norm = avoncap::normalise_data(rawData)
#> Normalising data using: normalise.avoncap_export.ed
#> Warning in norm_fn(rawData, ...): This hasn't been updated since the change to
#> admission_dates reconstruction
#> Admission date is derived from study week and hence approximate.
#> Some columns expected in the mappings were not present: ac_study_number, nhs_number, admission_type, c19_diagnosis, c19_adm_swab, c19_test_type, cc_critieria, cc_pos_date, age_march, ethnicity2, hapcovid_screening, hospital_covid, np_swab, adm_np_type, np_date, days_adm_npswab, np_swab_2, adm_np_type_2, np_date_2, np_swab_3, adm_np_type_3, np_date_3, saliva, saliva_date, days_adm_saliva, sputum, sputum_date, days_adm_sputum, pt_ad_ur, adm_ur_taken, nourine_reason, adm_np_type_2, adm_ur_date, days_adm_urine, adm_serum_tak, adm_seru_date, days_adm_serum, covidvax_date, covidvax_dose_2, covidvax_dose_3, covidvax_dose_4, covidvax_dose_5, covidvax_dose_6, flu_date, ppv23_date, c19_variant, adm_diagnosis, previousinfection_date, height, weight, bmi, first_radio, c19_peep, c19_hospadm, c17_high, c19icuon, c19_icudays, c19_vent, c19_ox, c19_ionotropes, c19_complication, c19_death7d, c19_meds, ip_death, days_in_icu, did_the_patient_have_respi, number_of_days_of_ventilat, ett_days, renal_replacement_therapy, complications, ventilatory_support, did_the_patient_receive_ec, inotropic_support_required, anosmia, ageusia, dysgeusia, malaise, myalgia, worse_confusion, general_det, antiplatelets, anticoagulants, statins, hypertensives
#> caching item: ~/.cache/avoncap/norm-0ef4812a2d1bc751062531c384a2b89e-aae482c14dabc5a9445fb3d15ae09be3.rda
#> mapping .optout to admin.opted_out
#> mapping .record_number to admin.record_number
#> mapping .what_was_the_first_surveil to admin.first_record_number
#> the input data set does not have a ac_study_number column (or column set)
#> the input data set does not have a nhs_number column (or column set)
#> mapping .duplicate to admin.duplicate
#> mapping .enrollment_date to admin.enrollment_date
#> the input data set does not have a admission_type column (or column set)
#> mapping .study_year to admin.study_year
#> mapping .file to admin.data_file
#> mapping .week_number to admin.week_number
#> the input data set does not have a c19_diagnosis column (or column set)
#> mapping .clinical_radio_diagnosis to diagnosis.clinical_or_radiological_LRTI_or_pneumonia
#> the input data set does not have a c19_adm_swab column (or column set)
#> the input data set does not have a c19_test_type column (or column set)
#> mapping .qualifying_symptoms_signs to diagnosis.qualifying_symptoms_signs
#> the input data set does not have a cc_critieria column (or column set)
#> the input data set does not have a cc_pos_date column (or column set)
#> mapping .gender to demog.gender
#> mapping .age_at_admission to demog.age
#> the input data set does not have a age_march column (or column set)
#> mapping .imd to demog.imd_decile
#> mapping .gp_practice to admin.gp_practice_old
#> mapping .gp_practice_drop_down to admin.gp_practice
#> mapping .smoking to demog.smoker
#> the input data set does not have a ethnicity2 column (or column set)
#> mapping .care_home to demog.care_home_resident
#> the input data set does not have a hapcovid_screening column (or column set)
#> the input data set does not have a hospital_covid column (or column set)
#> mapping .drugs___1 to demog.no_drug_abuse
#> mapping .drugs___2 to demog.alcohol_abuse
#> mapping .drugs___3 to demog.ivdu_abuse
#> mapping .drugs___4 to demog.marijuana_abuse
#> mapping .drugs___5 to demog.other_inhaled_drug_abuse
#> mapping .vaping to demog.vaping
#> mapping .alc_units to demog.units_of_alcohol
#> the input data set does not have a np_swab column (or column set)
#> the input data set does not have a adm_np_type column (or column set)
