run_rclade_cli: Run Rclade from the command line

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

Run Rclade from the command line

Description

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

Usage

run_rclade_cli(args = commandArgs(trailingOnly = TRUE))

Arguments

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

Value

An invisible integer exit code following standard Unix conventions: 0L (success), 1L (runtime error), 2L (parameter error), 3L (input-data error), 130L (user interrupt / SIGINT). The caller MUST pass this value to q(status = ...) or quit(status = ...) for the exit code to propagate to the operating system; simply calling run_rclade_cli() without forwarding the return value will always exit with code 0 regardless of errors.

Config-file override trap (L-E3 — READ BEFORE USING --config)

A --config YAML file supplies defaults for any option, with precedence CLI explicit argument > config file > built-in default. Because optparse does not expose "was this flag passed?", the override is applied by comparing each option against its built-in default: any option the user left at its default value is eligible to be overridden by the config file — even if the user explicitly typed a value identical to the default. Concretely:

• plot_timetree --rank phylum (where "phylum" is the default) will be overridden by rank: class in the config.

• plot_timetree --rank species (non-default) is preserved.

This is an optparse limitation, not a bug, and is intentional but surprising. To make an option immune to config, pass a non-default value, or avoid relying on config for options you care about. Unknown config keys are warned and ignored.

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