NEWS.md

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

Ramses 0.7.2

11 February 2024

Changed

• Now requires minimum AMR v2.0.0.
• Updated function calls and documentation following deprecation of AMR::as.rsi().

Ramses 0.7.1

19 November 2023

Changed

• Now requires minimum dbplyr v2.4.0.
• Unit test maintenance required by dbplyr v2.4.0.

Ramses 0.7.0

11 April 2023

Changed

• Now requires minimum R v4.0.0, dplyr v1.1.0, dbplyr v2.3.2 and tidyselect v1.2.0.
• Internal code maintenance in line with new tidy programming practice.
• Tolerance built into the timeline for handling of no growth results. Ramses does not currently prescribe whether no growth should be loaded into microbiology_isolates or not (#108). The timeline will now show specimens without an isolate record at the time of collection.

Ramses 0.6.0

23 October 2022

Improvements

• Changed validate_inpatient_diagnoses() to accept two optional fields diagnosis_start and diagnosis_end and take advantage of clinical systems such as problem lists
• Changed therapy_timeline() to take advantage of diagnosis_start and diagnosis_end variables if present
• Changed the inpatient_diagnoses mock dataset to removed episode start and end fields #103 which duplicated information in inpatient_episodes
• Changed bridge_*() functions to add a field antiinfective_type to bridge tables #76 and prevent unrelated generation issues #104
• General code maintenance and adaptation to ongoing changes to the dplyr data masking approach #105.

Ramses 0.5.2

13 September 2022

Improvements

• validate_investigations() now expects observation_code values to be associated with unique observation_name and observation_display values
• improvements to namespace handling in validate_microbiology().

Ramses 0.5.1

30 August 2022

Bug fix

• Fix bug affecting TherapyEpisode instances created for more than 3 therapy episodes (id with length > 3) #100

Ramses 0.5.0

27 August 2022

Improvements

• Local databases (connect_local_database() and create_mock_database()) are now powered by DuckDB rather than SQLite, bringing support for datetime variable types and increased performance. Ramses now depends on the duckdb library
• Added new S4 class Encounter #92 to manipulate hospitalisations (admissions) with associated methods for show(), compute(), collect(), Patient(), longitudinal_table(), clinical_feature_*(), therapy_timeline()
• TherapyEpisode() and Encounter() have a new optional extend_table_start input controlling their longitudinal table's start. This allows the creation of longitudinal tables starting before the therapy_start or admission_date, respectively. More detail is available from vignette("therapy-episodes")
• Added Patient() function to create a Patient object from any other object of class RamsesObject
• Improved documentation and export of S4 methods compute() and collect().

Breaking changes

• therapy_table() is now deprecated: use longitudinal_table() instead #86
• bridge_spell_therapy_overlap() is now deprecated : use bridge_encounter_therapy_overlap() instead #86
• Database table inpatient_episodes and documentation now refer to 'encounters' rather than 'spells'. Variable spell_id is now known as encounter_id #86. Databases built with previous versions of Ramses will not work with Ramses 0.5.0
• Function signatures for all methods are standardised: function arguments object are now changed to x, except for show(object).
• Support for SQLite databases is withdrawn.

Ramses 0.4.4

22 August 2022

Improvements

• clinical_feature_*() functions trigger a warning rather than an error if no value matching observation_code is found in theinpatient_investigations table.

Ramses 0.4.3

2 August 2022

Improvements

• upgrade dependency on packages dplyr version >= 1.0.1 and dbplyr version >= 2.1.0
• improve validate_inpatient_episodes() #85

Bug fixes

• fix bug in map_charlson_comorbidities() with tbl_df objects #84
• fix bug in compute() with TherapyEpisode objects #83
• fix uncommon bug in clinical_feature_*() functions with PostgreSQL #88

Ramses 0.4.2

28 January 2022

Improvements

• upgrade dependency on AMR package version >= 1.8.0
• better error messages in clinical_feature_*() functions #80
• spell_id is no longer required by validate_investigations() #77
• bridge tables will be generated by bridge_tables() even in the absence of defined daily doses (DDDs) in drug prescription and administration records
• improve vignette("Ramses")

Ramses 0.4.1

5 August 2021

Improvements

• clarifications on vignette("load-data")
• corrections to antibiotic_icd_indications

Ramses 0.4.0

7 July 2021

Improvements

• faster implementation of prescription linkage using igraph dependency
• TherapyEpisode class now supporting multiple therapy episodes
• support for integer *_id variables
• updated schema of drug prescriptions and administrations: drug_id refactored into drug_code; ATC_group retired in favour of drug_group
• updated schema of microbiology isolates and susceptibilities: isolates are now identified by isolate_id rather than organism_id
• updated schema of microbiology susceptibilities: drug_id, drug_name and drug_display_name refactored into agent_code, agent_name and agent_display_name
• faster execution of clinical_feature_*() functions on PostgreSQL
• uniform handling of prescription_status: therapy episodes and bridge table records will not be generated for prescriptions with status "draft", "entered-in-error", "cancelled", or "unknown".
• update reference_loinc to version 2.70 and expand to 10 new concepts

Bug fixes

• fix bug in validate_prescriptions() checks on daily_frequency
• fix bug in load_*() handling of data.table objects

Ramses 0.3.1

17 March 2021

Bug fix

• fix bug in handling data.table objects in arrange_variables() and validate_*()

Ramses 0.3.0

26 February 2021

Features

• introduce S4 classes Patient, MedicationRequest, TherapyEpisode
• introduce therapy methods therapy_table(), parenteral_changes(), clinical_feature_last(), clinical_feature_ols_trend(), clinical_feature_interval(), clinical_feature_mean()

Improvements

• remove dependencies
• improve handling of time data types by SQLite
• upgrade to units package version >=0.7-0

Documentation

• new ramses-objects vignette
• new therapy-episodes vignette

Ramses 0.2.1

8 February 2021

Bug fixes

• Corrected incorrect transitive closure settings
• Corrected prescription edge classification

Improvements

• Complete verification of prescription edge classification
• therapy_id now always set to the id of the first prescription in the episode

Ramses 0.2.0

25 January 2021

• Support PostgreSQL
• Introduce standalone patients table and dataset

Ramses 0.1.0

8 January 2021

• First minor version

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