PHOSP Variables Added During Cleaning - isaric4c/wiki GitHub Wiki

Variable / Field Name Description Field Type Field Label Choices or Calculations
tier Patient tier, defined by a 3 or 12 month visit numeric !is.na(crf3b_visit) = 2  ; is.na(crf3b_visit) = 1
age_admission_factor Age grouped into factors factor Age at admission (y) <30  ; 30-39  ; 40-49  ; 50-59  ; 60-69  ; 70-79
crf1b_eth_5levels Ethnicity grouped into character factors factor Ethnicity White  ; Black  ; Other  ; South Asian  ; Mixed
crf1b_eth_pft Ethnicity grouped into numeric factors factor Ethnicity 1, White  ; 2, Black  ; 3, Other  ; 4,South Asian  ; 5, Mixed
crf1a_com_mer_diab_yn Diabetes yes/no yesno Diabetes if_else(crf1a_com_mer_diab == "Type 1"
crf1a_com_mh_stm_yn Malignancy yes/no yesno Malignancy if_else(crf1a_com_mh_stm == "Localised"
no_comorbid Number of comorbidities numeric Number of comorbidities Sums "yes" for the following variables:crf1a_com_card_mi, crf1a_com_card_ihd, crf1a_com_card_af, crf1a_com_card_ht, crf1a_com_card_chf, crf1a_com_card_chd, crf1a_com_card_vhd, crf1a_com_card_pid, crf1a_com_card_pvd, crf1a_com_card_hcd, crf1a_com_neuspy_dem, crf1a_com_neuspy_da, crf1a_com_neuspy_chron, crf1a_com_neuspy_pam, crf1a_com_neuspy_ptm, crf1a_com_res_copd, crf1a_com_res_ast, crf1a_com_res_ild_yn, crf1a_com_res_bron, crf1a_com_res_osa, crf1a_com_res_ohs, crf1a_com_res_pe, crf1a_com_rheu_ctd, crf1a_com_rheu_ra, crf1a_com_rheu_ost, crf1a_com_gast_pud, crf1a_com_gast_gord, crf1a_com_gast_ibd, crf1a_com_gast_ibs, crf1a_com_mer_hypot, crf1a_com_mer_hypert, crf1a_com_mer_ckd_yn, crf1a_com_leuk_yn, crf1a_com_lymp_yn, crf1a_com_id_aids, crf1a_com_id_hiv, crf1a_com_id_other_yn
no_comorbid_3levels Number of comorbidies, grouped into three character factors factor Number of comorbidities (factor) Sum threshold from no_comorbid - No comorbidity ; 1 comorbidity ; 2+ comorbidity
no_comorbid_2levels Number of comorbidies, grouped into two character factors factor Number of comorbidities (factor) Sum threshold from no_comorbid - No comorbidity ; 1 comorbidity
crf1a_symptom_duration Duration of symptoms in days, from date of first symptom onset to date of admission to hospital numeric Symptom duration (days) crf1a_date_adm - crf1a_date_first_symptoms
crf1a_admission_duration Duration of admission in days, from date of admission to date of discharge from hospital numeric Admission duration (days) crf1a_date_dis - crf1a_date_adm
crf1a_com_card Summary variable for cardiovascular comorbidities yesno Cardiovascular "Yes" if any variable starting with "crf1a_com_card" and NOT containing "other" is "Yes", otherwise "No"
crf1a_com_res Summary variable for respiratory comorbidities yesno Respiratory "Yes" if any variable starting with "crf1a_com_res" and NOT containing "other" is "Yes", otherwise "No"
crf1a_com_gast Summary variable for gastrointestinal comorbidities yesno Gastrointestinal "Yes" if any variable starting with "crf1a_com_gast" and NOT containing "other" is "Yes", otherwise "No"
crf1a_com_neupsy Summary variable for neurological and psychiatric comorbidities yesno Neurological and psychiatric "Yes" if any variable starting with "crf1a_com_neupsy" and NOT containing "other" is "Yes", otherwise "No"
crf1a_com_rheu Summary variable for rheumatological comorbidities yesno Rheumatological "Yes" if any variable starting with "crf1a_com_rheu" and NOT containing "other" is "Yes", otherwise "No"
crf1a_com_mer Summary variable for metabolic/endocrine/renal comorbidities yesno Metabolic/endocrine/renal "Yes" if any variable starting with "crf1a_com_mer" and NOT containing "other" is "Yes", otherwise "No"
crf1a_com_mh Summary variable for malignancy comorbidities yesno Malignancy "Yes" if any variable starting with "crf1a_com_mh" and NOT containing "other" is "Yes", otherwise "No"
crf1a_com_id Summary variable for infectious disease comorbidities yesno Infectious disease "Yes" if any variable starting with "crf1a_com_id" and NOT containing "other" is "Yes", otherwise "No"
