A dichotomous key — dimoose • dimoose

An R6 object holding a dichotomous key as a table of the leads on every path from the root to a terminal taxon. Usually created by importFishbase() or parseFishbase(). See https://www.fishbase.se/keys/allkeys.php for FishBase keys.

Active bindings

desc: Key title or description (read-only).
df: Data frame with one row per lead (or per term, if terms were separated) per terminal taxon, with columns Statement, Choice, Character, Taxon, and pSt/pCh for the parent lead.
meta: Key/value data frame of metadata (citation, image URLs, ...).
taxa: Data frame of terminal taxa and their resolved names.
leads: Data frame with one row per lead: Statement, Choice, Character, Next (next couplet, or "-" if terminal) and Taxon, plus optional Prev, Image, ImageLink, TaxonUrl, Question, Feature, Test and Threshold. Derived from df when the object was created without one.
features: Data frame of features a machine can compute, one per row (see featureTable()), or NULL for keys meant only for people.

Methods

`dimoose$new()`

Create a new dimoose object.

Usage

dimoose$new(df, desc = NA, meta = NA, taxa = NA, leads = NULL, features = NULL)

Arguments

df: Data frame of leads (see the df field).
desc: Key title or description.
meta: Key/value metadata data frame.
taxa: Data frame of terminal taxa.
leads: Optional data frame of leads (see the leads field).
features: Optional data frame of machine-readable features (see featureTable()).

`dimoose$print()`

Print a short overview of the key.

Usage

dimoose$print(...)

Arguments

...: Unused.

`dimoose$summary()`

Counts describing the key.

Usage

dimoose$summary()

Returns

A one-row data frame: title, couplets, leads, taxa, depth (longest path in steps) and problems (see validate()).

`dimoose$validate()`

Check the key: leads to missing couplets, terminal leads without a taxon, couplets with fewer than two leads, couplets that cannot be reached from the first one, and (for keys with features) leads whose machine test is missing or inconsistent.

Usage

dimoose$validate()

Returns

A character vector of problems, invisibly if there are none.

`dimoose$toDataTree()`

Convert the key to a data.tree::Node: couplets are internal nodes and taxa leaves; each child node carries the lead label and the character text of the lead that leads to it. A couplet reached from several leads is attached under the first.

Usage

dimoose$toDataTree()

`dimoose$toNewick()`

Write the key's topology in Newick format, with couplets as internal node labels and taxa as leaves (labels quoted when needed). A couplet reached from several leads is placed under the first.

Usage

dimoose$toNewick()

Returns

A single string ending in ;.

`dimoose$clone()`

The objects of this class are cloneable with this method.

Usage

dimoose$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.