctb\"), person(\"Matthieu\", \"Stigler\", , \"Matthieu.Stigler@gmail.com\", role = \"ctb\"), person(\"Hugo\", \"Tavares\", , \"hm533@cam.ac.uk\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9373-2726\")), person(\"R. 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Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", + "License": "MIT + file LICENSE", + "URL": "https://broom.tidymodels.org/, https://github.com/tidymodels/broom", + "BugReports": "https://github.com/tidymodels/broom/issues", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "backports", + "cli", + "dplyr (>= 1.0.0)", + "generics (>= 0.0.2)", + "glue", + "lifecycle", + "purrr", + "rlang (>= 1.1.0)", + "stringr", + "tibble (>= 3.0.0)", + "tidyr (>= 1.0.0)" + ], + "Suggests": [ + "AER", + "AUC", + "bbmle", + "betareg (>= 3.2-1)", + "biglm", + "binGroup", + "boot", + "btergm (>= 1.10.6)", + "car (>= 3.1-2)", + "carData", + "caret", + 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"Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-25", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.3", + "Collate": "'aaa-documentation-helper.R' 'null-and-default.R' 'aer.R' 'auc.R' 'base.R' 'bbmle.R' 'betareg.R' 'biglm.R' 'bingroup.R' 'boot.R' 'broom-package.R' 'broom.R' 'btergm.R' 'car.R' 'caret.R' 'cluster.R' 'cmprsk.R' 'data-frame.R' 'deprecated-0-7-0.R' 'drc.R' 'emmeans.R' 'epiR.R' 'ergm.R' 'fixest.R' 'gam.R' 'geepack.R' 'glmnet-cv-glmnet.R' 'glmnet-glmnet.R' 'gmm.R' 'hmisc.R' 'import-standalone-obj-type.R' 'import-standalone-types-check.R' 'joinerml.R' 'kendall.R' 'ks.R' 'lavaan.R' 'leaps.R' 'lfe.R' 'list-irlba.R' 'list-optim.R' 'list-svd.R' 'list-xyz.R' 'list.R' 'lm-beta.R' 'lmodel2.R' 'lmtest.R' 'maps.R' 'margins.R' 'mass-fitdistr.R' 'mass-negbin.R' 'mass-polr.R' 'mass-ridgelm.R' 'stats-lm.R' 'mass-rlm.R' 'mclust.R' 'mediation.R' 'metafor.R' 'mfx.R' 'mgcv.R' 'mlogit.R' 'muhaz.R' 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It has also been used extensively in the book Fundamentals of Data Visualization.", + "URL": "https://wilkelab.org/cowplot/", + "BugReports": "https://github.com/wilkelab/cowplot/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "ggplot2 (>= 3.5.2)", + "grid", + "gtable", + "grDevices", + "methods", + "rlang", + "scales" + ], + "License": "GPL-2", + "Suggests": [ + "Cairo", + "covr", + "dplyr", + "forcats", + "gridGraphics (>= 0.4-0)", + "knitr", + "lattice", + "magick", + "maps", + "PASWR", + "patchwork", + "rmarkdown", + "ragg", + "testthat (>= 1.0.0)", + "tidyr", + "vdiffr (>= 0.3.0)", + "VennDiagram" + ], + "VignetteBuilder": "knitr", + "Collate": "'add_sub.R' 'align_plots.R' 'as_grob.R' 'as_gtable.R' 'axis_canvas.R' 'cowplot.R' 'draw.R' 'get_plot_component.R' 'get_axes.R' 'get_titles.R' 'get_legend.R' 'get_panel.R' 'gtable.R' 'key_glyph.R' 'plot_grid.R' 'save.R' 'set_null_device.R' 'setup.R' 'stamp.R' 'themes.R' 'utils_ggplot2.R'", + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Claus O. 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Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (ORCID: ), Jim Hester [aut] (ORCID: ), Romain François [aut] (ORCID: ), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "crosstalk": { + "Package": "crosstalk", + "Version": "1.2.2", + "Source": "Repository", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(, \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(, \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). 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Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.73): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" + ], + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "data.table": { + "Package": "data.table", + "Version": "1.18.2.1", + "Source": "Repository", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.4.0)" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils (>= 2.13.0)", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\", email=\"j.gorecki@wit.edu.pl\"), person(\"Michael\",\"Chirico\", role=\"aut\", email=\"michaelchirico4@gmail.com\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", email=\"toby.hocking@r-project.org\", comment = c(ORCID=\"0000-0002-3146-0865\")), 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Matthieu Gomez [ctb], Philippe Chataignon [ctb], Nello Blaser [ctb], Dmitry Selivanov [ctb], Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb] (GitHub user), Marc Halperin [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan [ctb], Leonardo Silvestri [ctb], Jim Hester [ctb], Anthony Damico [ctb], Sebastian Freundt [ctb], David Simons [ctb], Elliott Sales de Andrade [ctb], Cole Miller [ctb], Jens Peder Meldgaard [ctb], Vaclav Tlapak [ctb], Kevin Ushey [ctb], Dirk Eddelbuettel [ctb], Tony Fischetti [ctb], Ofek Shilon [ctb], Vadim Khotilovich [ctb], Hadley Wickham [ctb], Bennet Becker [ctb], Kyle Haynes [ctb], Boniface Christian Kamgang [ctb], Olivier Delmarcell [ctb], Josh O'Brien [ctb], Dereck de Mezquita [ctb], Michael Czekanski 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"Date": "2025-11-19", + "Title": "Create Compact Hash Digests of R Objects", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as 'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://eddelbuettel.github.io/digest/, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "utils" + ], + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown", + "rbenchmark" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Antoine Lucas [ctb] (ORCID: ), Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (ORCID: ), Simon Urbanek [ctb] (ORCID: ), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb] (ORCID: ), Duncan Murdoch [ctb], Jim Hester [ctb] (ORCID: ), Wush Wu [ctb] (ORCID: ), Qiang Kou [ctb] (ORCID: ), Thierry Onkelinx [ctb] (ORCID: ), Michel Lang [ctb] (ORCID: ), Viliam Simko [ctb], Kurt Hornik [ctb] (ORCID: ), Radford Neal [ctb] (ORCID: ), Kendon Bell [ctb] (ORCID: ), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb] (ORCID: ), Ion Suruceanu [ctb] (ORCID: ), Bill Denney [ctb] (ORCID: ), Dirk Schumacher [ctb], András Svraka [ctb] (ORCID: ), Sergey Fedorov [ctb] (ORCID: ), Will Landau [ctb] (ORCID: ), Floris Vanderhaeghe [ctb] (ORCID: ), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (ORCID: ), Mark van der Loo [ctb] (ORCID: ), Chris Muir [ctb] (ORCID: ), Moritz Beller [ctb] (ORCID: ), Sebastian Campbell [ctb] (ORCID: ), Winston Chang [ctb] (ORCID: ), Dean Attali [ctb] (ORCID: ), Michael Chirico [ctb] (ORCID: ), Kevin Ushey [ctb] (ORCID: ), Carl Pearson [ctb] (ORCID: )", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "doBy": { + "Package": "doBy", + "Version": "4.7.1", + "Source": "Repository", + "Title": "Groupwise Statistics, LSmeans, Linear Estimates, Utilities", + "Authors@R": "c( person(given = \"Ulrich\", family = \"Halekoh\", email = \"uhalekoh@health.sdu.dk\", role = c(\"aut\", \"cph\")), person(given = \"Søren\", family = \"Højsgaard\", email = \"sorenh@math.aau.dk\", role = c(\"aut\", \"cre\", \"cph\")) )", + "Description": "Utility package containing: Main categories: Working with grouped data: 'do' something to data when stratified 'by' some variables. General linear estimates. Data handling utilities. Functional programming, in particular restrict functions to a smaller domain. Miscellaneous functions for data handling. Model stability in connection with model selection. 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The 'farver' package provides a set of functions that gives access to very fast colour space conversion and comparisons implemented in C++, and offers speed improvements over the 'convertColor' function in the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://farver.data-imaginist.com, https://github.com/thomasp85/farver", + "BugReports": "https://github.com/thomasp85/farver/issues", + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Berendea Nicolae [aut] (Author of the ColorSpace C++ library), Romain François [aut] (), Posit, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "fastmap": { + "Package": "fastmap", + "Version": "1.2.0", + "Source": "Repository", + "Title": "Fast Data Structures", + "Authors@R": "c( person(\"Winston\", \"Chang\", email = \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Tessil\", role = \"cph\", comment = \"hopscotch_map library\") )", + "Description": "Fast implementation of data structures, including a key-value store, stack, and queue. 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Further the package makes it easy to manipulate and combine 'gtable' objects so that complex compositions can be built up sequentially.", + "License": "MIT + file LICENSE", + "URL": "https://gtable.r-lib.org, https://github.com/r-lib/gtable", + "BugReports": "https://github.com/r-lib/gtable/issues", + "Depends": [ + "R (>= 4.0)" + ], + "Imports": [ + "cli", + "glue", + "grid", + "lifecycle", + "rlang (>= 1.1.0)", + "stats" + ], + "Suggests": [ + "covr", + "ggplot2", + "knitr", + "profvis", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2024-10-25", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "gtools": { + "Package": "gtools", + "Version": "3.9.5", + "Source": "Repository", + "Title": "Various R Programming Tools", + "Description": "Functions to assist in R programming, including: - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse logit transformations ('logit', 'inv.logit'), - test if a value is missing, empty or contains only NA and NULL values ('invalid'), - manipulate R's .Last function ('addLast'), - define macros ('defmacro'), - detect odd and even integers ('odd', 'even'), - convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a binary search ('binsearch'), - sort strings containing both numeric and character components ('mixedsort'), - create a factor variable from the quantiles of a continuous variable ('quantcut'), - enumerate permutations and combinations ('combinations', 'permutation'), - calculate and convert between fold-change and log-ratio ('foldchange', 'logratio2foldchange', 'foldchange2logratio'), - calculate probabilities and generate random numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply a function over adjacent subsets of a vector ('running'), - modify the TCP_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of data frames, even if the column names don't match ('smartbind'), - generate significance stars from p-values ('stars.pval'), - convert characters to/from ASCII codes ('asc', 'chr'), - convert character vector to ASCII representation ('ASCIIfy'), - apply title capitalization rules to a character vector ('capwords').", + "Authors@R": "c(person(\"Gregory R.