edited visit outcome

[ekamau]

After discussion last week, this changes outcome = "recovered" to "discharged"

[github-actions]

Summary of the missing optional fields for the ccp-drc.toml parser:

table	missing	total_fields	percentage_coverage
subject	15	56	73.214286%
visit	21	53	60.377358%
observation	27	70	61.428571%

SUBJECT                                         
dataset_id                                      False
enrolment_date                                  False
sex_at_birth                                    False
pregnancy_whether_breastfed                     False
pregnancy_gestational_age_weeks                 False
preterm_infant                                  False
has_chronic_respiratory_disease                 False
diabetes_type                                   False
has_apnoea                                      False
has_inflammatory_bowel_disease                  False
has_rare_disease_inborn_metabolism_error        False
has_tuberculosis_past                           False
has_hiv_art                                     False
vaccinated_covid19                              False
vaccinated_covid19_dates                        False
VISIT                                           
dataset_id                                      False
phase                                           False
treatment_corticosteroid_type_other             False
treatment_oxygen_mask_prongs                    False
treatment_antifungal_agent                      False
treatment_antifungal_agent_type                 False
treatment_antiviral_type_other                  False
treatment_ace_inhibitors                        False
treatment_arb                                   False
treatment_steroids                              False
treatment_intravenous_fluids                    False
treatment_nsaid                                 False
treatment_cpr                                   False
treatment_offlabel                              False
treatment_respiratory_support                   False
treatment_colchicine                            False
treatment_immunoglobulins                       False
treatment_delirium                              False
treatment_delirium_type                         False
treatment_monoclonal_antibody                   False
treatment_pacing                                False
OBSERVATION                                     
avpu                                            False
acvpu                                           False
oxygen_flow_volume_max                          False
oxygen_flow_volume_max                          False
clinical_classification_critical_illness_scale  False
total_fluid_output_ml                           False
base_excess                                     False
clinical_frailty_score                          False
inability_to_walk_scale                         False
blantyre_coma_score                             False
mid_upper_arm_circumference_cm                  False
fio2_percent                                    False
pao2_mmHg                                       False
pco2_mmHg                                       False
richmond_agitation-sedation_scale               False
riker_sedation-agitation_scale                  False
mean_arterial_blood_pressure_mmHg               False
anorexia                                        False
bleeding                                        False
confusion                                       False
cyanosis                                        False
feeding_intolerance_pediatrics                  False
hepatomegaly                                    False
inability_to_walk                               False
irritability_pediatrics                         False
lung_sounds                                     False
severe_dehydration                              False
heart_sounds                                    False

[pipliggins]

@sadiekelly what do you think about changing those instances where the subject is actually recorded as 'recovered' in the study? I think my initial thought was just that we shouldn't be claiming people as 'recovered' if e.g., they were never admitted.

[sadiekelly]

@sadiekelly what do you think about changing those instances where the subject is actually recorded as 'recovered' in the study? I think my initial thought was just that we shouldn't be claiming people as 'recovered' if e.g., they were never admitted.

@pipliggins for the DRC, Ghana and Guinea datasets the original response option states "Recovered, confirmed with a negative COVID-19 test". This option is given alongside "Discharged". I think we might have gone for "Discharged" as the outcome for the patients recorded as "Recovered.." even if they were not ever admitted as there are plenty of patients in other databases who were admitted and discharged on the same day who also have "Discharged" captured for their outcome. So I think for being consistent that's why we decided to change these. We haven't captured any data on repeat testing though so have nowhere to record the final negative test result, but that's the same for all patients. Stating "recovered" could be misleading as you say, as we have no idea about ongoing symptoms. I think stick with "Discharged".