refactor all bridge_tables and add metrics tables #109

- remove bridge_encounter_therapy_overlap()
- add bridge_episode_therapy_overlap()
- add bridge_inpatient_episodes_date()
- add bridge_drug_prescriptions_date()
- add create_reporting_inpatient()
- add create_reporting_med_prescribing()
- begin rewriting Ramses.Rmd vignette (getting started)
- change name of Postgres database

.github/workflows/Postgres.yaml

@@ -17,7 +17,7 @@ jobs:
       postgres:
         image: ${{ matrix.config.postgres_image }} 
         env:
-          POSTGRES_DB: RamsesDB
+          POSTGRES_DB: RamsesDB_testing
           POSTGRES_USER: user
           POSTGRES_PASSWORD: password
         ports:

.github/workflows/R-CMD-check.yaml

@@ -21,7 +21,7 @@ jobs:
       postgres:
         image: postgres
         env:
-          POSTGRES_DB: RamsesDB
+          POSTGRES_DB: RamsesDB_testing
           POSTGRES_USER: user
           POSTGRES_PASSWORD: password
         ports:

DESCRIPTION

@@ -63,11 +63,12 @@ Suggests:
 Remotes: 
     ramses-antibiotics/snomedizer
 RdMacros: Rdpack    
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1
 VignetteBuilder: knitr,rmarkdown
 Collate: 
     'Ramses-deprecated.R'
     'Ramses-package.R'
+    'bridge_and_metrics.R'
     'objects.R'
     'clinical_features.R'
     'database.R'

NAMESPACE

@@ -8,9 +8,11 @@ export(Patient.RamsesObject)
 export(TherapyEpisode)
 export(TherapyEpisode.DBIConnection)
 export(TherapyEpisode.MedicationRequest)
-export(bridge_encounter_therapy_overlap)
+export(bridge_drug_prescriptions_date)
 export(bridge_episode_prescription_initiation)
 export(bridge_episode_prescription_overlap)
+export(bridge_episode_therapy_overlap)
+export(bridge_inpatient_episodes_date)
 export(bridge_spell_therapy_overlap)
 export(bridge_tables)
 export(clinical_feature_interval)
@@ -22,6 +24,8 @@ export(compute)
 export(compute_DDDs)
 export(connect_local_database)
 export(create_mock_database)
+export(create_reporting_inpatient)
+export(create_reporting_med_prescribing)
 export(create_therapy_episodes)
 export(download_icd10cm)
 export(get_ATC_name)