#> the input data set does not have a np_date column (or column set)
#> the input data set does not have a days_adm_npswab column (or column set)
#> the input data set does not have a np_swab_2 column (or column set)
#> the input data set does not have a adm_np_type_2 column (or column set)
#> the input data set does not have a np_date_2 column (or column set)
#> the input data set does not have a np_swab_3 column (or column set)
#> the input data set does not have a adm_np_type_3 column (or column set)
#> the input data set does not have a np_date_3 column (or column set)
#> the input data set does not have a saliva column (or column set)
#> the input data set does not have a saliva_date column (or column set)
#> the input data set does not have a days_adm_saliva column (or column set)
#> the input data set does not have a sputum column (or column set)
#> the input data set does not have a sputum_date column (or column set)
#> the input data set does not have a days_adm_sputum column (or column set)
#> the input data set does not have a pt_ad_ur column (or column set)
#> the input data set does not have a adm_ur_taken column (or column set)
#> the input data set does not have a nourine_reason column (or column set)
#> the input data set does not have a adm_np_type_2 column (or column set)
#> the input data set does not have a adm_ur_date column (or column set)
#> the input data set does not have a days_adm_urine column (or column set)
#> the input data set does not have a adm_serum_tak column (or column set)
#> the input data set does not have a adm_seru_date column (or column set)
#> the input data set does not have a days_adm_serum column (or column set)
#> mapping .contraindication to vaccination.covid_vaccine_contraindicated
#> mapping .covid19_vax to vaccination.covid_vaccination
#> the input data set does not have a covidvax_date column (or column set)
#> the input data set does not have a covidvax_dose_2 column (or column set)
#> the input data set does not have a covidvax_dose_3 column (or column set)
#> the input data set does not have a covidvax_dose_4 column (or column set)
#> the input data set does not have a covidvax_dose_5 column (or column set)
#> the input data set does not have a covidvax_dose_6 column (or column set)
#> mapping .brand_of_covid19_vaccinati to vaccination.first_dose_brand
#> mapping .covid19vax_brand_2 to vaccination.second_dose_brand
#> mapping .covid19vax_brand_3 to vaccination.third_dose_brand
#> mapping .covid19vax_brand_4 to vaccination.fourth_dose_brand
#> mapping .covid19vax_brand_5 to vaccination.fifth_dose_brand
#> mapping .covid19vax_brand_6 to vaccination.sixth_dose_brand
#> mapping .c19vaxd1_adm to admission.time_since_first_vaccine_dose
#> mapping .c19vaxd2_adm to admission.time_since_second_vaccine_dose
#> mapping .c19vaxd3_adm to admission.time_since_third_vaccine_dose
#> mapping .c19vaxd4_adm to admission.time_since_fourth_vaccine_dose
#> mapping .c19vax5_adm to admission.time_since_fifth_vaccine_dose
#> mapping .c19vax6_adm to admission.time_since_sixth_vaccine_dose
#> the input data set does not have a flu_date column (or column set)
#> mapping .fluvax_adm_d1 to admission.time_since_last_flu_vaccine_dose
#> the input data set does not have a ppv23_date column (or column set)
#> mapping .ppv23vax_adm_d to admission.time_since_last_pneumococcal_vaccine_dose
#> the input data set does not have a c19_variant column (or column set)
#> mapping .year to admission.year
#> mapping .study_week to admission.study_week
#> mapping .admission_date to admission.date
#> mapping .hospital to admin.hospital
#> the input data set does not have a adm_diagnosis column (or column set)
#> mapping .ics to admission.on_inhaled_corticosteroids
#> mapping .immsup to admission.on_immunosuppression
#> mapping .psi_class to admission.pneumonia_severity_index_class
