if (!rlang::is_installed("avoncap")) devtools::load_all()
# The data input directory on my development machine:
options("avoncap.input" = "~/Data/avoncap/")
# library(avoncap)
devtools::load_all()
#> ℹ Loading avoncaploading and normalising the central database
rawData = avoncap::load_data("avoncap-export","central", merge=FALSE)
#> caching item: ~/.cache/avoncap/data-6c0a3f301ee14020e3907a7472c55225-ceee88d5e0d35f4db6c42b5de999dc9e.rda
#> INCONSISTENT COLUMN(S) IN FILES: adm_ur_date_2;under5;eos;pmn;sars_cov2_antigen;weight;height;rsva_np;h5n1_np_conf;h7n9_np_conf;pn_st_2;pn_st_4;bnt162_date;bnt162b_batch;bnt162b_place;date_first_vax;date_second_vax;date_third_vax;date_fourth_vax;bnt162b_specify;bnt162b_further
#> NOT MERGING FILES
rawData2 = avoncap::load_data("avoncap-export","central", merge=TRUE)
#> using cached item: ~/.cache/avoncap/data-6c0a3f301ee14020e3907a7472c55225-fdcc9ea0386806423728b2d35efcb66f.rda
# devtools::load_all()
rawData3 = rawData2 %>% avoncap::validate_data()
#> validate data using: validate.avoncap_export.central
#> non-finite value in consented in 14 rows
#> non-finite value in ppc in 14 rows
#> non-finite value in include_patient in 14 rows
#> non-finite value in hosp in 21 rows
#> missing value in systolic_bp in 1 rows
#> missing value in diastolic_bp in 1 rows
#> missing value in imd in 33 rows
#> missing columns: ethnicity in 1 rows
#> non-finite value in care_home in 1 rows
#> non-finite value in ckd in 2 rows
#> non-finite value in liver_disease in 3 rows
#> non-finite value in diabetes in 2 rows
#> non-finite value in gastric_ulcers in 3 rows
#> non-finite value in pvd in 2 rows
#> non-finite value in ctd in 2 rows
#> non-finite value in immunodeficiency in 2 rows
#> non-finite value in other_pn_disease in 4 rows
#> non-finite value in cancer in 1 rows
#> non-finite value in transplant in 2 rows
#> non-finite value in lrtd_30d_outcome in 1 rows
#> non-finite value in week_number in 13 rows
#> non-finite value in ventilatory_support in 1 rows
#> both pneumonia and NP-LRTI in final SOC dx in 3 rows
#> 30 day and 1 yr survival duration different in 1 rows
#> length of stay > 30 day survival duration in 6 rows
#> length of stay > 1 yr survival duration in 13 rows
#> non-finite value in gp_practice_drop_down in 17 rows
#> non-finite value in dm_meds in 56 rows
#> non-finite value in current in 4 rows
#> using cached item: ~/.cache/avoncap/data-6c0a3f301ee14020e3907a7472c55225-7498859e4eaf9f364dc024b6ee4039c2.rda
normData2 = rawData3 %>% avoncap::normalise_data()
#> Normalising data using: normalise.avoncap_export.central
#> using cached item: ~/.cache/avoncap/data-6c0a3f301ee14020e3907a7472c55225-767899bd2d292ad780aeb94b72046017.rda
#> using cached item: ~/.cache/avoncap/data-6c0a3f301ee14020e3907a7472c55225-a8d3a7969f846ac52271754d8f1cb72e.rda
#> Some columns expected in the mappings were not present: nhs_number, np_swab_3, adm_np_type_3, covidvax_date, covidvax_dose_2, covidvax_dose_3, covidvax_dose_4, covidvax_dose_5, covidvax_dose_6, flu_date, ppv23_date, previousinfection_date
#> caching item: ~/.cache/avoncap/norm-0ef4812a2d1bc751062531c384a2b89e-868f1f3a8c39505c5f35a5cee23a61fb.rda
#> mapping .consented to admin.consented
#> mapping .ppc to admin.pp_consented
#> mapping .withdrawal to admin.withdrawal
#> mapping .consent_urine to admin.consent_for_urine
#> mapping .consent_blood to admin.consent_for_blood
#> mapping .consent_resp_samples1 to admin.consent_for_respiratory_samples
#> mapping .record_number to admin.record_number
#> mapping .what_was_the_first_surveil to admin.first_record_number
#> mapping .ac_study_number to admin.consented_record_number
#> 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
#> mapping .admission_type to admission.admission_route
#> mapping .study_year to admin.study_year
#> mapping .file to admin.data_file
#> mapping .week_number to admin.week_number