\", \"Warnes\", role = \"aut\"), person(\"Ben\", \"Bolker\", role = c(\"aut\", \"cre\"), email = \"bolker@mcmaster.ca\", comment=c(ORCID=\"0000-0002-2127-0443\")), person(\"Thomas\", \"Lumley\", role = \"aut\"), person(\"Arni\", \"Magnusson\", role = \"aut\"), person(\"Bill\", \"Venables\", role = \"aut\"), person(\"Genei\", \"Ryodan\", role = \"aut\"), person(\"Steffen\", \"Moeller\", role = \"aut\"), person(\"Ian\", \"Wilson\", role = \"ctb\"), person(\"Mark\", \"Davis\", role = \"ctb\"), person(\"Nitin\", \"Jain\", role=\"ctb\"), person(\"Scott\", \"Chamberlain\", role = \"ctb\"))", + "License": "GPL-2", + "Depends": [ + "methods", + "stats", + "utils" + ], + "URL": "https://github.com/r-gregmisc/gtools", + "BugReports": "https://github.com/r-gregmisc/gtools/issues", + "Language": "en-US", + "Suggests": [ + "car", + "gplots", + "knitr", + "rstudioapi", + "SGP", + "taxize" + ], + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Gregory R. 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Source code of other languages is supported via Andre Simon's highlight package ().", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "xfun (>= 0.18)" + ], + "Suggests": [ + "knitr", + "markdown", + "testit" + ], + "License": "GPL", + "URL": "https://github.com/yihui/highr", + "BugReports": "https://github.com/yihui/highr/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (ORCID: ), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "htmltools": { + "Package": "htmltools", + "Version": "0.5.9", + "Source": "Repository", + "Type": "Package", + "Title": "Tools for HTML", + "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Barret\", \"Schloerke\", , \"barret@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Yihui\", \"Xie\", , \"yihui@posit.co\", role = \"aut\"), person(\"Jeff\", \"Allen\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Tools for HTML generation and output.", + "License": "GPL (>= 2)", + "URL": "https://github.com/rstudio/htmltools, https://rstudio.github.io/htmltools/", + "BugReports": "https://github.com/rstudio/htmltools/issues", + "Depends": [ + "R (>= 2.14.1)" + ], + "Imports": [ + "base64enc", + "digest", + "fastmap (>= 1.1.0)", + "grDevices", + "rlang (>= 1.0.0)", + "utils" + ], + "Suggests": [ + "Cairo", + "markdown", + "ragg", + "shiny", + "testthat", + "withr" + ], + "Enhances": [ + "knitr" + ], + "Config/Needs/check": "knitr", + "Config/Needs/website": "rstudio/quillt, bench", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "Collate": "'colors.R' 'fill.R' 'html_dependency.R' 'html_escape.R' 'html_print.R' 'htmltools-package.R' 'images.R' 'known_tags.R' 'selector.R' 'staticimports.R' 'tag_query.R' 'utils.R' 'tags.R' 'template.R'", + "NeedsCompilation": "yes", + "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (ORCID: ), Barret Schloerke [aut] (ORCID: ), Winston Chang [aut] (ORCID: ), Yihui Xie [aut], Jeff Allen [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" + }, + "htmlwidgets": { + "Package": "htmlwidgets", + "Version": "1.6.4", + "Source": "Repository", + "Type": "Package", + "Title": "HTML Widgets for R", + "Authors@R": "c( person(\"Ramnath\", \"Vaidyanathan\", role = c(\"aut\", \"cph\")), person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"JJ\", \"Allaire\", role = \"aut\"), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Kenton\", \"Russell\", role = c(\"aut\", \"cph\")), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/ramnathv/htmlwidgets", + "BugReports": "https://github.com/ramnathv/htmlwidgets/issues", + "Imports": [ + "grDevices", + "htmltools (>= 0.5.7)", + "jsonlite (>= 0.9.16)", + "knitr (>= 1.8)", + "rmarkdown", + "yaml" + ], + "Suggests": [ + "testthat" + ], + "Enhances": [ + "shiny (>= 1.1)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Ramnath Vaidyanathan [aut, cph], Yihui Xie [aut], JJ Allaire [aut], Joe Cheng [aut], Carson Sievert [aut, cre] (), Kenton Russell [aut, cph], Ellis Hughes [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" + }, + "httpuv": { + "Package": "httpuv", + "Version": "1.6.17", + "Source": "Repository", + "Type": "Package", + "Title": "HTTP and WebSocket Server Library", + "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")), person(\"Hector\", \"Corrada Bravo\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Andrzej\", \"Krzemienski\", role = \"cph\", comment = \"optional.hpp\"), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library, see src/libuv/AUTHORS file\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library, see src/libuv/AUTHORS file; and http-parser library, see src/http-parser/AUTHORS file\"), person(\"Niels\", \"Provos\", role = \"cph\", comment = \"libuv subcomponent: tree.h\"), person(\"Internet Systems Consortium, Inc.\", role = \"cph\", comment = \"libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c\"), person(\"Alexander\", \"Chemeris\", role = \"cph\", comment = \"libuv subcomponent: stdint-msvc2008.h (from msinttypes)\"), person(\"Google, Inc.\", role = \"cph\", comment = \"libuv subcomponent: pthread-fixes.c\"), person(\"Sony Mobile Communcations AB\", role = \"cph\", comment = \"libuv subcomponent: pthread-fixes.c\"), person(\"Berkeley Software Design Inc.\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Kenneth\", \"MacKay\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016)\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Steve\", \"Reid\", role = \"aut\", comment = \"SHA-1 implementation\"), person(\"James\", \"Brown\", role = \"aut\", comment = \"SHA-1 implementation\"), person(\"Bob\", \"Trower\", role = \"aut\", comment = \"base64 implementation\"), person(\"Alexander\", \"Peslyak\", role = \"aut\", comment = \"MD5 implementation\"), person(\"Trantor Standard Systems\", role = \"cph\", comment = \"base64 implementation\"), person(\"Igor\", \"Sysoev\", role = \"cph\", comment = \"http-parser\") )", + "Description": "Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)", + "License": "GPL (>= 2) | file LICENSE", + "URL": "https://rstudio.github.io/httpuv/, https://github.com/rstudio/httpuv", + "BugReports": "https://github.com/rstudio/httpuv/issues", + "Depends": [ + "R (>= 2.15.1)" + ], + "Imports": [ + "later (>= 0.8.0)", + "promises", + "R6", + "Rcpp (>= 1.0.7)", + "utils" + ], + "Suggests": [ + "callr", + "curl", + "jsonlite", + "testthat (>= 3.0.0)", + "websocket" + ], + "LinkingTo": [ + "later", + "Rcpp" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-07-01", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "SystemRequirements": "GNU make, zlib", + "Collate": "'RcppExports.R' 'httpuv-package.R' 'httpuv.R' 'random_port.R' 'server.R' 'staticServer.R' 'static_paths.R' 'utils.R'", + "NeedsCompilation": "yes", + "Author": "Joe Cheng [aut], Winston Chang [aut, cre], Posit, PBC [cph, fnd] (ROR: ), Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Andrzej Krzemienski [cph] (optional.hpp), libuv project contributors [cph] (libuv library, see src/libuv/AUTHORS file), Joyent, Inc. and other Node contributors [cph] (libuv library, see src/libuv/AUTHORS file; and http-parser library, see src/http-parser/AUTHORS file), Niels Provos [cph] (libuv subcomponent: tree.h), Internet Systems Consortium, Inc. [cph] (libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c), Alexander Chemeris [cph] (libuv subcomponent: stdint-msvc2008.h (from msinttypes)), Google, Inc. [cph] (libuv subcomponent: pthread-fixes.c), Sony Mobile Communcations AB [cph] (libuv subcomponent: pthread-fixes.c), Berkeley Software Design Inc. [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Kenneth MacKay [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016) [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Steve Reid [aut] (SHA-1 implementation), James Brown [aut] (SHA-1 implementation), Bob Trower [aut] (base64 implementation), Alexander Peslyak [aut] (MD5 implementation), Trantor Standard Systems [cph] (base64 implementation), Igor Sysoev [cph] (http-parser)", + "Maintainer": "Winston Chang ", + "Repository": "CRAN" + }, + "httr": { + "Package": "httr", + "Version": "1.4.8", + "Source": "Repository", + "Title": "Tools for Working with URLs and HTTP", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).", + "License": "MIT + file LICENSE", + "URL": "https://httr.r-lib.org/, https://github.com/r-lib/httr", + "BugReports": "https://github.com/r-lib/httr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "curl (>= 5.1.0)", + "jsonlite", + "mime", + "openssl (>= 0.8)", + "R6" + ], + "Suggests": [ + "covr", + "httpuv", + "jpeg", + "knitr", + "png", + "readr", + "rmarkdown", + "testthat (>= 0.8.0)", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "isoband": { + "Package": "isoband", + "Version": "0.3.0", + "Source": "Repository", + "Title": "Generate Isolines and Isobands from Regularly Spaced Elevation Grids", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Claus O.\", \"Wilke\", , \"wilke@austin.utexas.edu\", role = \"aut\", comment = c(\"Original author\", ORCID = \"0000-0002-7470-9261\")), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "A fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.", + "License": "MIT + file LICENSE", + "URL": "https://isoband.r-lib.org, https://github.com/r-lib/isoband", + "BugReports": "https://github.com/r-lib/isoband/issues", + "Imports": [ + "cli", + "grid", + "rlang", + "utils" + ], + "Suggests": [ + "covr", + "ggplot2", + "knitr", + "magick", + "bench", + "rmarkdown", + "sf", + "testthat (>= 3.0.0)", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-12-05", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "Config/build/compilation-database": "true", + "LinkingTo": [ + "cpp11" + ], + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut] (ORCID: ), Claus O. Wilke [aut] (Original author, ORCID: ), Thomas Lin Pedersen [aut, cre] (ORCID: ), Posit, PBC [cph, fnd] (ROR: )", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "jquerylib": { + "Package": "jquerylib", + "Version": "0.1.4", + "Source": "Repository", + "Title": "Obtain 'jQuery' as an HTML Dependency Object", + "Authors@R": "c( person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@rstudio.com\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@rstudio.com\"), person(family = \"RStudio\", role = \"cph\"), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt\") )", + "Description": "Obtain any major version of 'jQuery' () and use it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', and 'rmarkdown'). Most R users don't need to use this package directly, but other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package to avoid bundling redundant copies of 'jQuery'.