crf1a_com_diab Special diabetes variable - only includes Type 2 (Type 1 set to 'No') factor Diabetes Takes crf1a_com_mer_diab, recodes "Type 1" as "No", keeps only "Type 2"
crf3a_bmi BMI variable, taken from CRF3a resting weight/height numeric BMI (crf3a_rest_weight / (crf3a_rest_height / 100)^2)
crf3a_bmi_5levels BMI, grouped into five character factors factor BMI (5 levels) Underweight (<18.5) ; Normal weight (18.5 to 24.9) ; Overweight (25 to 29.9) ; Obese (30 to 39.9)
crf3a_bmi_2levels BMI, grouped into two character factors factor BMI (2 levels) BMI < 30 kg/m^2 ; BMI 30+ kg/m^2
eq5d5l_summary_delta Difference in self-reported health pre vs post hospitalisation numeric How good or bad is your health overall? 3 months vs pre-covid eq5d5l_summary - eq5d5l_summary_pre
eq5d5l_summary_delta_change Difference in self-reported health pre vs post hospitalisation, grouped into three character factors factor No change ; Improvement ; Worse
eq5d5l_total_pre EQ5D sum across domains pre hospitalisation numeric EQ5D sum of domains pre-covid sum(eq5d5l_q1_pre:eq5d5l_q5_pre)
eq5d5l_total EQ5D sum across domains post hospitalisation numeric EQ5D sum of domains sum(eq5d5l_q1:eq5d5l_q5)
eq5d5l_total_delta EQ5D change in sum of domains factor EQ5D change in sum of domains No change ; Improvement ; Worse
eq5d5l_q_numeric EQ5D numeric post covid numeric as.numeric(eq5d5l_q1:eq5d5l_q5)
eq5d5l_q_pre_numeric EQ5D numeric pre covid numeric as.numeric(eq5d5l_q1_pre:eq5d5l_q5_pre)
eq5d5l_q_delta EQ5D change numeric eq5d5l_q_numeric - eq5d5l__q_pre_numeric
eq5d5l_q_delta_change EQ5D change, grouped into three character factors factor No change ; Improvement ; Worse
eq5d_population_norm EQSD population norms numeric age_admission < 25 = 0.940 ; age_admission < 35 = 0.927 ; age_admission < 45 = 0.911 ; age_admission < 55 = 0.847 ; age_admission < 65 = 0.799 ; age_admission < 75 = 0.779
eq5d5l_utility_index_pre EQSD utility index pre covid numeric
eq5d5l_utility_index EQSD utility index post covid numeric
eq5d5l_utility_index_delta EQSD utility index change numeric EQ5D utility index (difference)
patient_sq_l_*_numeric Numeric versions of columns starting with patient_sq_l_ numeric
patient_sq_l_t_seeing_delta Change in difficulty seeing, from precovid to today, in numeric format numeric
patient_sq_l_t_hearing_delta Change in difficulty hearing, from precovid to today, in numeric format numeric
patient_sq_l_t_walking_delta Change in difficulty walking, from precovid to today, in numeric format numeric
patient_sq_l_t_remembering_delta Change in difficulty remembering, from precovid to today, in numeric format numeric
patient_sq_l_t_self_care_delta Change in difficulty taking care of yourself, from precovid to today, in numeric format numeric
patient_sq_l_t_communicate_delta Change in difficulty communicating, from precovid to today, in numeric format numeric
patient_sq_l_t_seeing_delta_change Change in difficulty seeing, from precovid to today, grouped into three character factors Factor No change ; Improvement ; Worse
patient_sq_l_t_hearing_delta_change Change in difficulty hearing, from precovid to today, grouped into three character factors Factor No change ; Improvement ; Worse
patient_sq_l_t_walking_delta_change Change in difficulty walking, from precovid to today, grouped into three character factors Factor No change ; Improvement ; Worse
patient_sq_l_t_remembering_delta_change Change in difficulty remembering, from precovid to today, grouped into three character factors Factor No change ; Improvement ; Worse
patient_sq_l_t_self_care_delta_change Change in difficulty taking care of yourself, from precovid to today, grouped into three character factors Factor No change ; Improvement ; Worse
patient_sq_l_t_communicate_delta_change Change in difficulty communicating, from precovid to today, grouped into three character factors Factor No change ; Improvement ; Worse
