Re-create therapy episodes and therapy combinations

This function should be used to recreate therapy episodes and therapy combinations, for example in order to try new transitive_closure_controls parameters.

create_therapy_episodes(
  conn,
  transitive_closure_controls = transitive_closure_control(),
  silent = FALSE
)

Arguments

conn: a connection to a database containing a drug_prescriptions table previously created with load_medications())
transitive_closure_controls: parameters controlling (see transitive_closure_control())
silent: if TRUE, the progress bar will be hidden. The default is FALSE.

Overview

Electronic prescribing and administration systems do not usually define:

combination therapy: prescribing two or more antimicrobials concurrently for the same indication
therapy episodes: the set of antimicrobial prescriptions administered consecutively or concurrently and corresponding to a single indication and intent.

When loading medication records, load_medications() first examines all prescriptions authored in a given hospital admission to ascertain such links between prescriptions. This involves looking at patterns of overlap and succession of prescriptions, and using a graph theory method known as 'transitive closure'.

Ramses links prescriptions together if:

prescriptions share the same antiinfective_type: antibacterials are linked with antibacterials, antifungals with antifungals, etc.
prescription_status is *not* 'cancelled', 'draft', 'entered-in-error', or 'unknown'.

Operations

This function performs the following operations:

verify that a valid drug_prescriptions table exists
delete any existing drug_prescription_edges and drug_therapy_episodes table
recreate the drug_prescription_edges table
overwrite therapy_id and combination_id fields in drug_prescriptions table
recreate the drug_therapy_episodes table

Arguments

Overview

Operations

See also