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Canonicalize Location Data

Source: R/imuGAP.R
canonicalize_locations.Rd

Canonicalize Location Data

Usage

canonicalize_locations(locations)

Arguments

locations

a [data.frame()], with columns loc_id and parent_id, of the same type. See Details for restrictions.

Value

a data.table, with:

  • loc_id, parent_id columns as originally supplied, possibly reordered

  • loc_c_id, loc_cp_id columns, canonicalized id/parent_id columns, representing the order that will be used in the sampler

  • layer column, an integer from 1 (root), 2 (root children), 3 (grandchildren), &c

  • layer_bound column, an integer starting from 1 by layer. This provides index slice information used in the stan model.

Details

The [imuGAP()] sampler works on a hierarchical model of locations, and must be provided that structure. This method checks location structure validity, and returns a canonical version including the layer membership.

A valid structure has:

  • a unique root,

  • no cycles, and

  • no duplicate loc_ids

Users may explicitly identify the root loc_id by providing a row with parent_id equal to NA. Otherwise, any parent_id that does not appear in loc_id is treated as the root.

If the input is valid, this method will create the canonicalized version. In that version, all ids run from 1:N, where N is the number of distinct ids. That order is determined by layer order, then position of parent within its layer, then "natural" order (i.e., whatever base R sort() yields).