Additional Fields

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_mer_diab_yn, crf1a_com_card_mi, crf1a_com_mh_stm_yn, 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"