#> mapping .crb_test_mai to admission.curb_65_severity_score
#> mapping .news_2_total to admission.news2_score
#> mapping .pulse_ox to admission.oximetry
#> mapping .rr to admission.respiratory_rate
#> mapping .fio2 to admission.max_oxygen
#> mapping .systolic_bp to admission.systolic_bp
#> mapping .diastolic_bp to admission.diastolic_bp
#> mapping .hr to admission.heart_rate
#> mapping .temperature to admission.temperature
#> mapping .symptom_days_preadmit to admission.duration_symptoms
#> mapping .previous_infection to admission.previous_covid_infection
#> the input data set does not have a previousinfection_date column (or column set)
#> mapping .c19d_preadm to admission.time_since_covid_diagnosis
#> mapping .rockwood to admission.rockwood_score
#> mapping .cci_total_score to admission.charlson_comorbidity_index
#> the input data set does not have a height column (or column set)
#> the input data set does not have a weight column (or column set)
#> the input data set does not have a bmi column (or column set)
#> the input data set does not have a first_radio column (or column set)
#> the input data set does not have a c19_peep column (or column set)
#> the input data set does not have a c19_hospadm column (or column set)
#> the input data set does not have a c17_high column (or column set)
#> the input data set does not have a c19icuon column (or column set)
#> the input data set does not have a c19_icudays column (or column set)
#> the input data set does not have a c19_vent column (or column set)
#> the input data set does not have a c19_ox column (or column set)
#> the input data set does not have a c19_ionotropes column (or column set)
#> the input data set does not have a c19_complication column (or column set)
#> the input data set does not have a c19_death7d column (or column set)
#> the input data set does not have a c19_meds column (or column set)
#> mapping .hospital_length_of_stay to outcome.length_of_stay
#> mapping .survival_days to outcome.survival_duration
#> the input data set does not have a ip_death column (or column set)
#> the input data set does not have a days_in_icu column (or column set)
#> the input data set does not have a did_the_patient_have_respi column (or column set)
#> the input data set does not have a number_of_days_of_ventilat column (or column set)
#> the input data set does not have a ett_days column (or column set)
#> the input data set does not have a renal_replacement_therapy column (or column set)
#> the input data set does not have a complications column (or column set)
#> the input data set does not have a ventilatory_support column (or column set)
#> the input data set does not have a did_the_patient_receive_ec column (or column set)
#> the input data set does not have a inotropic_support_required column (or column set)
#> mapping .lrtd_30d_outcome to outcome.functional_status
#> mapping .survive_1yr to outcome.one_year_survival
#> mapping .survival_1yr_days to outcome.one_year_survival_duration
#> mapping .yr_survival_complete to outcome.one_year_survival_complete
#> mapping .fever2 to symptom.abnormal_temperature
#> mapping .pleurtic_cp to symptom.pleuritic_chest_pain
#> mapping .cough2 to symptom.cough
#> mapping .sput_prod to symptom.productive_sputum
#> mapping .dyspnoea to symptom.dyspnoea
#> mapping .tachypnoea2 to symptom.tachypnoea
#> mapping .confusion to symptom.confusion
#> the input data set does not have a anosmia column (or column set)
#> the input data set does not have a ageusia column (or column set)
#> the input data set does not have a dysgeusia column (or column set)
#> mapping .fever to symptom.fever
#> mapping .hypothermia to symptom.hypothermia
#> mapping .chills to symptom.chills
#> mapping .headache to symptom.headache
#> the input data set does not have a malaise column (or column set)