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "RoxygenNote": "7.0.2", + "Imports": [ + "htmltools" + ], + "Suggests": [ + "testthat" + ], + "NeedsCompilation": "no", + "Author": "Carson Sievert [aut, cre] (), Joe Cheng [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt)", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" + }, + "jsonlite": { + "Package": "jsonlite", + "Version": "2.0.0", + "Source": "Repository", + "Title": "A Simple and Robust JSON Parser and Generator for R", + "License": "MIT + file LICENSE", + "Depends": [ + "methods" + ], + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Duncan\", \"Temple Lang\", role = \"ctb\"), person(\"Lloyd\", \"Hilaiel\", role = \"cph\", comment=\"author of bundled libyajl\"))", + "URL": "https://jeroen.r-universe.dev/jsonlite https://arxiv.org/abs/1403.2805", + "BugReports": "https://github.com/jeroen/jsonlite/issues", + "Maintainer": "Jeroen Ooms ", + "VignetteBuilder": "knitr, R.rsp", + "Description": "A reasonably fast JSON parser and generator, optimized for statistical data and the web. Offers simple, flexible tools for working with JSON in R, and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.", + "Suggests": [ + "httr", + "vctrs", + "testthat", + "knitr", + "rmarkdown", + "R.rsp", + "sf" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Duncan Temple Lang [ctb], Lloyd Hilaiel [cph] (author of bundled libyajl)", + "Repository": "CRAN" + }, + "knitr": { + "Package": "knitr", + "Version": "1.51", + "Source": "Repository", + "Type": "Package", + "Title": "A General-Purpose Package for Dynamic Report Generation in R", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\", URL = \"https://yihui.org\")), person(\"Abhraneel\", \"Sarma\", role = \"ctb\"), person(\"Adam\", \"Vogt\", role = \"ctb\"), person(\"Alastair\", \"Andrew\", role = \"ctb\"), person(\"Alex\", 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The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).", + "Collate": "'block.R' 'cache.R' 'citation.R' 'hooks-html.R' 'plot.R' 'utils.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'otel.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (ORCID: , URL: https://yihui.org), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (ORCID: ), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. 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Kamvar [ctb] (ORCID: ), Posit Software, PBC [cph, fnd]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "labeling": { + "Package": "labeling", + "Version": "0.4.3", + "Source": "Repository", + "Type": "Package", + "Title": "Axis Labeling", + "Date": "2023-08-29", + "Author": "Justin Talbot,", + "Maintainer": "Nuno Sempere ", + "Description": "Functions which provide a range of axis labeling algorithms.", + "License": "MIT + file LICENSE | Unlimited", + "Collate": "'labeling.R'", + "NeedsCompilation": "no", + "Imports": [ + "stats", + "graphics" + ], + "Repository": "CRAN" + }, + "later": { + "Package": "later", + "Version": "1.4.8", + "Source": "Repository", + "Type": "Package", + "Title": "Utilities for Scheduling Functions to Execute Later with Event Loops", + "Authors@R": "c( person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Charlie\", \"Gao\", , \"charlie.gao@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0750-061X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")), person(\"Marcus\", \"Geelnard\", role = c(\"ctb\", \"cph\"), comment = \"TinyCThread library, https://tinycthread.github.io/\"), person(\"Evan\", \"Nemerson\", role = c(\"ctb\", \"cph\"), comment = \"TinyCThread library, https://tinycthread.github.io/\") )", + "Description": "Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. The functions are scheduled in an event loop.", + "License": "MIT + file LICENSE", + "URL": "https://later.r-lib.org, https://github.com/r-lib/later", + "BugReports": "https://github.com/r-lib/later/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "Rcpp (>= 1.0.10)", + "rlang" + ], + "Suggests": [ + "knitr", + "nanonext", + "promises", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "Rcpp" + ], + "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-07-18", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "yes", + "Author": "Winston Chang [aut] (ORCID: ), Joe Cheng [aut], Charlie Gao [aut, cre] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: ), Marcus Geelnard [ctb, cph] (TinyCThread library, https://tinycthread.github.io/), Evan Nemerson [ctb, cph] (TinyCThread library, https://tinycthread.github.io/)", + "Maintainer": "Charlie Gao ", + "Repository": "CRAN" + }, + "lattice": { + "Package": "lattice", + "Version": "0.22-9", + "Source": "Repository", + "Date": "2026-02-03", + "Priority": "recommended", + "Title": "Trellis Graphics for R", + "Authors@R": "c(person(\"Deepayan\", \"Sarkar\", role = c(\"aut\", \"cre\"), email = \"deepayan.sarkar@r-project.org\", comment = c(ORCID = \"0000-0003-4107-1553\")), person(\"Felix\", \"Andrews\", role = \"ctb\"), person(\"Kevin\", \"Wright\", role = \"ctb\", comment = \"documentation\"), person(\"Neil\", \"Klepeis\", role = \"ctb\"), person(\"Johan\", \"Larsson\", role = \"ctb\", comment = \"miscellaneous improvements\"), person(\"Zhijian (Jason)\", \"Wen\", role = \"cph\", comment = \"filled contour code\"), person(\"Paul\", \"Murrell\", role = \"ctb\", email = \"paul@stat.auckland.ac.nz\"), person(\"Stefan\", \"Eng\", role = \"ctb\", comment = \"violin plot improvements\"), person(\"Achim\", \"Zeileis\", role = \"ctb\", comment = \"modern colors\"), person(\"Alexandre\", \"Courtiol\", role = \"ctb\", comment = \"generics for larrows, lpolygon, lrect and lsegments\") )", + "Description": "A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. 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Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", ,\"hadley@rstudio.com\", c(\"aut\", \"cre\")), person(\"RStudio\", role = \"cph\") )", + "License": "GPL-3", + "LazyData": "true", + "Depends": [ + "R (>= 3.1.0)" + ], + "Suggests": [ + "knitr", + "rmarkdown (>= 0.2.65)", + "testthat", + "covr" + ], + "VignetteBuilder": "knitr", + "RoxygenNote": "6.1.1", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], RStudio [cph]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "lifecycle": { + "Package": "lifecycle", + "Version": "1.0.5", + "Source": "Repository", + "Title": "Manage the Life Cycle of your Package Functions", + "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Manage the life cycle of your exported functions with shared conventions, documentation badges, and user-friendly deprecation warnings.", + "License": "MIT + file LICENSE", + "URL": "https://lifecycle.r-lib.org/, https://github.com/r-lib/lifecycle", + "BugReports": "https://github.com/r-lib/lifecycle/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "knitr", + "lintr (>= 3.1.0)", + "rmarkdown", + "testthat (>= 3.0.1)", + "tibble", + "tidyverse", + "tools", + "vctrs", + "withr", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate, usethis", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut] (ORCID: ), Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" + }, + "lme4": { + "Package": "lme4", + "Version": "2.0-1", + "Source": "Repository", + "Title": "Linear Mixed-Effects Models using 'Eigen' and S4", + "Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = \"aut\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Ben\", \"Bolker\", role = c(\"cre\", \"aut\"), email = \"bbolker+lme4@gmail.com\", comment = c(ORCID = \"0000-0002-2127-0443\")), person(\"Steven\", \"Walker\", role = \"aut\", comment = c(ORCID = \"0000-0002-4394-9078\")), person(\"Rune Haubo Bojesen\", \"Christensen\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4494-3399\")), person(\"Henrik\", \"Singmann\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4842-3657\")), person(\"Bin\", \"Dai\", role = \"ctb\"), person(\"Fabian\", \"Scheipl\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8172-3603\")), person(\"Gabor\", \"Grothendieck\", role = \"ctb\"), person(\"Peter\", \"Green\", role = \"ctb\", comment = c(ORCID = \"0000-0002-0238-9852\")), person(\"John\", \"Fox\", role = \"ctb\"), person(\"Alexander\", \"Bauer\", role = \"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role = c(\"ctb\", \"cph\"), comment = c(ORCID = \"0000-0002-9101-3362\", \"shared copyright on simulate.formula\")), person(\"Emi\", \"Tanaka\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1455-259X\")), person(\"Mikael\", \"Jagan\", role = \"aut\", comment = c(ORCID = \"0000-0002-3542-2938\")), person(\"Ross D.