#> mapping .c19_diagnosis to diagnosis.standard_of_care_COVID_diagnosis
#> mapping .clinical_radio_diagnosis to diagnosis.clinical_or_radiological_LRTI_or_pneumonia
#> mapping .c19_adm_swab to diagnosis.admission_swab
#> mapping .c19_test_type to diagnosis.test_type
#> mapping .qualifying_symptoms_signs to diagnosis.qualifying_symptoms_signs
#> mapping .cc_critieria to diagnosis.meets_case_control_criteria
#> mapping .cc_pos_date to diagnosis.first_COVID_positive_swab_date
#> mapping .gender to demog.gender
#> mapping .age_at_admission to demog.age
#> mapping .age_march to demog.age_in_march_2021
#> 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
#> mapping .ethnicity2 to demog.ethnicity
#> mapping .care_home to demog.care_home_resident
#> mapping .hapcovid_screening to admission.non_lrtd_hospital_acquired_covid
#> mapping .hospital_covid to admission.hospital_acquired_covid
#> 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
#> mapping .np_swab to admin.np_swab_taken_1
#> mapping .adm_np_type to admin.np_swab_site_1
#> mapping .np_date to admin.np_swab_date_1
#> mapping .days_adm_npswab to admin.np_swab_day_since_admission
#> mapping .np_swab_2 to admin.np_swab_taken_2
#> mapping .adm_np_type_2 to admin.np_swab_site_2
#> mapping .np_date_2 to admin.np_swab_date_2
#> 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)
#> mapping .np_date_3 to admin.np_swab_date_3
#> mapping .saliva to admin.saliva_sample_taken
#> mapping .saliva_date to admin.saliva_sample_date
#> mapping .days_adm_saliva to admin.saliva_sample_day_since_admission
#> mapping .sputum to admin.sputum_sample_taken
#> mapping .sputum_date to admin.sputum_sample_date
#> mapping .days_adm_sputum to admin.sputum_sample_day_since_admission
#> mapping .pt_ad_ur to admin.urine_sample_needed
#> mapping .adm_ur_taken to admin.urine_sample_taken
#> mapping .nourine_reason to admin.urine_sample_failure_reason
#> the input data set does not have a adm_np_type_2 column (or column set)
#> mapping .adm_ur_date to admin.urine_sample_date
#> mapping .days_adm_urine to admin.urine_sample_day_since_admission
#> mapping .adm_serum_tak to admin.serum_sample_taken
#> mapping .adm_seru_date to admin.serum_sample_date
#> mapping .days_adm_serum to admin.serum_sample_day_since_admission
#> 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
#> mapping .c19_variant to genomic.variant
#> mapping .year to admission.year
#> mapping .study_week to admission.study_week
#> mapping .admission_date to admission.date
#> mapping .hospital to admin.hospital
#> mapping .adm_diagnosis___1 to admission.presumed_CAP_radiologically_confirmed
#> mapping .adm_diagnosis___2 to admission.presumed_CAP_clinically_confirmed
#> mapping .adm_diagnosis___3 to admission.presumed_CAP_no_radiology
#> mapping .adm_diagnosis___4 to admission.presumed_LRTI
#> mapping .adm_diagnosis___5 to admission.presumed_Empyema_or_abscess
#> mapping .adm_diagnosis___6 to admission.presumed_exacerbation_COPD
#> mapping .adm_diagnosis___7 to admission.presumed_exacerbation_non_COPD
#> mapping .adm_diagnosis___8 to admission.presumed_congestive_heart_failure
#> mapping .adm_diagnosis___9 to admission.presumed_non_infectious_process
#> mapping .adm_diagnosis___10 to admission.presumed_non_LRTI
#> 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
#> mapping .height to admission.height
#> mapping .weight to admission.weight
#> mapping .bmi to admission.BMI
#> mapping .first_radio___1 to admission.cxr_normal
#> mapping .first_radio___2 to admission.cxr_pneumonia
#> mapping .first_radio___3 to admission.cxr_heart_failure
#> mapping .first_radio___4 to admission.cxr_pleural_effusion
#> mapping .first_radio___5 to admission.cxr_covid_changes
#> mapping .first_radio___6 to admission.cxr_other
#> mapping .c19_peep to day_7.max_peep
#> mapping .c19_hospadm to day_7.length_of_stay