#> mapping .wheeze to symptom.wheeze
#> the input data set does not have a myalgia column (or column set)
#> the input data set does not have a worse_confusion column (or column set)
#> the input data set does not have a general_det column (or column set)
#> mapping .ox_on_admission to symptom.oxygen_required_on_admission
#> mapping .resp_disease___1 to comorbid.no_resp_dx
#> mapping .resp_disease___2 to comorbid.copd
#> mapping .resp_disease___3 to comorbid.asthma
#> mapping .resp_disease___4 to comorbid.resp_other
#> mapping .other_respiratory_disease___1 to comorbid.bronchiectasis
#> mapping .other_respiratory_disease___2 to comorbid.interstitial_lung_dx
#> mapping .other_respiratory_disease___3 to comorbid.cystic_fibrosis
#> mapping .other_respiratory_disease___4 to comorbid.pulmonary_hypertension
#> mapping .other_respiratory_disease___5 to comorbid.chronic_pleural_dx
#> mapping .other_respiratory_disease___6 to comorbid.other_chronic_resp_dx
#> mapping .chd___1 to comorbid.no_heart_dx
#> mapping .chd___2 to comorbid.ccf
#> mapping .chd___3 to comorbid.ihd
#> mapping .chd___4 to comorbid.hypertension
#> mapping .chd___5 to comorbid.other_heart_dx
#> mapping .mi to comorbid.previous_mi
#> mapping .other_chd___1 to comorbid.congenital_heart_dx
#> mapping .other_chd___2 to comorbid.af
#> mapping .other_chd___3 to comorbid.other_arrythmia
#> mapping .other_chd___4 to comorbid.pacemaker
#> mapping .other_chd___5 to comorbid.valvular_heart_dx
#> mapping .other_chd___6 to comorbid.other_other_heart_dx
#> mapping .diabetes to comorbid.diabetes
#> mapping .dm_meds to comorbid.diabetes_medications
#> mapping .neurological_disease___1 to comorbid.neuro_other
#> mapping .neurological_disease___2 to comorbid.cva
#> mapping .neurological_disease___3 to comorbid.tia
#> mapping .neurological_disease___4 to comorbid.hemiplegia
#> mapping .neurological_disease___5 to comorbid.paraplegia
#> mapping .neurological_disease___6 to comorbid.no_neuro_dx
#> mapping .dementia___1 to comorbid.no_dementia
#> mapping .dementia___2 to comorbid.dementia
#> mapping .dementia___3 to comorbid.cognitive_impairment
#> mapping .cancer to comorbid.solid_cancer
#> mapping .haem_malig___1 to comorbid.no_haemotological_cancer
#> mapping .haem_malig___2 to comorbid.leukaemia
#> mapping .haem_malig___3 to comorbid.lymphoma
#> mapping .ckd to comorbid.ckd
#> mapping .liver_disease to comorbid.liver_disease
#> mapping .gastric_ulcers to comorbid.gastric_ulcers
#> mapping .pvd to comorbid.periph_vasc_dx
#> mapping .ctd to comorbid.connective_tissue_dx
#> mapping .immunodeficiency to comorbid.immunodeficiency
#> mapping .other_pn_disease to comorbid.other_pneumococcal_risks
#> mapping .transplant to comorbid.transplant_recipient
#> mapping .pregnancy to comorbid.pregnancy
#> mapping .hiv___1 to comorbid.no_HIV
#> mapping .hiv___2 to comorbid.HIV
#> mapping .hiv___3 to comorbid.AIDS
#> mapping .final_soc_lrtd_diagnosis___1 to diagnosis.SOC_CAP_radiologically_confirmed
#> mapping .final_soc_lrtd_diagnosis___2 to diagnosis.SOC_CAP_clinically_confirmed
#> mapping .final_soc_lrtd_diagnosis___3 to diagnosis.SOC_CAP_no_radiology
#> mapping .final_soc_lrtd_diagnosis___4 to diagnosis.SOC_LRTI
#> mapping .final_soc_lrtd_diagnosis___5 to diagnosis.SOC_Empyema_or_abscess
#> mapping .final_soc_lrtd_diagnosis___6 to diagnosis.SOC_exacerbation_COPD
#> mapping .final_soc_lrtd_diagnosis___7 to diagnosis.SOC_exacerbation_non_COPD
#> mapping .final_soc_lrtd_diagnosis___8 to diagnosis.SOC_congestive_heart_failure
#> mapping .final_soc_lrtd_diagnosis___9 to diagnosis.SOC_non_infectious_process
#> mapping .final_soc_lrtd_diagnosis___10 to diagnosis.SOC_non_LRTI
#> mapping .covid_19_diagnosis to diagnosis.covid_19_diagnosis
#> mapping .ppv23 to vaccination.pneumovax
