NEWS.md
11 April 2023
dplyr v1.1.0, dbplyr v2.3.2 and tidyselect v1.2.0.microbiology_isolates or not (#108). The timeline will now show specimens without an isolate record at the time of collection.23 October 2022
validate_inpatient_diagnoses() to accept two optional fields diagnosis_start and diagnosis_end and take advantage of clinical systems such as problem liststherapy_timeline() to take advantage of diagnosis_start and diagnosis_end variables if presentinpatient_diagnoses mock dataset to removed episode start and end fields #103 which duplicated information in inpatient_episodes
bridge_*() functions to add a field antiinfective_type to bridge tables #76 and prevent unrelated generation issues #104
dplyr data masking approach #105.13 September 2022
validate_investigations() now expects observation_code values to be associated with unique observation_name and observation_display valuesvalidate_microbiology().30 August 2022
TherapyEpisode instances created for more than 3 therapy episodes (id with length > 3) #100
27 August 2022
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 libraryEncounter #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")
Patient() function to create a Patient object from any other object of class RamsesObject
compute() and collect().therapy_table() is now deprecated: use longitudinal_table() instead #86
bridge_spell_therapy_overlap() is now deprecated : use bridge_encounter_therapy_overlap() instead #86
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 0.5.0object are now changed to x, except for show(object).2 August 2022
dplyr version >= 1.0.1 and dbplyr version >= 2.1.0validate_inpatient_episodes() #85
map_charlson_comorbidities() with tbl_df objects #84
compute() with TherapyEpisode objects #83
clinical_feature_*() functions with PostgreSQL #88
28 January 2022
AMR package version >= 1.8.0clinical_feature_*() functions #80
spell_id is no longer required by validate_investigations() #77
bridge_tables() even in the absence of defined daily doses (DDDs) in drug prescription and administration recordsvignette("Ramses")
5 August 2021
vignette("load-data")
antibiotic_icd_indications
7 July 2021
igraph dependencyTherapyEpisode class now supporting multiple therapy episodes*_id variablesdrug_id refactored into drug_code; ATC_group retired in favour of drug_group
isolate_id rather than organism_id
drug_id, drug_name and drug_display_name refactored into agent_code, agent_name and agent_display_name
clinical_feature_*() functions on PostgreSQLprescription_status: therapy episodes and bridge table records will not be generated for prescriptions with status "draft", "entered-in-error", "cancelled", or "unknown".reference_loinc to version 2.70 and expand to 10 new conceptsvalidate_prescriptions() checks on daily_frequency
load_*() handling of data.table objects26 February 2021
Patient, MedicationRequest, TherapyEpisode
therapy_table(), parenteral_changes(), clinical_feature_last(), clinical_feature_ols_trend(), clinical_feature_interval(), clinical_feature_mean()