#> mapping .c17_high to day_7.max_care_level
#> mapping .c19icuon to day_7.still_on_icu
#> mapping .c19_icudays to day_7.icu_length_of_stay
#> mapping .c19_vent to day_7.max_ventilation_level
#> mapping .c19_ox to day_7.max_o2_level
#> mapping .c19_ionotropes to day_7.ionotropes_needed
#> mapping .c19_complication___1 to day_7.PE
#> mapping .c19_complication___2 to day_7.DVT
#> mapping .c19_complication___3 to day_7.ARF
#> mapping .c19_complication___4 to day_7.NSTEMI
#> mapping .c19_complication___5 to day_7.STEMI
#> mapping .c19_complication___6 to day_7.cardiac_failure
#> mapping .c19_complication___7 to day_7.new_AF
#> mapping .c19_complication___8 to day_7.new_other_arrythmia
#> mapping .c19_complication___9 to day_7.inpatient_fall
#> mapping .c19_complication___10 to day_7.other_complication
#> mapping .c19_complication___11 to day_7.no_complication
#> mapping .c19_death7d to day_7.death
#> mapping .c19_meds___1 to treatment.dexamethasone
#> mapping .c19_meds___2 to treatment.remdesevir
#> mapping .c19_meds___3 to treatment.tocilizumab
#> mapping .c19_meds___4 to treatment.sarilumab
#> mapping .c19_meds___5 to treatment.in_drug_trial
#> mapping .c19_meds___6 to treatment.no_drug_treatment
#> mapping .c19_meds___7 to treatment.sotrovimab
#> mapping .hospital_length_of_stay to outcome.length_of_stay
#> mapping .survival_days to outcome.survival_duration
#> mapping .ip_death to outcome.inpatient_death
#> mapping .days_in_icu to outcome.icu_duration
#> mapping .did_the_patient_have_respi to outcome.respiratory_support_needed
#> mapping .number_of_days_of_ventilat to outcome.ventilator_duration
#> mapping .ett_days to outcome.endotracheal_tube_duration
#> mapping .renal_replacement_therapy to outcome.renal_support_duration
#> mapping .complications___1 to outcome.acute_renal_failure
#> mapping .complications___2 to outcome.liver_dysfunction
#> mapping .complications___3 to outcome.hospital_acquired_infection
#> mapping .complications___4 to outcome.acute_respiratory_distress_syndrome
#> mapping .complications___5 to outcome.NSTEMI
#> mapping .complications___6 to outcome.STEMI
#> mapping .complications___7 to outcome.new_AF
#> mapping .complications___8 to outcome.new_other_arrhthmia
#> mapping .complications___9 to outcome.stroke
#> mapping .complications___10 to outcome.DVT
#> mapping .complications___11 to outcome.PE
#> mapping .complications___12 to outcome.heart_failure
#> mapping .complications___13 to outcome.fall_in_hospital
#> mapping .complications___14 to outcome.reduced_mobility
#> mapping .complications___15 to outcome.increasing_care_requirement
#> mapping .complications___16 to outcome.no_complications
#> mapping .ventilatory_support to outcome.highest_level_ventilatory_support
#> mapping .did_the_patient_receive_ec to outcome.received_ecmo
#> mapping .inotropic_support_required to outcome.received_ionotropes
#> 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
#> mapping .anosmia to symptom.anosmia
#> mapping .ageusia to symptom.ageusia
#> mapping .dysgeusia to symptom.dysguesia
#> mapping .fever to symptom.fever
#> mapping .hypothermia to symptom.hypothermia
#> mapping .chills to symptom.chills
#> mapping .headache to symptom.headache
#> mapping .malaise to symptom.malaise
#> mapping .wheeze to symptom.wheeze
#> mapping .myalgia to symptom.myalgia
#> mapping .worse_confusion to symptom.worsening_confusion
#> mapping .general_det to symptom.general_deterioration
#> 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
#> mapping .antiplatelets to admission.antiplatelet_therapy
#> mapping .anticoagulants to admission.anticoagulant_therapy
#> mapping .statins to admission.cholesterol_lowering_therapy
#> mapping .hypertensives to admission.antihypertensive_therapy
#> Mapped 299 columns
#> Did not map 3463 columns
failures = rawData3 %>% avoncap::write_issues("~/avoncap-issues")
tmp = failures %>%