#> mapping .flu_vaccine to vaccination.influenza_vaccination
#> mapping .abx_14d_prior to admission.pre_admission_antibiotics_given
#> the input data set does not have a antiplatelets column (or column set)
#> the input data set does not have a anticoagulants column (or column set)
#> the input data set does not have a statins column (or column set)
#> the input data set does not have a hypertensives column (or column set)
#> mapping .ed_hours to outcome.emergency_dept_length_of_stay
#> mapping .ed_reattendance to admin.ed_episodes_in_last_30_days
#> mapping .hosp_adm_30d to outcome.admitted_within_30_days
#> mapping .hosp_adm_7d to outcome.admitted_within_7_days
#> mapping .home_d_1 to outcome.days_since_last_ed_episode
#> mapping .radiology_result_1___2 to radio.consistent_with_pneumonia_1
#> mapping .radiology_result_2___2 to radio.consistent_with_pneumonia_2
#> Mapped 180 columns
#> Did not map 558 columns
aug = avoncap::augment_data(norm)
#> Augmenting data using: augment.avoncap_export.ed
#> caching item: ~/.cache/avoncap/augment-4c0c0c577381837fb7b8ee36b440288a-ea6d42c46140aa8048d730d9a7451335.rda
#> Created admission.cxr_pneumonia, admission.admission_route, outcome.admitted_to_hospital, outcome.death_within_30_days using: radio.consistent_with_pneumonia_1, radio.consistent_with_pneumonia_2, outcome.functional_status, outcome.survival_duration
#> Created demog.age_category, demog.age_eligible, admission.cci_category, admission.cci_category_alternate, admission.rockwood_category, admission.curb_65_category using: demog.age, admission.charlson_comorbidity_index, admission.rockwood_score, admission.curb_65_severity_score
#> Created admin.patient_identifier using: admin.first_record_number, admin.record_number
#> Created admission.episode, admission.interval using: admission.date
#> Skipping function due to error: In argument: `admin.linked_gp_practice = ~...`.
#> Created admin.catchment_status using: admin.gp_practice
#> Created comorbid.diabetes_type, comorbid.solid_cancer_present, comorbid.haemotological_cancer_present, comorbid.any_cancer_present, comorbid.any_chronic_lung_disease, comorbid.any_chronic_heart_disease, comorbid.cva_or_tia, comorbid.any_immune_compromise using: comorbid.diabetes, comorbid.solid_cancer, comorbid.leukaemia, comorbid.lymphoma, comorbid.no_haemotological_cancer, comorbid.asthma, comorbid.bronchiectasis, comorbid.chronic_pleural_dx, comorbid.copd, comorbid.interstitial_lung_dx, comorbid.cystic_fibrosis, comorbid.other_chronic_resp_dx, comorbid.pulmonary_hypertension, comorbid.ccf, comorbid.ihd, comorbid.previous_mi, comorbid.congenital_heart_dx, comorbid.hypertension, comorbid.af, comorbid.other_arrythmia, comorbid.other_heart_dx, comorbid.other_other_heart_dx, comorbid.cva, comorbid.tia, comorbid.immunodeficiency, admission.on_immunosuppression
#> Skipping function due to error: In argument: `admission.initial_presentation_3_class = `%>%`(...)`.
#> Skipping function due to error: In argument: `admission.hospital_acquired = `%>%`(...)`.
#> Created admission.covid_pcr_result, admission.is_covid using: diagnosis.covid_19_diagnosis
#> Created diagnosis.pneumonia, diagnosis.LRTI, diagnosis.exacerbation_of_chronic_respiratory_disease, diagnosis.heart_failure using: diagnosis.SOC_CAP_clinically_confirmed, diagnosis.SOC_CAP_radiologically_confirmed, diagnosis.SOC_CAP_no_radiology, diagnosis.SOC_Empyema_or_abscess, diagnosis.SOC_LRTI, diagnosis.SOC_exacerbation_COPD, diagnosis.SOC_exacerbation_non_COPD, diagnosis.SOC_congestive_heart_failure
#> Created admission.infective_cause using: diagnosis.SOC_non_infectious_process, diagnosis.SOC_non_LRTI
#> Created admission.category, admission.presentation_3_class using:
#> Created diagnosis.infection_context using: admission.date
#> Skipping function due to error: In argument: `genomic.variant_inferred = `%>%`(...)`.
