inst/docs/en/reference/cli-interactive.md

In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

Command-line & Interactive Interfaces

Run Rclade from the command line, launch the Shiny app, run the self-test, and batch with interruption handling.

This module contains the following functions:

• run_rclade_cli — Run Rclade from the command line
• run_rclade_shiny — Launch Rclade Shiny app
• run_rclade_selftest — Run Rclade self-test
• batch_with_interrupt — Execute batch operation with interrupt handling and progress
• with_graceful_interrupt — Execute expression with graceful interrupt handling

run_rclade_cli

Provides a command-line interface for Rclade. Requires the optparse package.

Usage:

run_rclade_cli(args = commandArgs(trailingOnly = TRUE))

Arguments:

| Argument | Description | |----------|-------------| | args | Character vector of command-line arguments (default: commandArgs(trailingOnly = TRUE)) |

Examples:

# At the system command line run:
# Rscript -e 'Rclade::run_rclade_cli()' -- --help
run_rclade_cli(c("--help"))

run_rclade_shiny

Provides an interactive web interface for Rclade. Requires the shiny package.

Usage:

run_rclade_shiny()

Examples:

run_rclade_shiny()

run_rclade_selftest

Performs comprehensive self-check:

1. Required package availability and versions
2. Example tree parsing and taxonomy extraction
3. Monophyly logic validation

Usage:

run_rclade_selftest()

Value:

Integer. Exit code (0 = all passed, 1 = failures).

Examples:

run_rclade_selftest()

batch_with_interrupt

Processes a list of items with progress tracking and graceful interrupt handling. If interrupted, reports how many items were completed before stopping.

Usage:

batch_with_interrupt(items, fun, label_fun = NULL)

Arguments:

| Argument | Description | |----------|-------------| | items | List or vector of items to process. | | fun | Function to apply to each item. Receives (item, index). | | label_fun | Optional function to generate label for each item. |

Value:

List of results (NULL for items not processed due to interrupt).

Examples:

trees <- list(tree1, tree2, tree3)
results <- batch_with_interrupt(trees, function(t, i) {
  plot_timetree(t, rank = "phylum")
})

with_graceful_interrupt

Wraps an expression so that SIGINT (Ctrl+C) is caught gracefully: progress is reported, resources are cleaned up, and the function returns NULL instead of throwing an error.

Usage:

with_graceful_interrupt(expr, total = 0)

Arguments:

| Argument | Description | |----------|-------------| | expr | Expression to evaluate. | | total | Integer. Total items for progress tracking (batch mode). |

Value:

Result of expr, or NULL if interrupted.

Examples:

result <- with_graceful_interrupt({
  for (i in 1:100) {
    Sys.sleep(0.1)
  }
  "done"
})

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Rclade documentation built on Sept. 26, 2026, 5:07 p.m.