\", \"Boylan\", role = \"ctb\", comment = c(ORCID = \"0009-0003-4123-8090\")), person(\"Anna\", \"Ly\", role = \"aut\", comment = c(ORCID = \"0000-0002-0210-0342\")))", + "Description": "Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' \"glue\".", + "Depends": [ + "R (>= 3.6)", + "Matrix", + "methods", + "stats" + ], + "LinkingTo": [ + "Matrix (>= 1.5-0)", + "Rcpp (>= 0.10.5)", + "RcppEigen (>= 0.3.3.9.4)" + ], + "Imports": [ + "MASS", + "Rdpack", + "boot", + "graphics", + "grid", + "lattice", + "minqa (>= 1.1.15)", + "nlme (>= 3.1-123)", + "nloptr (>= 1.0.4)", + "parallel", + "reformulas (>= 0.4.3.1)", + "rlang", + "splines", + "utils" + ], + "Suggests": [ + "HSAUR3", + "MEMSS", + "car", + "dfoptim", + "gamm4", + "ggplot2", + "glmmTMB", + "knitr", + "merDeriv", + "mgcv", + "mlmRev", + "numDeriv", + "optimx (>= 2013.8.6)", + "pbkrtest", + "rmarkdown", + "rr2", + "semEff", + "statmod", + "testthat (>= 0.8.1)", + "tibble" + ], + "Enhances": [ + "DHARMa", + "performance" + ], + "RdMacros": "Rdpack", + "VignetteBuilder": "knitr", + "LazyData": "yes", + "License": "GPL (>= 2)", + "URL": "https://github.com/lme4/lme4/", + "BugReports": "https://github.com/lme4/lme4/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "yes", + "Author": "Douglas Bates [aut] (ORCID: ), Martin Maechler [aut] (ORCID: ), Ben Bolker [cre, aut] (ORCID: ), Steven Walker [aut] (ORCID: ), Rune Haubo Bojesen Christensen [ctb] (ORCID: ), Henrik Singmann [ctb] (ORCID: ), Bin Dai [ctb], Fabian Scheipl [ctb] (ORCID: ), Gabor Grothendieck [ctb], Peter Green [ctb] (ORCID: ), John Fox [ctb], Alexander Bauer [ctb], Pavel N. Krivitsky [ctb, cph] (ORCID: , shared copyright on simulate.formula), Emi Tanaka [ctb] (ORCID: ), Mikael Jagan [aut] (ORCID: ), Ross D. Boylan [ctb] (ORCID: ), Anna Ly [aut] (ORCID: )", + "Maintainer": "Ben Bolker ", + "Repository": "CRAN" + }, + "lmtest": { + "Package": "lmtest", + "Version": "0.9-40", + "Source": "Repository", + "Title": "Testing Linear Regression Models", + "Date": "2022-03-21", + "Authors@R": "c(person(given = \"Torsten\", family = \"Hothorn\", role = \"aut\", email = \"Torsten.Hothorn@R-project.org\", comment = c(ORCID = \"0000-0001-8301-0471\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = c(\"Richard\", \"W.\"), family = \"Farebrother\", role = \"aut\", comment = \"pan.f\"), person(given = \"Clint\", family = \"Cummins\", role = \"aut\", comment = \"pan.f\"), person(given = \"Giovanni\", family = \"Millo\", role = \"ctb\"), person(given = \"David\", family = \"Mitchell\", role = \"ctb\"))", + "Description": "A collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.", + "LazyData": "yes", + "Depends": [ + "R (>= 3.0.0)", + "stats", + "zoo" + ], + "Suggests": [ + "car", + "strucchange", + "sandwich", + "dynlm", + "stats4", + "survival", + "AER" + ], + "Imports": [ + "graphics" + ], + "License": "GPL-2 | GPL-3", + "NeedsCompilation": "yes", + "Author": "Torsten Hothorn [aut] (), Achim Zeileis [aut, cre] (), Richard W. 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There is flexible support for the type of right-hand side expressions. For more information, see package vignette. 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Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.", + "License": "MIT + file LICENSE", + "URL": "https://jeroen.r-universe.dev/openssl", + "BugReports": "https://github.com/jeroen/openssl/issues", + "SystemRequirements": "OpenSSL >= 1.0.2", + "VignetteBuilder": "knitr", + "Imports": [ + "askpass" + ], + "Suggests": [ + "curl", + "testthat (>= 2.1.0)", + "digest", + "knitr", + "rmarkdown", + "jsonlite", + "jose", + "sodium" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Oliver Keyes [ctb]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "otel": { + "Package": "otel", + "Version": "0.2.0", + "Source": "Repository", + "Title": "OpenTelemetry R API", + "Authors@R": "person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\"))", + "Description": "High-quality, ubiquitous, and portable telemetry to enable effective observability. 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Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. 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Portfolio selection methods based on expected shortfall risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press, and Koenker, R. et al. (2017) Handbook of Quantile Regression, CRC Press, .", + "Authors@R": "c( person(\"Roger\", \"Koenker\", role = c(\"cre\",\"aut\"), email = \"rkoenker@illinois.edu\"), person(\"Stephen\", \"Portnoy\", role = c(\"ctb\"), comment = \"Contributions to Censored QR code\", email = \"sportnoy@illinois.edu\"), person(c(\"Pin\", \"Tian\"), \"Ng\", role = c(\"ctb\"), comment = \"Contributions to Sparse QR code\", email = \"pin.ng@nau.edu\"), person(\"Blaise\", \"Melly\", role = c(\"ctb\"), comment = \"Contributions to preprocessing code\", email = \"mellyblaise@gmail.com\"), person(\"Achim\", \"Zeileis\", role = c(\"ctb\"), comment = \"Contributions to dynrq code essentially identical to his dynlm code\", email = \"Achim.Zeileis@uibk.ac.at\"), person(\"Philip\", \"Grosjean\", role = c(\"ctb\"), comment = \"Contributions to nlrq code\", email = \"phgrosjean@sciviews.org\"), person(\"Cleve\", \"Moler\", role = c(\"ctb\"), comment = \"author of several linpack routines\"), person(\"Yousef\", \"Saad\", role = c(\"ctb\"), comment = \"author of sparskit2\"), person(\"Victor\", \"Chernozhukov\", role = c(\"ctb\"), comment = \"contributions to extreme value inference code\"), person(\"Ivan\", \"Fernandez-Val\", role = c(\"ctb\"), comment = \"contributions to extreme value inference code\"), person(\"Martin\", \"Maechler\", role = \"ctb\", comment = c(\"tweaks (src/chlfct.f, 'tiny','Large')\", ORCID = \"0000-0002-8685-9910\")), person(c(\"Brian\", \"D\"), \"Ripley\", role = c(\"trl\",\"ctb\"), comment = \"Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice\", email = \"ripley@stats.ox.ac.uk\"))", + "Maintainer": "Roger Koenker ", + "Repository": "CRAN", + "Depends": [ + "R (>= 3.5)", + "stats", + "SparseM" + ], + "Imports": [ + "methods", + "graphics", + "Matrix", + "MatrixModels", + "survival", + "MASS" + ], + "Suggests": [ + "interp", + "rgl", + "logspline", + "nor1mix", + "Formula", + "zoo", + "R.rsp", + "conquer" + ], + "License": "GPL (>= 2)", + "URL": "https://www.r-project.org", + "NeedsCompilation": "yes", + "VignetteBuilder": "R.rsp", + "Author": "Roger Koenker [cre, aut], Stephen Portnoy [ctb] (Contributions to Censored QR code), Pin Tian Ng [ctb] (Contributions to Sparse QR code), Blaise Melly [ctb] (Contributions to preprocessing code), Achim Zeileis [ctb] (Contributions to dynrq code essentially identical to his dynlm code), Philip Grosjean [ctb] (Contributions to nlrq code), Cleve Moler [ctb] (author of several linpack routines), Yousef Saad [ctb] (author of sparskit2), Victor Chernozhukov [ctb] (contributions to extreme value inference code), Ivan Fernandez-Val [ctb] (contributions to extreme value inference code), Martin Maechler [ctb] (tweaks (src/chlfct.f, 'tiny','Large'), ), Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice)" + }, + "rappdirs": { + "Package": "rappdirs", + "Version": "0.3.4", + "Source": "Repository", + "Type": "Package", + "Title": "Application Directories: Determine Where to Save Data, Caches, and Logs", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"trl\", \"cre\", \"cph\")), person(\"Sridhar\", \"Ratnakumar\", role = \"aut\"), person(\"Trent\", \"Mick\", role = \"aut\"), person(\"ActiveState\", role = \"cph\", comment = \"R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs\"), person(\"Eddy\", \"Petrisor\", role = \"ctb\"), person(\"Trevor\", \"Davis\", role = c(\"trl\", \"aut\"), comment = c(ORCID = \"0000-0001-6341-4639\")), person(\"Gabor\", \"Csardi\", role = \"ctb\"), person(\"Gregory\", \"Jefferis\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "An easy way to determine which directories on the users computer you should use to save data, caches and logs. 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Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods. Details can be found in Zeileis et al. 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Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.", + "License": "MIT + file LICENSE", + "URL": "https://withr.r-lib.org, https://github.com/r-lib/withr#readme", + "BugReports": "https://github.com/r-lib/withr/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "graphics", + "grDevices" + ], + "Suggests": [ + "callr", + "DBI", + "knitr", + "methods", + "rlang", + "rmarkdown (>= 2.12)", + "RSQLite", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'aaa.R' 'collate.R' 'connection.R' 'db.R' 'defer-exit.R' 'standalone-defer.R' 'defer.R' 'devices.R' 'local_.R' 'with_.R' 'dir.R' 'env.R' 'file.R' 'language.R' 'libpaths.R' 'locale.R' 'makevars.R' 'namespace.R' 'options.R' 'par.R' 'path.R' 'rng.R' 'seed.R' 'wrap.R' 'sink.R' 'tempfile.R' 'timezone.R' 'torture.R' 'utils.R' 'with.R'", + "NeedsCompilation": "no", + "Author": "Jim Hester [aut], Lionel Henry [aut, cre], Kirill Müller [aut], Kevin Ushey [aut], Hadley Wickham [aut], Winston Chang [aut], Jennifer Bryan [ctb], Richard Cotton [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" + }, + "xfun": { + "Package": "xfun", + "Version": "0.57", + "Source": "Repository", + "Type": "Package", + "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\", URL = \"https://yihui.org\")), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Daijiang\", \"Li\", role = \"ctb\"), person(\"Xianying\", \"Tan\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", role = \"ctb\", email = \"salim-b@pm.me\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person() )", + "Description": "Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ + "grDevices", + "stats", + "tools" + ], + "Suggests": [ + "testit", + "parallel", + "codetools", + "methods", + "rstudioapi", + "tinytex (>= 0.30)", + "mime", + "litedown (>= 0.6)", + "commonmark", + "knitr (>= 1.50)", + "remotes", + "pak", + "curl", + "xml2", + "jsonlite", + "magick", + "yaml", + "data.table", + "qs2" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/xfun", + "BugReports": "https://github.com/yihui/xfun/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "VignetteBuilder": "litedown", + "NeedsCompilation": "yes", + "Author": "Yihui Xie [aut, cre, cph] (ORCID: , URL: https://yihui.org), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (ORCID: ), Christophe Dervieux [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-8", + "Source": "Repository", + "Date": "2026-02-20", + "Title": "Export Tables to LaTeX or HTML", + "Authors@R": "c(person(\"David B.