patient_sq_l_t_disability Summary variable for those with a disability (any of the above patient_sq_l_t variables) Factor WG-SS: any 'Yes - lot of difficulty' "Yes" if any variable starting with "patient_sq_l_t_" is "Yes", otherwise "No"
patient_sq_l_t__new_disability Summary variable for those with a new disability, derived from patient_sq_l_t_*_delta variables Factor WG-SS: new disability "Yes" ; "No" (see 03_prep.R for detailed calculation)
psq_scale_blness_delta Change in breathlessness, within 24h - precovid numeric
psq_scale_fatigue_delta Change in fatigue, within 24h - precovid numeric
psq_scale_cough_delta Change in cough, within 24h - precovid numeric
psq_scale_pain_delta Change in pain, within 24h - precovid numeric
psq_scale_sleep_delta Change in sleep quality, within 24h - precovid numeric
psq_scale_blness_delta _change Change in sleep quality, within 24h - precovid, grouped into three character factors factor No change ; Improvement ; Worse
psq_scale_fatigue_delta _change Change in sleep quality, within 24h - precovid, grouped into three character factors factor No change ; Improvement ; Worse
psq_scale_cough_delta _change Change in sleep quality, within 24h - precovid, grouped into three character factors factor No change ; Improvement ; Worse
psq_scale_pain_delta _change Change in sleep quality, within 24h - precovid, grouped into three character factors factor No change ; Improvement ; Worse
psq_scale_sleep_delta _change Change in sleep quality, within 24h - precovid, grouped into three character factors factor No change ; Improvement ; Worse
gad7_summary_2levels GAD7, grouped into two character factors factor Anxiety (GAD7 >8) "Yes" ; "No"
phq9_summary_2levels PHQ9, grouped into two character factors factor Depression (PHQ-9 >= 10) "Yes" ; "No"
pcl5_summary_2levels PCL5, grouped into two character factors factor PTSD (PCL-5 >= 38) "Yes" ; "No"
dyspnoea12_summary Summary variable for those with dyspnoea numeric Dyspnoea-12 score Sum all columns starting with "dysp"
bpi_severity_summary Summary variable for those with BPI numeric BPI severity Sum all columns between "bpi_worst" and "bpi_rightnow"
bpi_interference_summary Summary variable for those with BPI interference numeric BPI interference Sum all columns between "bpi_past24_general" and "bpi_past24_enjoyment"
sppb_score_summary SPPB, grouped into two character factors factor SPPB (mobility disability <=10 "Yes" ; "No"
rcf_score_numeric Rockwood clinical frailty score, as numeric numeric RCF score (numeric) as.numeric(rcf_score)
rcf_score_summary Rockwood clinical frailty score, grouped into two character factors factor Rockwood clinical frailty score >=5 "Yes" ; "No"
mocal_total_summary Summary MOCA variable factor MOCA <23 If < 23 then "Yes" ; If >= 23 then "No"
crf1a_resp_support_8levels Respiratory support variable, grouped into eight character factors factor Maximal organ support "ECMO" ; "RRT" ; "IMV" ; "HFN" ; "BIPAP" ; "CPAP" ; "O2" ; "No respiratory support"
crf1a_resp_support_4levels Respiratory support variable, grouped into four character factors according to the WHO clinical progression scale factor WHO clinical progression scale "WHO – class 3-4" ; "WHO – class 5" ; "WHO – class 6" ; "WHO – class 7-9"
mocal_total_corrected MOCA adjusted for level of education attainment numeric If crf1b_edu == "None", "Primary School" or "Secondary School", mocal_total + 1 otherwise mocal_total
mocal_total_corrected_summary Summary corrected MOCA variable factor MOCA (corrected) <23 "Yes" ; "No"
bnp_summary Summary variable for BNP/NT-Pro_BNP over threshold factor BNP/NT-Pro-BNP above threshold "Yes" ; "No"
hba1c_summary Summary variable for HbA1c greater than 6.0 factor HbA1C above threshold (>=6.0%) "Yes" ; "No"
egfr_summary Summary variable for eGFR greater than 60 factor eGFR < 60 ml/min/1.73 m2 "Yes" ; "No"
ddi_summary Summary variable for D-dimer greater than 500 factor D-dimer (>= 500 ng/ml) "Yes" ; "No"
