cr_create_analysis_dataset_sept2020.do

********************************************************************************
*
*	Do-file:		cr_create_analysis_dataset.do
*
*	Project:		Risk factors for poor outcomes in Covid-19
*
*	Programmed by:	Fizz & Krishnan
*
*	Data used:		Data in memory (from input.csv)
*
*	Data created:	cr_create_analysis_dataset.dta  (main analysis dataset)
*					Same data but already stset (to avoid re-doing):
*						cr_create_analysis_dataset_STSET_cpnsdeath.dta 
*						cr_create_analysis_dataset_STSET_onscoviddeath.dta
*
*	Other output:	None
*
********************************************************************************
*
*	Purpose:		This do-file creates the variables required for the 
*					main analysis and saves into Stata datasets.
*  
********************************************************************************



* Open a log file
cap log close
log using ./analysis/output/cr_create_analysis_dataset_sept2020, replace t

clear
import delimited ./output/input.csv

di "STARTING COUNT FROM IMPORT:"
cou

rename hiv hiv_code

****************************
*  Create required cohort  *
****************************

* Age: Exclude children
noi di "DROPPING AGE<18:" 
drop if age<18


* Age: Exclude those with implausible ages
assert age<.
noi di "DROPPING AGE<105:" 
drop if age>105

* Sex: Exclude categories other than M and F
assert inlist(sex, "M", "F", "I", "U")
noi di "DROPPING GENDER NOT M/F:" 
drop if inlist(sex, "I", "U")


******************************
*  Convert strings to dates  *
******************************

* Covariates
foreach var of varlist 	bp_sys_date 					///
						bp_dias_date 					///
						hba1c_percentage_date			///
						hba1c_mmol_per_mol_date			///
						hypertension					///
						bmi_date_measured				///
						chronic_respiratory_disease 	///
						chronic_cardiac_disease 		///
						diabetes 						///
						lung_cancer 					///
						haem_cancer						///
						other_cancer 					///
						chronic_liver_disease 			///
						stroke							///
						dementia		 				///
						other_neuro 					///
						organ_transplant 				///	
						dysplenia						///
						sickle_cell 					///
						aplastic_anaemia 				///
						hiv_date						///
						permanent_immunodeficiency 		///
						temporary_immunodeficiency		///
						ra_sle_psoriasis  dialysis 	{
	confirm string variable `var'
	replace `var' = `var' + "-15"
	rename `var' `var'_dstr
	replace `var'_dstr = " " if `var'_dstr == "-15"
	gen `var'_date = date(`var'_dstr, "YMD") 
	order `var'_date, after(`var'_dstr)
	drop `var'_dstr
	format `var'_date %td
}

rename bmi_date_measured_date      bmi_date_measured
rename bp_dias_date_measured_date  bp_dias_date
rename bp_sys_date_measured_date   bp_sys_date
rename hba1c_percentage_date_date  hba1c_percentage_date
rename hba1c_mmol_per_mol_date_date  hba1c_mmol_per_mol_date
rename hiv_date_date hiv_date

* Dates of: CPNS death, ONS-covid death
foreach var of varlist 	died_date_ons died_date_cpns died_date_1ocare {
		confirm string variable `var'
		rename `var' _tmp
		gen `var' = date(_tmp, "YMD")
		drop _tmp
		format %d `var'
}
 
********* DEFAULT CENSORING IS MAX OUTCOME DATE MINUS 7 **********
foreach var of varlist 	died_date_ons died_date_cpns {
		*Set default censoring date as max observed minus 7 days
		local globstem = substr("`var'",11,.)
		summ `var'
		global `globstem'deathcensor = r(max)-7
}
global primarycaredeathcensor = $onsdeathcensor

******************INPUT HERE TO OVERRIDE******************
*Set censoring dates manually here if needed
*global cpnsdeathcensor 		= d("25/04/2020")
*global onscoviddeathcensor 	= d("06/05/2020")
*******************************************************************************


*******************************
*  Recode implausible values  *
*******************************


* BMI 

* Only keep if within certain time period? using bmi_date_measured ?
* NB: Some BMI dates in future or after cohort entry

* Set implausible BMIs to missing:
replace bmi = . if !inrange(bmi, 15, 50)




**********************
*  Recode variables  *
**********************

* Sex
assert inlist(sex, "M", "F")
gen male = (sex=="M")
drop sex


* Smoking
label define smoke 1 "Never" 2 "Former" 3 "Current" 

gen     smoke = 1  if smoking_status=="N"
replace smoke = 2  if smoking_status=="E"
replace smoke = 3  if smoking_status=="S"
replace smoke = . if smoking_status=="M"
label values smoke smoke
drop smoking_status