\", \"Dahl\", role=\"aut\"), person(\"David\", \"Scott\", role=c(\"aut\",\"cre\"), email=\"d.scott@auckland.ac.nz\"), person(\"Charles\", \"Roosen\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"), person(\"Jonathan\", \"Swinton\", role=\"aut\"), person(\"Ajay\", \"Shah\", role=\"ctb\"), person(\"Arne\", \"Henningsen\", role=\"ctb\"), person(\"Benno\", \"Puetz\", role=\"ctb\"), person(\"Bernhard\", \"Pfaff\", role=\"ctb\"), person(\"Claudio\", \"Agostinelli\", role=\"ctb\"), person(\"Claudius\", \"Loehnert\", role=\"ctb\"), person(\"David\", \"Mitchell\", role=\"ctb\"), person(\"David\", \"Whiting\", role=\"ctb\"), person(\"Fernando da\", \"Rosa\", role=\"ctb\"), person(\"Guido\", \"Gay\", role=\"ctb\"), person(\"Guido\", \"Schulz\", role=\"ctb\"), person(\"Ian\", \"Fellows\", role=\"ctb\"), person(\"Jeff\", \"Laake\", role=\"ctb\"), person(\"John\", \"Walker\", role=\"ctb\"), person(\"Jun\", \"Yan\", role=\"ctb\"), person(\"Liviu\", \"Andronic\", role=\"ctb\"), person(\"Markus\", \"Loecher\", role=\"ctb\"), person(\"Martin\", \"Gubri\", role=\"ctb\"), person(\"Matthieu\", \"Stigler\", role=\"ctb\"), person(\"Robert\", \"Castelo\", role=\"ctb\"), person(\"Seth\", \"Falcon\", role=\"ctb\"), person(\"Stefan\", \"Edwards\", role=\"ctb\"), person(\"Sven\", \"Garbade\", role=\"ctb\"), person(\"Uwe\", \"Ligges\", role=\"ctb\"))", + "Maintainer": "David Scott ", + "Imports": [ + "stats", + "utils", + "methods" + ], + "Suggests": [ + "knitr", + "zoo", + "survival", + "glue", + "tinytex" + ], + "VignetteBuilder": "knitr", + "Description": "Coerce data to LaTeX and HTML tables.", + "URL": "http://xtable.r-forge.r-project.org/", + "Depends": [ + "R (>= 2.10.0)" + ], + "License": "GPL (>= 2)", + "Repository": "CRAN", + "NeedsCompilation": "no", + "Author": "David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.12", + "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"cre\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Shawn\", \"Garbett\", , \"shawn.garbett@vumc.org\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4079-5621\")), person(\"Jeremy\", \"Stephens\", role = c(\"aut\", \"ctb\")), person(\"Kirill\", \"Simonov\", role = \"aut\"), person(\"Yihui\", \"Xie\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Zhuoer\", \"Dong\", role = \"ctb\"), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"reikoch\", role = \"ctb\"), person(\"Will\", \"Beasley\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5613-5006\")), person(\"Brendan\", \"O'Connor\", role = \"ctb\"), person(\"Michael\", \"Quinn\", role = \"ctb\"), person(\"Charlie\", \"Gao\", role = \"ctb\"), person(c(\"Gregory\", \"R.\"), \"Warnes\", role = \"ctb\"), person(c(\"Zhian\", \"N.\"), \"Kamvar\", role = \"ctb\") )", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://yaml.r-lib.org, https://github.com/r-lib/yaml/", + "BugReports": "https://github.com/r-lib/yaml/issues", + "Suggests": [ + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "VignetteBuilder": "knitr", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [cre] (ORCID: ), Shawn Garbett [ctb] (ORCID: ), Jeremy Stephens [aut, ctb], Kirill Simonov [aut], Yihui Xie [ctb] (ORCID: ), Zhuoer Dong [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb] (ORCID: ), Brendan O'Connor [ctb], Michael Quinn [ctb], Charlie Gao [ctb], Gregory R. Warnes [ctb], Zhian N. Kamvar [ctb]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-15", + "Source": "Repository", + "Date": "2025-12-15", + "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", + "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", + "Depends": [ + "R (>= 3.1.0)", + "stats" + ], + "Suggests": [ + "AER", + "coda", + "chron", + "ggplot2 (>= 3.5.0)", + "mondate", + "scales", + "stinepack", + "strucchange", + "timeDate", + "timeSeries", + "tinyplot", + "tis", + "tseries", + "xts" + ], + "Imports": [ + "utils", + "graphics", + "grDevices", + "lattice (>= 0.20-27)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://zoo.R-Forge.R-project.org/", + "NeedsCompilation": "yes", + "Author": "Achim Zeileis [aut, cre] (ORCID: ), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" + } + } +} diff --git a/renv/.gitignore b/renv/.gitignore new file mode 100644 index 0000000..0ec0cbb --- /dev/null +++ b/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 0000000..93d4f65 --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,1438 @@ + +local({ + + # the requested version of renv + version <- "1.2.0" + attr(version, "md5") <- "b7d230b07507f361d3bcf794d157a188" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-run:\\1\a\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + # also check for config environment variables that should suppress messages + # https://github.com/rstudio/renv/issues/2214 + enabled <- Sys.getenv("RENV_CONFIG_STARTUP_QUIET", unset = NA) + if (!is.na(enabled) && tolower(enabled) %in% c("true", "1")) + return(invisible()) + + enabled <- Sys.getenv("RENV_CONFIG_SYNCHRONIZED_CHECK", unset = NA) + if (!is.na(enabled) && tolower(enabled) %in% c("false", "0")) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + text <- paste(substring(lines, common), collapse = "\n") + + # substitute in ANSI links for executable renv code + ansify(text) + + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # ensure the target library path exists; required for file.copy(..., recursive = TRUE) + dir.create(library, showWarnings = FALSE, recursive = TRUE) + + # try to install renv from cache + md5 <- attr(version, "md5", exact = TRUE) + if (length(md5)) { + pkgpath <- renv_bootstrap_find(version) + if (length(pkgpath) && file.exists(pkgpath)) { + ok <- file.copy(pkgpath, library, recursive = TRUE) + if (isTRUE(ok)) + return(invisible()) + } + } + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # split on ';' if present + parts <- strsplit(repos, ";", fixed = TRUE)[[1L]] + + # split into named repositories if present + idx <- regexpr("=", parts, fixed = TRUE) + keys <- substring(parts, 1L, idx - 1L) + vals <- substring(parts, idx + 1L) + names(vals) <- keys + + # if we have a single unnamed repository, call it CRAN + if (length(vals) == 1L && identical(keys, "")) + names(vals) <- "CRAN" + + return(vals) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + # retrieve package database + db <- tryCatch( + as.data.frame( + do.call(utils::available.packages, args), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_find <- function(version) { + + path <- renv_bootstrap_find_cache(version) + if (length(path) && file.exists(path)) { + catf("- Using renv %s from global package cache", version) + return(path) + } + + } + + renv_bootstrap_find_cache <- function(version) { + + md5 <- attr(version, "md5", exact = TRUE) + if (is.null(md5)) + return() + + # infer path to renv cache + cache <- Sys.getenv("RENV_PATHS_CACHE", unset = "") + if (!nzchar(cache)) { + root <- Sys.getenv("RENV_PATHS_ROOT", unset = NA) + if (!is.na(root)) + cache <- file.path(root, "cache") + } + + if (!nzchar(cache)) { + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) { + root <- tools$R_user_dir("renv", "cache") + cache <- file.path(root, "cache") + } + } + + # start completing path to cache + file.path( + cache, + renv_bootstrap_cache_version(), + renv_bootstrap_platform_prefix(), + "renv", + version, + md5, + "renv" + ) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + token <- renv_bootstrap_github_token() + if (is.null(token)) + token <- "" + + if (nzchar(Sys.which("curl")) && nzchar(token)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix_default <- function() { + + # read version component + version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v") + + # expand placeholders + placeholders <- list( + list("%v", format(getRversion()[1, 1:2])), + list("%V", format(getRversion()[1, 1:3])) + ) + + for (placeholder in placeholders) + version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE) + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + version <- paste(version, R.version[["svn rev"]], sep = "-r") + + version + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- renv_bootstrap_platform_prefix_default() + + # build list of path components + components <- c(version, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + + expected <- description[["RemoteSha"]] + if (!is.character(expected)) + return(FALSE) + + pattern <- sprintf("^\\Q%s\\E", version) + grepl(pattern, expected, perl = TRUE) + + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(c(expected), c(version)) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(project, libpath, version) + } + + renv_bootstrap_run <- function(project, libpath, version) { + tryCatch( + renv_bootstrap_run_impl(project, libpath, version), + error = function(e) { + msg <- paste( + "failed to bootstrap renv: the project will not be loaded.", + paste("Reason:", conditionMessage(e)), + "Use `renv::activate()` to re-initialize the project.", + sep = "\n" + ) + warning(msg, call. = FALSE) + } + ) + } + + renv_bootstrap_run_impl <- function(project, libpath, version) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = project)) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_bootstrap_cache_version <- function() { + # NOTE: users should normally not override the cache version; + # this is provided just to make testing easier + Sys.getenv("RENV_CACHE_VERSION", unset = "v5") + } + + renv_bootstrap_cache_version_previous <- function() { + version <- renv_bootstrap_cache_version() + number <- as.integer(substring(version, 2L)) + paste("v", number - 1L, sep = "") + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_patterns <- function() { + + list( + + # objects + list("{", "\t\n\tobject(\t\n\t", TRUE), + list("}", "\t\n\t)\t\n\t", TRUE), + + # arrays + list("[", "\t\n\tarray(\t\n\t", TRUE), + list("]", "\n\t\n)\n\t\n", TRUE), + + # maps + list(":", "\t\n\t=\t\n\t", TRUE), + + # newlines + list("\\u000a", "\n", FALSE) + + ) + + } + + renv_json_read_envir <- function() { + + envir <- new.env(parent = emptyenv()) + + envir[["+"]] <- `+` + envir[["-"]] <- `-` + + envir[["object"]] <- function(...) { + result <- list(...) + names(result) <- as.character(names(result)) + result + } + + envir[["array"]] <- list + + envir[["true"]] <- TRUE + envir[["false"]] <- FALSE + envir[["null"]] <- NULL + + envir + + } + + renv_json_read_remap <- function(object, patterns) { + + # repair names if necessary + if (!is.null(names(object))) { + + nms <- names(object) + for (pattern in patterns) + nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) + names(object) <- nms + + } + + # repair strings if necessary + if (is.character(object)) { + for (pattern in patterns) + object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) + } + + # recurse for other objects + if (is.recursive(object)) + for (i in seq_along(object)) + object[i] <- list(renv_json_read_remap(object[[i]], patterns)) + + # return remapped object + object + + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # read json text + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + + # convert into