detect_taxonomy_format: Detect taxonomy format from tip labels

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

Detect taxonomy format from tip labels

Description

Detects Format A (embedded: _d_Bacteria_p_...) or Format B (semicolon-delimited: d__Bacteria;p__...).

Usage

detect_taxonomy_format(labels)

Arguments

labels

Character vector of tip labels

Value

Format name: "embedded", "GTDB", "Silva", "NCBI", or "unknown"

Regex heuristic boundaries (L-C3)

Detection and parsing here are heuristic regex passes, not a strict grammar. Known boundaries the caller must respect:

• Underscores in names: under delimiter_mode = "reverse" the pattern uses [^_]+?, so an underscore inside a taxon name (e.g. _g_Clostridium_sensu_stricto_s_X) can be mis-read as a rank separator. Names that contain underscores should use delimiter_mode = "segment" (delimiter-to-delimiter extraction), which preserves embedded underscores. For Format B (;-delimited) underscores are safe.

• Custom regex backtracking: caller-supplied custom_patterns are inserted verbatim into the parser. Unbounded repeating groups (e.g. (.+)+) can cause catastrophic backtracking on adversarial labels. Patterns are rejected above the 200-character limit, but keep sub-patterns bounded and anchored.

• Detection is content-based: detect_taxonomy_format samples labels; a mixed or malformed corpus may return "unknown", in which case the caller must fall back to an explicit format=.

• GTDB requires a semicolon majority (M-B3): the GTDB rule additionally requires that more than half of sampled labels contain a semicolon. Accession-prefixed embedded labels with double-underscore rank separators (e.g. GCA_xxx_d__Archaea_p__Nanoarchaeota) satisfy the [dpcofgsk]__ pattern but contain no semicolons; they are detected as "embedded" rather than misclassified as GTDB. The embedded parsers also tolerate double-underscore separators.

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