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Normalise the avoncap pneumococcal data

Source: R/mapping-pneumococcal.R
map_avoncap_pneumococcal.Rd

  • participant_number -> admin.record_number (name)

  • hospital -> admin.hospital (list)

  • nhs_number -> admin.patient_identifier (ppi)

  • age_at_admission -> demog.age (double)

  • sex -> demog.gender (list)

  • test_date -> pneumo.test_date (date)

  • test -> pneumo.test_type (list)

  • serotype -> pneumo.phe_serotype (pneumo_serotype)

  • smoker -> demog.smoker (list)

  • resp_disease -> comorbid.no_resp_dx, comorbid.copd, comorbid.asthma, comorbid.bronchiectasis, comorbid.pulmonary_fibrosis, comorbid.resp_other (checkboxes)

  • chd -> comorbid.no_heart_dx, comorbid.ccf, comorbid.ihd, comorbid.hypertension, comorbid.af, comorbid.other_heart_dx (checkboxes)

  • mi -> comorbid.previous_mi (yesno)

  • ckd -> comorbid.ckd (list)

  • liver_disease -> comorbid.liver_disease (list)

  • diabetes -> comorbid.diabetes (list)

  • dm_meds -> comorbid.diabetes_medications (list)

  • dementia -> comorbid.no_dementia, comorbid.dementia, comorbid.cognitive_impairment (checkboxes)

  • neurological_disease -> comorbid.neuro_other, comorbid.cva, comorbid.tia, comorbid.hemiplegia, comorbid.paraplegia, comorbid.no_neuro_dx (checkboxes)

  • gastric_ulcers -> comorbid.gastric_ulcers (yesno)

  • dysphagia -> comorbid.dysphagia (yesno)

  • pvd -> comorbid.periph_vasc_dx (yesno)

  • ctd -> comorbid.connective_tissue_dx (yesno)

  • immunodeficiency -> comorbid.immunodeficiency (yesno)

  • other_pn_disease -> comorbid.other_pneumococcal_risks (yesno)

  • hiv -> comorbid.no_HIV, comorbid.HIV, comorbid.AIDS (checkboxes)

  • cancer -> comorbid.solid_cancer (list)

  • haem_malig -> comorbid.no_haemotological_cancer, comorbid.leukaemia, comorbid.lymphoma (checkboxes)

  • recent_chemo -> comorbid.recent_chemotherapy (yesno)

  • recent_radiotherapy -> comorbid.recent_radiotherapy (yesno)

  • transplant -> comorbid.transplant_recipient (yesno)

  • pregnancy -> comorbid.pregnancy (list)

  • drugs -> demog.no_drug_abuse, demog.alcohol_abuse, demog.ivdu_abuse, demog.marijuana_abuse, demog.other_inhaled_drug_abuse (checkboxes)

  • immsup -> admission.on_immunosuppression (yesno)

  • weight_problem -> comorbid.bmi_status (list)

  • concomittant_flu -> comorbid.influenza_infection (yesno)

  • hcv -> comorbid.hepatitis_c (yesno)

  • ppv23 -> vaccination.ppv23_vaccination (list)

  • flu_vaccine -> vaccination.flu (list)

  • cci_total_score -> admission.charlson_comorbidity_index (name)

  • los_days -> outcome.length_of_stay (double)

  • amts -> admission.triage_score (list)

  • resp_rate -> admission.respiratory_rate (double)

  • sats_ra -> admission.saturations_on_room_air (double)

  • systolic_bp -> admission.systolic_bp (double)

  • diastolic_bp -> admission.diastolic_bp (double)

  • crb65_score -> admission.crb_65_severity_score (list)

  • curb65_score -> admission.curb_65_severity_score (list)

  • antibiotic_route -> outcome.antibiotic_route (list)

  • antibiotic_days -> outcome.antibiotic_duration (double)

  • infection_site -> admission.infection_site (list)

  • deranged_lfts -> outcome.abnormal_lft (yesno)

  • aki -> outcome.acute_kidney_injury (yesno)

  • pleural_effusion -> outcome.pleural_effusion (yesno)

  • empyema -> outcome.empyema (yesno)

  • discharge_destination -> outcome.discharge_to (list)

  • icu -> outcome.admitted_icu (yesno)

  • niv -> outcome.non_invasive_ventilation (yesno)

  • intubation -> outcome.intubation (yesno)

  • recurrent_pneumonia -> outcome.recurrent_pneumonia (yesno)

  • ecmo -> outcome.received_ecmo (yesno)

  • inotropes -> outcome.received_ionotropes (yesno)

  • trachy -> outcome.tracheostomy (yesno)

  • inpatient_death -> outcome.inpatient_death (yesno)

  • death_30days -> outcome.death_within_30_days (yesno)

  • death_1year -> outcome.death_within_1_year (yesno)

  • survival_days -> outcome.survival_duration (name)

  • albumin -> haem.albumin (double)

  • wcc -> haem.white_cell_count (double)

  • hb -> haem.haemoglobin (double)

  • pmn -> haem.neutrophils (double)

  • lymphocytes -> haem.lymphocytes (double)

  • crp -> haem.crp (double)

  • na_result -> haem.sodium (double)

  • ur_result -> haem.urea (double)

  • egfr -> haem.egfr (double)

  • creatinine -> haem.creatinine (double)

  • cxr_sides -> radio.cxr_infection (list)

  • cxr_lobes -> radio.cxr_lobar_changes (list)

  • death_5year -> outcome.death_within_5_years (yesno)

  • survival_days_2 -> outcome.5_yr_survival_duration (name)

  • imd_decile -> demog.imd_decile (name)

Usage

map_avoncap_pneumococcal()

Value

a list