filter(.error_type %in% c("none checked in checkbox","missing value")) %>%
inner_join(rawData2, by="record_number", suffix=c("",".raw")) %>%
group_by(.variable) %>%
filter(
!is.na(enrollment_date) &
!is.na(hosp)
) %>%
filter(
n()>20
)
if (nrow(tmp) > 0) {
ggplot(tmp, aes(x=enrollment_date, fill=as.factor(hosp)))+
geom_histogram(binwidth = 7)+
scale_x_date(date_breaks = "1 month", date_labels = "%m-%Y")+
theme(axis.text.x.bottom = element_text(angle = 90, vjust=0.5, hjust=1))+
facet_wrap(~.variable,scales = "free_y")
} else {
message("No systematically missing values in checked items")
}
# normData2 = rawData2 %>%
# avoncap::normalise_data(.nocache = TRUE)
augData2 = normData2 %>% avoncap::augment_data()
#> Augmenting data using: augment.avoncap_export.central
#> caching item: ~/.cache/avoncap/augment-4c0c0c577381837fb7b8ee36b440288a-fe06990bee8ad645fd3f23a321feec45.rda
#> Created outcome.admitted_to_hospital using:
#> 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
#> Created admission.initial_presentation_3_class using: admission.presumed_CAP_clinically_confirmed, admission.presumed_CAP_radiologically_confirmed, admission.presumed_CAP_no_radiology, admission.presumed_Empyema_or_abscess, admission.presumed_LRTI, admission.presumed_exacerbation_COPD, admission.presumed_exacerbation_non_COPD, admission.presumed_congestive_heart_failure
#> Created admission.hospital_acquired, admission.days_before_enrollment using: admission.hospital_acquired_covid, admission.non_lrtd_hospital_acquired_covid, admission.date, admin.enrollment_date
#> Created admission.covid_pcr_result, admission.is_covid using: diagnosis.covid_19_diagnosis, diagnosis.admission_swab, diagnosis.test_type
#> 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, admission.cxr_pneumonia, 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.hospital_acquired_covid, admission.non_lrtd_hospital_acquired_covid, diagnosis.first_COVID_positive_swab_date, admission.date
#> Created genomic.variant_inferred using: genomic.variant, admission.date
#> 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
#> Created day_7.WHO_clinical_progression, outcome.WHO_clinical_progression using: day_7.death, day_7.max_ventilation_level, day_7.ionotropes_needed, day_7.max_o2_level, outcome.survival_duration, outcome.functional_status, outcome.highest_level_ventilatory_support, outcome.received_ionotropes, outcome.respiratory_support_needed
#> Created outcome.icu_admission, outcome.death_within_30_days, outcome.death_within_1_year, outcome.death_during_follow_up using: outcome.icu_duration, day_7.death, outcome.survival_duration, outcome.one_year_survival_duration, outcome.one_year_survival_complete, outcome.inpatient_death, outcome.functional_status
#> 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 survival.length_of_stay_quintile using:
#> Created day_7.max_o2_gt_28, day_7.max_o2_gt_35, day_7.max_o2_gt_50, day_7.WHO_score_gt_6, day_7.WHO_score_gt_5, day_7.los_gt_3, day_7.los_gt_5, day_7.los_gt_7 using: day_7.max_o2_level, day_7.length_of_stay, outcome.survival_duration
#> Created using:
#> Created admission.pre_admission_antivirals_given using: admission.pre_admission_antiviral
avoncap::find_new_field_names(normData2, "adm_diagnosis")
#> adm_diagnosis___1
#> "admission.presumed_CAP_radiologically_confirmed"
#> adm_diagnosis___2
#> "admission.presumed_CAP_clinically_confirmed"
#> adm_diagnosis___3
#> "admission.presumed_CAP_no_radiology"
#> adm_diagnosis___4
#> "admission.presumed_LRTI"
#> adm_diagnosis___5
#> "admission.presumed_Empyema_or_abscess"
#> adm_diagnosis___6
#> "admission.presumed_exacerbation_COPD"
#> adm_diagnosis___7
#> "admission.presumed_exacerbation_non_COPD"
#> adm_diagnosis___8
#> "admission.presumed_congestive_heart_failure"
#> adm_diagnosis___9
#> "admission.presumed_non_infectious_process"
#> adm_diagnosis___10
#> "admission.presumed_non_LRTI"