something the R parser will understand + patterns <- renv_json_read_patterns() + transformed <- text + for (pattern in patterns) + transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) + + # parse it + rfile <- tempfile("renv-json-", fileext = ".R") + on.exit(unlink(rfile), add = TRUE) + writeLines(transformed, con = rfile) + json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]] + + # evaluate in safe environment + result <- eval(json, envir = renv_json_read_envir()) + + # fix up strings if necessary -- do so only with reversible patterns + patterns <- Filter(function(pattern) pattern[[3L]], patterns) + renv_json_read_remap(result, patterns) + + } + + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 0000000..4aa5441 --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,20 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.dev": false, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/results_analysis.R b/results_analysis.R index 3551ed8..bb8abe9 100644 --- a/results_analysis.R +++ b/results_analysis.R @@ -2,86 +2,121 @@ # OBJECTIVE: Send an HTML file of an IC50 Calculation plot and a dataframe # of IC50 statistical results to a Benchling analysis # -# This code requires a dataframe (df) in order to work -# The dataframe should contain the columns Cell Concentration and Cell Mortality -# The code also requires values for subdomain, analysis_id, and access_token -# (see get_dataframe.R for more detail) -# -# Steps -> calculate IC50 -# -> calculate result dataframe and send to Benchling S3 Bucket -# -> create IC50 plot file and send to Benchling S3 Bucket -# -> Patch analysis +# Prerequisites: +# - Run get_dataframe.R first in the same R session +# - Required variables: df, subdomain, analysis_id, access_token, folder_id ########################################################################################## library(httr) library(jsonlite) -library(drc) -library(plotly) library(htmlwidgets) library(rstudioapi) -library(pracma) + +# Source utility functions +source("utils.R") ################################################################################ -# Calculate IC50 -# In this example, we use the drc library and a 4 parameter log-logistics model -# to calculate a slope and IC50 value +# Verify Prerequisites ################################################################################ -model <- - drm( - Cell.Mortality.Mortality.24h ~ Cell.Mortality.Concentration, - data = df, - fct = LL.4( - fixed = c(NA, 0, 100, NA), - names = c("Slope", "LS Inferior", "LS Superior", "IC50") - ) - ) -summary <- summary(model) - -#Create an IC50 list composed of value and slope -IC50_result <- list( - value = round(summary$coefficients[2],2), - slope = round(summary$coefficients[1],2)) - -# Create CSV file -cell <- c(df$Cell.Line.Name[1]) -hours <- c(24) -fit_function <- c('LL.4') -IC50 <- c(round(summary$coefficients[2],2)) -std <- c(round(summary$coefficients[4],2)) -t_Value <- c(round(summary$coefficients[6],2)) -p_Value <- summary$coefficients[8] - -# Transform p-Value to scientific notation -formatC(p_Value, format = "e", digits = 4) -p_Value <-signif(p_Value, digits=3) - -# create CSV dataframe -csv_df <- - data.frame(cell, hours, fit_function, IC50, std, t_Value, p_Value) - -# 4 parameter Logisitic function plot curve -logistic4 <- function(x, A, B, C, D) { - return ((A-D) / (1.0 + ((x / C) ** B))) + D +required_vars <- c("df", "base_domain", "analysis_id", "access_token", "folder_id") +missing_vars <- required_vars[!sapply(required_vars, exists)] + +if (length(missing_vars) > 0) { + stop(paste( + "Missing required variables:", paste(missing_vars, collapse = ", "), + "\nPlease run get_dataframe.R first in the same R session", + sep = "\n" + )) +} + +cat("✓ All required variables present\n") +cat(" Dataset:", nrow(df), "rows x", ncol(df), "columns\n\n") + +# Create tmp directory for temporary files +tmp_dir <- "tmp" +if (!dir.exists(tmp_dir)) { + dir.create(tmp_dir) } +# Verify required columns exist +required_cols <- c("Cell.Name", "Concentration", "Mortality.24h", "Mortality.48h") +missing_cols <- required_cols[!required_cols %in% names(df)] + +if (length(missing_cols) > 0) { + stop(paste( + "Dataset missing required columns:", paste(missing_cols, collapse = ", "), + "\nAvailable columns:", paste(names(df), collapse = ", "), + sep = "\n" + )) +} + +################################################################################ +# Calculate IC50 using utility function +################################################################################ + +cat("Calculating IC50 for 24h data...\n") + +result_24h <- calculate_ic50( + df, + concentration_col = "Concentration", + mortality_col = "Mortality.24h" +) + +cat("✓ 24h IC50 calculation complete\n") +cat(" IC50 Value:", result_24h$ic50, "\n") +cat(" Slope:", result_24h$slope, "\n\n") + +cat("Calculating IC50 for 48h data...\n") + +result_48h <- calculate_ic50( + df, + concentration_col = "Concentration", + mortality_col = "Mortality.48h" +) + +cat("✓ 48h IC50 calculation complete\n") +cat(" IC50 Value:", result_48h$ic50, "\n") +cat(" Slope:", result_48h$slope, "\n\n") + +################################################################################ +# Create Results Dataframe +################################################################################ + +cat("Preparing results dataframe...\n") + +# Extract cell line name from Cell.Name column +cell_line <- unique(df$Cell.Name)[1] + +# Create dataframe with both 24h and 48h results +csv_df <- data.frame( + cell = c(cell_line, cell_line), + hours = c(24, 48), + fit_function = c('LL.4', 'LL.4'), + IC50 = c(result_24h$ic50, result_48h$ic50), + std = c(result_24h$std_error, result_48h$std_error), + t_Value = c(result_24h$t_value, result_48h$t_value), + p_Value = c(result_24h$p_value, result_48h$p_value) +) + +cat("✓ Results dataframe created (24h and 48h)\n\n") + ########################################################################################## # Calculate result dataframe and send to Benchling S3 Bucket ########################################################################################## -# Save CSV on local path +cat("Uploading results dataframe to Benchling...\n") + +# Save CSV to tmp directory csv_name <- "mortality.csv" -path <- dirname(rstudioapi::getSourceEditorContext()$path) -csv_file <- paste(path, '/', csv_name, sep = "") +csv_file <- file.path(tmp_dir, csv_name) write.csv(csv_df, csv_file, row.names = FALSE) - ############ Use the POST dataframe endpoint to create a new dataframe ############ # Construct url -# The resulting URL should look like: https://.benchling.com/api/v2-beta/data-frames api_path <- "/api/v2-beta/data-frames" -url <- paste("https://", subdomain, api_path, sep = "") +url <- paste("https://", base_domain, api_path, sep = "") # Create a binary file my_data <- readBin(csv_file, "raw", 10e6) @@ -92,10 +127,21 @@ dataframe_payload <- # Convert payload to Json format and use POST endpoint to create dataframe dataframe_request <- - httr::POST(url = url, + httr::POST( + url = url, body = toJSON(dataframe_payload, pretty = TRUE, auto_unbox = TRUE), - httr::accept('application/json'),httr::content_type('application/json'), - httr::add_headers ('Authorization' = paste("Bearer", access_token))) + httr::accept('application/json'), + httr::content_type('application/json'), + httr::add_headers('Authorization' = paste("Bearer", access_token)) + ) + +# Check for errors +if (dataframe_request$status_code != 200) { + stop(paste( + "Failed to create dataframe! Status code:", dataframe_request$status_code, + sep = "" + )) +} # Use the jsonLite library to read the Json body dataframe_body <- @@ -107,177 +153,317 @@ result_dataframe_id <- dataframe_body$id # Retrieve S3 PUT url from previous call s3_put_url <- dataframe_body$manifest$url - ####### Use the PUT file endpoint to upload file in a Benchling S3 Bucket ###### + # Put file in S3 bucket and add [;x-amz-server-side-encryption': 'AES256'] to # the request headers, because we use server-side encryption s3_file_request <- httr::PUT( url = s3_put_url, body = my_data, - httr::add_headers ('x-amz-server-side-encryption' = 'AES256')) - -# Change dataframe status to IN PROGRESS after uploading to S3 -if (s3_file_request$status_code == '200') -{ - # Construct url - # The resulting URL should look like: https://.benchling.com/api/v2-beta/data-frames/data_cACYhKlo) - api_path <- "/api/v2-beta/data-frames/" - url <- - paste("https://", subdomain, api_path, result_dataframe_id, sep = "") - - # Set Payload list as IN PROGRESS - dataframe_payload <-list(uploadStatus = "IN_PROGRESS") - - # Convert payload to Json format and use Patch endpoint to mark dataframe upload as in Progress - dataframe_request <- - httr::PATCH( - url = url, - body = toJSON(dataframe_payload, pretty = TRUE, auto_unbox = TRUE), - httr::accept('application/json'),httr::content_type('application/json'), - httr::add_headers ('Authorization' = paste("Bearer", access_token))) - - # Use the jsonLite library to read the Json body - dataframe_body <-jsonlite::fromJSON(rawToChar(dataframe_request$content)) - - # Print status code - 200 = Successful - print(dataframe_request$status_code) - -}else { - print('ERROR: Upload to S3 unsuccessful') + httr::add_headers('x-amz-server-side-encryption' = 'AES256') + ) + +# Check if upload succeeded +if (s3_file_request$status_code != 200) { + stop(paste( + "Failed to upload dataframe to S3! Status code:", s3_file_request$status_code, + sep = "" + )) } -################################################################################ -# Use plotly to create a html plot to embed in Benchling Analysis ############## -################################################################################ +# Change dataframe status to IN_PROGRESS after uploading to S3 +api_path <- "/api/v2-beta/data-frames/" +url <- + paste("https://", base_domain, api_path, result_dataframe_id, sep = "") -# Set Image Name and Path (path is set here are the local directory of the R script) -image_name <- "mortality_24h.html" +# Set Payload list as IN_PROGRESS +dataframe_payload <- list(uploadStatus = "IN_PROGRESS") -# Save html file on local path -path <- dirname(rstudioapi::getSourceEditorContext()$path) -image_file <- paste(path, '/', image_name, sep = "") +# Convert payload to Json format and use Patch endpoint to mark dataframe upload as in Progress +dataframe_request <- + httr::PATCH( + url = url, + body = toJSON(dataframe_payload, pretty = TRUE, auto_unbox = TRUE), + httr::accept('application/json'), + httr::content_type('application/json'), + httr::add_headers('Authorization' = paste("Bearer", access_token)) + ) + +cat("✓ Results dataframe uploaded (ID:", result_dataframe_id, ")\n\n") -# Use plotly to plot the IC50 -plot <- - plot_ly( - data = df, - x = df$Cell.Mortality.Concentration, - y = df$Cell.Mortality.Mortality.24h, - type = "scatter", - mode = "markers") +################################################################################ +# Create interactive plots using utility function +################################################################################ -plot <- layout(plot, xaxis = list(type = "log")) +cat("Creating interactive plots...