#> Created symptom_onset.date_of_symptoms, symptom_onset.time_of_symptoms_since_first_vaccine_dose, symptom_onset.time_of_symptoms_since_second_vaccine_dose, symptom_onset.time_of_symptoms_since_third_vaccine_dose, symptom_onset.time_of_symptoms_since_fourth_vaccine_dose, vaccination.dose_interval, vaccination.booster_interval, vaccination.second_booster_interval using: admission.date, admission.duration_symptoms, admission.time_since_first_vaccine_dose, admission.time_since_second_vaccine_dose, admission.time_since_third_vaccine_dose, admission.time_since_fourth_vaccine_dose
#> Created vaccination.protection using: vaccination.covid_vaccination, admission.time_since_fourth_vaccine_dose, admission.duration_symptoms, admission.time_since_third_vaccine_dose, admission.time_since_second_vaccine_dose, admission.time_since_first_vaccine_dose, admission.previous_covid_infection
#> Created vaccination.vaccination using: vaccination.covid_vaccination, admission.time_since_sixth_vaccine_dose, admission.duration_symptoms, admission.time_since_fifth_vaccine_dose, admission.time_since_fourth_vaccine_dose, admission.time_since_third_vaccine_dose, admission.time_since_second_vaccine_dose, admission.time_since_first_vaccine_dose
#> Created vaccination.brand_combination using: vaccination.first_dose_brand, vaccination.second_dose_brand, vaccination.third_dose_brand
#> Created pneumo.presentation_CAP, pneumo.presentation_RAD, pneumo.presentation_class using: diagnosis.SOC_CAP_radiologically_confirmed
#> Created admission.pneumococcal_high_risk using: demog.age, comorbid.other_pneumococcal_risks, comorbid.copd, comorbid.interstitial_lung_dx, comorbid.cystic_fibrosis, comorbid.hypertension, comorbid.ccf, comorbid.ihd, comorbid.ckd, comorbid.liver_disease, comorbid.diabetes, comorbid.immunodeficiency, comorbid.asthma, admission.on_immunosuppression
#> Created admission.pneumococcal_risk_classification using: comorbid.cva, comorbid.immunodeficiency, comorbid.leukaemia, comorbid.lymphoma, comorbid.no_haemotological_cancer, admission.on_immunosuppression, comorbid.transplant_recipient, comorbid.ckd, comorbid.HIV, comorbid.solid_cancer, demog.care_home_resident, demog.smoker, demog.age, demog.alcohol_abuse, comorbid.diabetes, comorbid.diabetes_medications, comorbid.paraplegia, comorbid.copd, comorbid.interstitial_lung_dx, comorbid.cystic_fibrosis, comorbid.asthma, comorbid.liver_disease, comorbid.ccf, comorbid.ihd, comorbid.other_pneumococcal_risks
#> Skipping function due to error: In argument: `day_7.WHO_clinical_progression = `%>%`(...)`.
#> Skipping function due to error: In argument: `outcome.icu_admission = `%>%`(...)`.
#> Created survival.length_of_stay, survival.uncensored_time_to_death, survival.last_observed_event using: admin.enrollment_date, outcome.length_of_stay, outcome.survival_duration, outcome.one_year_survival_duration, admission.date
#> Created survival.length_of_stay_category, survival.30_day_death_time, survival.30_day_death_event, survival.1_yr_death_time, survival.1_yr_death_event, survival.30_day_discharge_time, survival.30_day_discharge_event using:
#> Created using:
#> Created admission.pre_admission_antivirals_given using: admission.pre_admission_antiviral