crp_summary Summary variable for CRP greater than 10 factor CRP (>10 mg/L) "Yes" ; "No"
social_status_after Variable to evaluate if occupation/working status has changed since COVID factor Occupation/working status since COVID-19 If patient_sq_q == "Same as before" then social_status_before, if patient_sq_q == "Different from before" and social_status_before != patient_sq_q_today then patient_sq_q_today
working_status_change Variable to evaluate if occupation/working status has changed factor If patient_sq_q == "Different from before" then "Yes" ; if patient_sq_q == "Same as before" then "No"
working_less Variable to evaluate if patient is working less factor If working_status_change == "Yes" AND social_status_before == "Working full-time" AND patient_sq_q_today == "Working part-time" THEN "Yes" ; If working_status_change == "Yes" OR working_status_change == "No" THEN "No"
working_before Variable to evaluate if patient was working before COVID factor If social_status_before == "Working full-time" OR "Working part-time" THEN "Yes", otherwise "No"
no_longer_working Variable to evaluate if patient is no longer working factor If working_status_change == "Yes" AND patient_sq_q_today == "Full time carer (children or other)" OR "Unemployed" OR "Unable to work due to chronic illness" OR "Student" OR "Retired" OR "Medically retired" OR "Prefer not to say" then "Yes", otherwise "No"
health_reasons Variable to evaluate if patient has an altered working status due to health reasons factor If patient_sq_q_change == "Poor health" OR "Sick leave" THEN "Yes", otherwise "No"
employer_reasons Variable to evaluate if patient has an altered working status due to employer reasons factor If patient_sq_q_change == "Made redundant" OR "Working hours reduced by employer" THEN "Yes", otherwise "No"
other_reasons Variable to evaluate if patient has an altered working status due to other reasons factor If patient_sq_q_change == "New caring responsibility" OR "Other" OR "Prefer not to say" THEN "Yes", otherwise "No"
pft_fev1 Mean of PFT FEV1 readings numeric FEV1 If variable starts with "pft_fev1_r" then calculate mean between variables
pft_fvc Mean of PFT FVC readings numeric FVC If variable starts with "pft_fvc_r" then calculate mean between variables
pft_fev1_fvc Ratio FEV1:FVC numeric FEV1/FVC pft_fev1 / pft_fvc
pft_tlco Mean of PFT TLCO readings numeric TLCO If variable starts with "pft_tlco_r" then calculate mean between variables
pft_kco Mean of PFT KCO readings numeric KCO If variable starts with "pft_kco_r" then calculate mean between variables
pft_mip Mean of PFT MIP readings numeric MIP If variable starts with "pft_mip_r" then calculate mean between variables
pft_mep Mean of PFT MEP readings numeric MEP If variable starts with "pft_mep_r" then calculate mean between variables
pft_fev1_pred Prediction of FEV1 readings using GLI equations numeric pred_GLI(age_admission, crf3a_rest_height / 100, crf1a_sex, crf1b_eth_pft, param = c("FEV1"))
pft_fvc_pred Prediction of FVC readings using GLI equations numeric pred_GLI(age_admission, crf3a_rest_height / 100, crf1a_sex, crf1b_eth_pft, param = c("FVC"))
pft_fev1_perc_pred Percentage of FEV1 predicted numeric FEV1 % predicted 100 * pft_fev1 / pft_fev1_pred
pft_fvc_perc_pred Percentage of FVC predicted numeric FVC % predicted 100 * pft_fvc / pft_fvc_pred
pft_fev1_perc_pred_80 Percentage of FEV1 predicted over 80% numeric FEV1 % pred <80% If < 80 then "Yes" ; If >= 80 then "No"
pft_fvc_perc_pred_80 Percentage of FVC predicted over 80% numeric FVC % pred <80% If < 80 then "Yes" ; If >= 80 then "No"
pft_fev1_fvc_70 Ratio FEV1:FVC less than 0.7 numeric FEV1/FVC <0.7 If < 0.7 then "Yes" ; If >= 0.7 then "No"
imd Index of Multiple Deprivation (IMD) numeric See 03_prep.R for full calculation
imd_quintile Index of Multiple Deprivation (IMD) quintile factor Index of multiple deprivation See 03_prep.R for full calculation
swab_pcr_result COVID swab PCR test result factor SARS-CoV-2 swab "Positive" ; "Indeterminate" ; "Negative"