\n") + +# Set Image Names and Paths (save to tmp directory) +image_name_24h <- "mortality_24h.html" +image_name_48h <- "mortality_48h.html" +image_file_24h <- file.path(tmp_dir, image_name_24h) +image_file_48h <- file.path(tmp_dir, image_name_48h) + +# Create 24h plot +plot_24h <- create_ic50_plot( + df, + concentration_col = "Concentration", + mortality_col = "Mortality.24h", + ic50_value = result_24h$ic50, + slope = result_24h$slope, + title = paste0("IC50 Dose-Response Curve - 24h (", cell_line, ")") +) + +# Save 24h plot +saveWidget( + widget = plot_24h, + file = image_file_24h, + selfcontained = TRUE +) + +cat("✓ 24h plot created and saved locally\n") + +# Create 48h plot +plot_48h <- create_ic50_plot( + df, + concentration_col = "Concentration", + mortality_col = "Mortality.48h", + ic50_value = result_48h$ic50, + slope = result_48h$slope, + title = paste0("IC50 Dose-Response Curve - 48h (", cell_line, ")") +) + +# Save 48h plot +saveWidget( + widget = plot_48h, + file = image_file_48h, + selfcontained = TRUE +) + +cat("✓ 48h plot created and saved locally\n\n") -xs <- - linspace(min(df$Cell.Mortality.Concentration), - max(df$Cell.Mortality.Concentration), - n=1000) +################################################################################ +# Upload Plots to Benchling +################################################################################ -plot <- - add_lines(plot, - line = list(shape = "scatter"), - x = xs, - y = logistic4(xs, 100, IC50_result$slope, IC50_result$value, 0)) +cat("Uploading plots to Benchling...\n") -# Save html file -saveWidget(widget = plot, - file = image_file, - selfcontained = TRUE) +# Upload 24h plot +cat(" Uploading 24h plot...\n") ### Create a binary file -my_data <- readBin(image_file, "raw", 10e6) - +my_data_24h <- readBin(image_file_24h, "raw", 10e6) ############### Use the POST File endpoint to create a new File ############### # Construct url -# The resulting URL should look like: https://.benchling.com/api/v2-beta/files) api_path <- "/api/v2-beta/files" -url <- paste("https://", subdomain, api_path, sep = "") +url <- paste("https://", base_domain, api_path, sep = "") # Provide name of file as a payload in a list -file_payload <- list(name = image_name, filename = image_name, folderId = folder_id) +file_payload_24h <- list(name = image_name_24h, filename = image_name_24h, folderId = folder_id) # Convert payload to Json format and use POST endpoint to create File -file_request <- - httr::POST(url = url, - body = toJSON(file_payload, pretty = TRUE, auto_unbox = TRUE), - httr::accept('application/json'),httr::content_type('application/json'), - httr::add_headers ('Authorization' = paste("Bearer", access_token))) +file_request_24h <- + httr::POST( + url = url, + body = toJSON(file_payload_24h, pretty = TRUE, auto_unbox = TRUE), + httr::accept('application/json'), + httr::content_type('application/json'), + httr::add_headers('Authorization' = paste("Bearer", access_token)) + ) + +# Check for errors +if (file_request_24h$status_code != 200) { + stop(paste( + "Failed to create 24h file! Status code:", file_request_24h$status_code, + sep = "" + )) +} # Use the jsonLite library to read the Json body -file_body <-jsonlite::fromJSON(rawToChar(file_request$content)) +file_body_24h <- jsonlite::fromJSON(rawToChar(file_request_24h$content)) # Retrieve the file id -file_id <- file_body$id +file_id_24h <- file_body_24h$id # Retrieve S3 PUT url from previous call -s3_put_url <- file_request$headers$`content-location` +s3_put_url_24h <- file_request_24h$headers$`content-location` ####### Use the PUT file endpoint to upload file in a Benchling S3 Bucket ###### -# Put file in S3 bucket and add [;x-amz-server-side-encryption': 'AES256'] to the request headers, because we use server-side encryption -s3_file_request <- - httr::PUT(url = s3_put_url, - body = my_data, - httr::add_headers ('x-amz-server-side-encryption' = 'AES256')) - -# Change dataframe status to SUCCEEDED after uploading to S3 -if (s3_file_request$status_code == '200') -{ - # Construct url - # The resulting URL should look like: https://.benchling.com/api/v2-beta/files/file_cGCGhKqh) - api_path <- "/api/v2-beta/files/" - url <- paste("https://", subdomain, api_path, file_id, sep = "") - - # Set Payload list as SUCCEEDED - file_payload <-list (uploadStatus = 'SUCCEEDED') - - # Convert payload to Json format and use Patch endpoint to mark file upload as completed - file_request <- - httr::PATCH(url = url, - body = toJSON(file_payload, pretty = TRUE, auto_unbox = TRUE), - httr::accept('application/json'),httr::content_type('application/json'), - httr::add_headers ('Authorization' = paste("Bearer", access_token))) - - # Use the jsonLite library to read the Json body - file_body <-jsonlite::fromJSON(rawToChar(file_request$content)) - - # Print status code - 200 = Successful - print(file_request$status_code) - -}else { - print('ERROR: Upload to S3 unsuccessful') + +# Put file in S3 bucket and add [;x-amz-server-side-encryption': 'AES256'] to the request headers +s3_file_request_24h <- + httr::PUT( + url = s3_put_url_24h, + body = my_data_24h, + httr::add_headers('x-amz-server-side-encryption' = 'AES256') + ) + +# Check if upload succeeded +if (s3_file_request_24h$status_code != 200) { + stop(paste( + "Failed to upload 24h plot to S3! Status code:", s3_file_request_24h$status_code, + sep = "" + )) } +# Change file status to SUCCEEDED after uploading to S3 +api_path <- "/api/v2-beta/files/" +url_24h <- paste("https://", base_domain, api_path, file_id_24h, sep = "") + +# Set Payload list as SUCCEEDED +file_payload_24h <- list(uploadStatus = 'SUCCEEDED') + +# Convert payload to Json format and use Patch endpoint to mark file upload as completed +file_request_24h <- + httr::PATCH( + url = url_24h, + body = toJSON(file_payload_24h, pretty = TRUE, auto_unbox = TRUE), + httr::accept('application/json'), + httr::content_type('application/json'), + httr::add_headers('Authorization' = paste("Bearer", access_token)) + ) + +cat(" ✓ 24h plot uploaded (ID:", file_id_24h, ")\n") + +# Upload 48h plot +cat(" Uploading 48h plot...\n") + +### Create a binary file +my_data_48h <- readBin(image_file_48h, "raw", 10e6) + +# Provide name of file as a payload in a list +file_payload_48h <- list(name = image_name_48h, filename = image_name_48h, folderId = folder_id) + +# Convert payload to Json format and use POST endpoint to create File +file_request_48h <- + httr::POST( + url = url, + body = toJSON(file_payload_48h, pretty = TRUE, auto_unbox = TRUE), + httr::accept('application/json'), + httr::content_type('application/json'), + httr::add_headers('Authorization' = paste("Bearer", access_token)) + ) + +# Check for errors +if (file_request_48h$status_code != 200) { + stop(paste( + "Failed to create 48h file! Status code:", file_request_48h$status_code, + sep = "" + )) +} + +# Use the jsonLite library to read the Json body +file_body_48h <- jsonlite::fromJSON(rawToChar(file_request_48h$content)) + +# Retrieve the file id +file_id_48h <- file_body_48h$id + +# Retrieve S3 PUT url from previous call +s3_put_url_48h <- file_request_48h$headers$`content-location` + +####### Use the PUT file endpoint to upload file in a Benchling S3 Bucket ###### + +# Put file in S3 bucket +s3_file_request_48h <- + httr::PUT( + url = s3_put_url_48h, + body = my_data_48h, + httr::add_headers('x-amz-server-side-encryption' = 'AES256') + ) + +# Check if upload succeeded +if (s3_file_request_48h$status_code != 200) { + stop(paste( + "Failed to upload 48h plot to S3! Status code:", s3_file_request_48h$status_code, + sep = "" + )) +} + +# Change file status to SUCCEEDED after uploading to S3 +url_48h <- paste("https://", base_domain, api_path, file_id_48h, sep = "") + +# Set Payload list as SUCCEEDED +file_payload_48h <- list(uploadStatus = 'SUCCEEDED') + +# Convert payload to Json format and use Patch endpoint to mark file upload as completed +file_request_48h <- + httr::PATCH( + url = url_48h, + body = toJSON(file_payload_48h, pretty = TRUE, auto_unbox = TRUE), + httr::accept('application/json'), + httr::content_type('application/json'), + httr::add_headers('Authorization' = paste("Bearer", access_token)) + ) + +cat(" ✓ 48h plot uploaded (ID:", file_id_48h, ")\n\n") + ################################################################################ -# Use the PATCH analyses endpoint to upload file into analyses ################# +# Use the PATCH analyses endpoint to attach outputs to analysis ################################################################################ +cat("Attaching outputs to analysis...