validate_newick_syntax: Validate Newick string syntax

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

Validate Newick string syntax

Description

Performs deep syntax validation on a raw Newick string before parsing. Checks bracket balance, negative branch lengths, empty node names, duplicate node names, and self-loops.

Usage

validate_newick_syntax(text, filepath = "<string>")

Arguments

text	Character. Raw Newick string.
filepath	Character. File path for error messages.

Value

Invisibly returns TRUE if valid. Stops on CRITICAL errors.

Heuristics & error contract (L-C3 / L-E3)

The syntax checks are regex heuristics over the raw string and may occasionally false-positive or false-negative on exotic input (e.g. unusual quoting, deeply nested labels). They are a fast pre-filter; the authoritative correctness check is the structural validation that runs after the tree is parsed. Do not treat a clean heuristic pass as a full guarantee.

On failure these validators raise via rlang::abort(message, class = "Rclade_validate_error") (or "Rclade_read_error" for I/O problems). Callers must branch on the condition class, never grep the message text — this is the supported contract and prevents brittle tests when wording changes.

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