create_therapy_episodes: Re-create therapy episodes and therapy combinations

In ramses-antibiotics/ramses-package: R Package for Antimicrobial Stewardship & Surveillance

Re-create therapy episodes and therapy combinations

Description

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

Usage

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:

1. verify that a valid drug_prescriptions table exists

2. delete any existing drug_prescription_edges and drug_therapy_episodes table

3. recreate the drug_prescription_edges table

4. overwrite therapy_id and combination_id fields in drug_prescriptions table

5. recreate the drug_therapy_episodes table

See Also

For more details please consult vignette("therapy-episodes", package = "Ramses")

ramses-antibiotics/ramses-package documentation built on Feb. 13, 2024, 1:01 p.m.