\n") + # Construct url -# The resulting URL should look like: https://.benchling.com/api/v2-beta/analyses/ana_Tx98nkEm) api_path <- "/api/v2-beta/analyses/" -url <- paste("https://", subdomain, api_path, analysis_id, sep = "") - +url <- paste("https://", base_domain, api_path, analysis_id, sep = "") # Create nested list containing output files and output dataframes analysis_body <- - list(fileIds = list(file_id), + list(fileIds = list(file_id_24h, file_id_48h), dataFrameIds = list(result_dataframe_id)) -# Convert payload to Json format and use Patch endpoint to update Analyis to include output files and output dataframes -analysis_request <- - httr::PATCH(url = url, - body = toJSON(analysis_body, pretty = TRUE, auto_unbox = TRUE), - httr::accept('application/json'),httr::content_type('application/json'), - httr::add_headers ('Authorization' = paste("Bearer", access_token))) +# Convert payload to Json format and use Patch endpoint to update Analysis +analysis_request <- + httr::PATCH( + url = url, + body = toJSON(analysis_body, pretty = TRUE, auto_unbox = TRUE), + httr::accept('application/json'), + httr::content_type('application/json'), + httr::add_headers('Authorization' = paste("Bearer", access_token)) + ) + +# Check for errors +if (analysis_request$status_code != 200) { + stop(paste( + "Failed to update analysis! Status code:", analysis_request$status_code, + sep = "" + )) +} # Use the jsonLite library to read the Json body -analysis_body <-jsonlite::fromJSON(rawToChar(analysis_request$content)) +analysis_body <- jsonlite::fromJSON(rawToChar(analysis_request$content)) -# Print status code - 200 = Successful -print(analysis_request$status_code) +cat("✓ Outputs attached to analysis\n") +cat(" Analysis status:", analysis_body$status, "\n\n") + +################################################################################ +# Clean up temporary files +################################################################################ + +cat("Cleaning up temporary files...\n") + +# Delete tmp directory and all contents +if (dir.exists(tmp_dir)) { + unlink(tmp_dir, recursive = TRUE) +} + +cat("✓ Temporary files cleaned up\n\n") + +################################################################################ +# Success Summary +################################################################################ -# Initial status will be running and move to succeeded -# We recommend that can build a wait function to verify that it succeeded -print(analysis_body$status) +cat("==========================================\n") +cat("SUCCESS! Analysis complete\n") +cat("==========================================\n") +cat("Results:\n") +cat(" 24h IC50:", result_24h$ic50, " Slope:", result_24h$slope, " p-value:", result_24h$p_value, "\n") +cat(" 48h IC50:", result_48h$ic50, " Slope:", result_48h$slope, " p-value:", result_48h$p_value, "\n\n") +cat("Uploaded to Benchling:\n") +cat(" ✓ Results CSV (", result_dataframe_id, ")\n", sep = "") +cat(" ✓ 24h plot (", file_id_24h, ")\n", sep = "") +cat(" ✓ 48h plot (", file_id_48h, ")\n", sep = "") +cat("\nView your analysis at:\n") +cat(" https://", base_domain, "/analyses/", analysis_id, "\n", sep = "") diff --git a/utils.R b/utils.R new file mode 100644 index 0000000..9852edc --- /dev/null +++ b/utils.R @@ -0,0 +1,242 @@ +################################################################################ +# Utility Functions for IC50 Analysis +# +# This file contains reusable functions for IC50 dose-response curve analysis. +# These utilities are used by multiple scripts in this repository to reduce +# code duplication while keeping the main workflow scripts readable. +# +# Functions: +# - calculate_ic50(): Fit 4-parameter log-logistic model to dose-response data +# - create_ic50_plot(): Generate interactive plotly visualization +################################################################################ + +library(drc) +library(plotly) +library(pracma) + +################################################################################ +# calculate_ic50 +# +# Calculates IC50 (half maximal inhibitory concentration) using a 4-parameter +# log-logistic model (LL.4). This is the most common model for dose-response +# curves in pharmacology. +# +# Parameters: +# df - Data frame containing the dose-response data +# concentration_col - Name of the column containing drug concentrations +# mortality_col - Name of the column containing mortality/response values +# +# Returns: +# A list containing: +# $ic50 - IC50 value (concentration at 50% response) +# $slope - Slope of the dose-response curve +# $std_error - Standard error of IC50 estimate +# $t_value - t-statistic for IC50 +# $p_value - p-value for IC50 significance +# $model - The fitted drc model object (for advanced users) +# +# Model Details: +# The LL.4 model has 4 parameters: +# - Slope: Steepness of the curve +# - Lower limit: Fixed at 0 (minimum response) +# - Upper limit: Fixed at 100 (maximum response) +# - IC50: Concentration at 50% response (what we're solving for) +# +# Example: +# df <- read.csv("examples/sample_ic50_data.csv") +# result <- calculate_ic50(df, "Cell.Mortality.Concentration", "Cell.Mortality.Mortality.24h") +# print(paste("IC50:", result$ic50)) +# print(paste("p-value:", result$p_value)) +################################################################################ + +calculate_ic50 <- function(df, concentration_col, mortality_col) { + + # Validate inputs + if (!concentration_col %in% names(df)) { + stop(paste("Column not found:", concentration_col, + "\nAvailable columns:", paste(names(df), collapse = ", "))) + } + + if (!mortality_col %in% names(df)) { + stop(paste("Column not found:", mortality_col, + "\nAvailable columns:", paste(names(df), collapse = ", "))) + } + + # Create formula for drc model + formula <- as.formula(paste(mortality_col, "~", concentration_col)) + + # Fit 4-parameter log-logistic model + # fixed = c(NA, 0, 100, NA) means: + # Slope: NA (estimate from data) + # Lower limit: 0 (fixed) + # Upper limit: 100 (fixed) + # IC50: NA (estimate from data) + tryCatch({ + model <- drm( + formula, + data = df, + fct = LL.4( + fixed = c(NA, 0, 100, NA), + names = c("Slope", "LS Inferior", "LS Superior", "IC50") + ) + ) + + # Extract model summary + summary_result <- summary(model) + coefficients <- summary_result$coefficients + + # Extract key statistics + # Coefficients matrix has rows: [1]=Slope, [2]=IC50 + # Columns: [1]=Estimate, [2]=Std.Error, [3]=t-value, [4]=p-value + result <- list( + ic50 = round(coefficients[2, 1], 2), # IC50 estimate + slope = round(coefficients[1, 1], 2), # Slope estimate + std_error = round(coefficients[2, 2], 2), # Std error of IC50 + t_value = round(coefficients[2, 3], 2), # t-statistic + p_value = signif(coefficients[2, 4], 3), # p-value (3 sig figs) + model = model # Full model object + ) + + return(result) + + }, error = function(e) { + stop(paste( + "IC50 calculation failed:", + e$message, + "\nPlease check:", + " 1. Data has sufficient range of concentrations", + " 2. Response values are between 0-100", + " 3. No missing values in concentration or response columns", + sep = "\n" + )) + }) +} + +################################################################################ +# create_ic50_plot +# +# Creates an interactive plotly visualization of dose-response data with +# fitted IC50 curve. The plot shows: +# - Scatter points: Original data +# - Smooth curve: Fitted 4-parameter log-logistic model +# - Log scale on x-axis (standard for dose-response curves) +# +# Parameters: +# df - Data frame containing the data +# concentration_col - Name of column with drug concentrations +# mortality_col - Name of column with mortality/response values +# ic50_value - IC50 value (from calculate_ic50 function) +# slope - Slope value (from calculate_ic50 function) +# title - Optional: Custom title for the plot (default: auto-generated) +# +# Returns: +# A plotly object that can be: +# - Displayed interactively in RStudio +# - Saved with htmlwidgets::saveWidget() +# - Embedded in Shiny apps +# +# The Logistic Function: +# The 4-parameter logistic equation is: +# y = D + (A - D) / (1 + (x/C)^B) +# Where: +# A = upper limit (100) +# B = slope +# C = IC50 (inflection point) +# D = lower limit (0) +# +# Example: +# result <- calculate_ic50(df, "Cell.Mortality.Concentration", "Cell.Mortality.Mortality.24h") +# plot <- create_ic50_plot(df, "Cell.Mortality.Concentration", "Cell.Mortality.Mortality.24h", +# result$ic50, result$slope) +# htmlwidgets::saveWidget(plot, "ic50_plot.html", selfcontained = TRUE) +################################################################################ + +create_ic50_plot <- function(df, concentration_col, mortality_col, + ic50_value, slope, title = NULL) { + + # Validate inputs + if (!concentration_col %in% names(df)) { + stop(paste("Column not found:", concentration_col)) + } + + if (!mortality_col %in% names(df)) { + stop(paste("Column not found:", mortality_col)) + } + + # Define 4-parameter logistic function + # This is the mathematical model that describes the dose-response curve + logistic4 <- function(x, A, B, C, D) { + return((A - D) / (1.0 + ((x / C) ** B)) + D) + } + + # Extract data columns + conc_data <- df[[concentration_col]] + mort_data <- df[[mortality_col]] + + # Create scatter plot of observed data + plot <- plot_ly( + data = df, + x = conc_data, + y = mort_data, + type = "scatter", + mode = "markers", + name = "Observed Data", + marker = list(size = 10, color = 'rgba(50, 120, 200, 0.8)') + ) + + # Generate default title if not provided + if (is.null(title)) { + title <- paste("IC50 Dose-Response Curve (IC50 =", ic50_value, ")") + } + + # Configure plot layout + plot <- layout( + plot, + xaxis = list( + type = "log", # Log scale for concentrations (standard practice) + title = "Concentration" + ), + yaxis = list( + title = paste(mortality_col, "(%)") + ), + title = title, + hovermode = "closest" + ) + + # Generate smooth curve using the fitted model + # linspace creates evenly spaced points for a smooth curve + xs <- linspace(min(conc_data), max(conc_data), n = 1000) + + # Calculate fitted y-values using the logistic function + # Parameters: A=100 (upper), B=slope, C=IC50, D=0 (lower) + ys <- logistic4(xs, 100, slope, ic50_value, 0) + + # Add fitted curve to plot (line only, no markers) + plot <- add_trace( + plot, + x = xs, + y = ys, + type = "scatter", + mode = "lines", + name = "Fitted Curve", + line = list( + color = 'rgba(200, 50, 50, 0.8)', + width = 2 + ), + inherit = FALSE # Don't inherit data from previous trace + ) + + return(plot) +} + +################################################################################ +# End of utils.R +# +# Usage Notes: +# - Always source this file before using the functions: source("utils.R") +# - Both functions include input validation and helpful error messages +# - The calculate_ic50() function is designed to work with any column names +# - The create_ic50_plot() function returns a plotly object, not a static image +# +# For more examples, see the scripts in the examples/ directory +################################################################################