* Ethnicity (5 category)
replace ethnicity = . if ethnicity==.
label define ethnicity 	1 "White"  					///
						2 "Mixed" 					///
						3 "Asian or Asian British"	///
						4 "Black"  					///
						5 "Other"					
						
label values ethnicity ethnicity


* Ethnicity (16 category)
replace ethnicity_16 = . if ethnicity==.
label define ethnicity_16 									///
						1 "British or Mixed British" 		///
						2 "Irish" 							///
						3 "Other White" 					///
						4 "White + Black Caribbean" 		///
						5 "White + Black African"			///
						6 "White + Asian" 					///
 						7 "Other mixed" 					///
						8 "Indian or British Indian" 		///
						9 "Pakistani or British Pakistani" 	///
						10 "Bangladeshi or British Bangladeshi" ///
						11 "Other Asian" 					///
						12 "Caribbean" 						///
						13 "African" 						///
						14 "Other Black" 					///
						15 "Chinese" 						///
						16 "Other" 							
						
label values ethnicity_16 ethnicity_16


* Ethnicity (16 category grouped further)
* Generate a version of the full breakdown with mixed in one group
gen ethnicity_16_combinemixed = ethnicity_16
recode ethnicity_16_combinemixed 4/7 = 4
label define ethnicity_16_combinemixed 	///
						1 "British or Mixed British" ///
						2 "Irish" ///
						3 "Other White" ///
						4 "All mixed" ///
						8 "Indian or British Indian" ///
						9 "Pakistani or British Pakistani" ///
						10 "Bangladeshi or British Bangladeshi" ///
						11 "Other Asian" ///
						12 "Caribbean" ///
						13 "African" ///
						14 "Other Black" ///
						15 "Chinese" ///
						16 "Other" 
						
label values ethnicity_16_combinemixed ethnicity_16_combinemixed
						

* STP 
rename stp stp_old
bysort stp_old: gen stp = 1 if _n==1
replace stp = sum(stp)
drop stp_old




**************************
*  Categorise variables  *
**************************


/*  Age variables  */ 

* Create categorised age
recode age 18/39.9999=1 40/49.9999=2 50/59.9999=3 ///
	60/69.9999=4 70/79.9999=5 80/max=6, gen(agegroup) 

label define agegroup 	1 "18-<40" ///
						2 "40-<50" ///
						3 "50-<60" ///
						4 "60-<70" ///
						5 "70-<80" ///
						6 "80+"
label values agegroup agegroup


* Create binary age
recode age min/69.999=0 70/max=1, gen(age70)

* Check there are no missing ages
assert age<.
assert agegroup<.
assert age70<.

* Create restricted cubic splines fir age
mkspline age = age, cubic nknots(4)



/*  Body Mass Index  */

* BMI (NB: watch for missingness)
gen 	bmicat = .
recode  bmicat . = 1 if bmi<18.5
recode  bmicat . = 2 if bmi<25
recode  bmicat . = 3 if bmi<30
recode  bmicat . = 4 if bmi<35
recode  bmicat . = 5 if bmi<40
recode  bmicat . = 6 if bmi<.
replace bmicat = . if bmi>=.

label define bmicat 1 "Underweight (<18.5)" 	///
					2 "Normal (18.5-24.9)"		///
					3 "Overweight (25-29.9)"	///
					4 "Obese I (30-34.9)"		///
					5 "Obese II (35-39.9)"		///
					6 "Obese III (40+)"			
					
label values bmicat bmicat

* Create more granular categorisation
recode bmicat 1/3 . = 1 4=2 5=3 6=4, gen(obese4cat)

label define obese4cat 	1 "No record of obesity" 	///
						2 "Obese I (30-34.9)"		///
						3 "Obese II (35-39.9)"		///
						4 "Obese III (40+)"		
label values obese4cat obese4cat
order obese4cat, after(bmicat)



/*  Smoking  */


* Create non-missing 3-category variable for current smoking
recode smoke .=1, gen(smoke_nomiss)
order smoke_nomiss, after(smoke)
label values smoke_nomiss smoke



/*  Asthma  */


* Asthma  (coded: 0 No, 1 Yes no OCS, 2 Yes with OCS)
rename asthma asthmacat
recode asthmacat 0=1 1=2 2=3 .=1
label define asthmacat 1 "No" 2 "Yes, no OCS" 3 "Yes with OCS"
label values asthmacat asthmacat

gen asthma = (asthmacat==2|asthmacat==3)





/*  Blood pressure   */

* Categorise
gen     bpcat = 1 if bp_sys < 120 &  bp_dias < 80
replace bpcat = 2 if inrange(bp_sys, 120, 130) & bp_dias<80
replace bpcat = 3 if inrange(bp_sys, 130, 140) | inrange(bp_dias, 80, 90)
replace bpcat = 4 if (bp_sys>=140 & bp_sys<.) | (bp_dias>=90 & bp_dias<.) 
replace bpcat = . if bp_sys>=. | bp_dias>=. | bp_sys==0 | bp_dias==0

label define bpcat 1 "Normal" 2 "Elevated" 3 "High, stage I"	///
					4 "High, stage II" 
label values bpcat bpcat

recode bpcat .=1, gen(bpcat_nomiss)
label values bpcat_nomiss bpcat

* Create non-missing indicator of known high blood pressure
gen bphigh = (bpcat==4)
order bpcat bphigh, after(bp_dias_date)




/*  IMD  */

* Group into 5 groups
rename imd imd_o
egen imd = cut(imd_o), group(5) icodes
replace imd = imd + 1
replace imd = . if imd_o==-1
drop imd_o

* Reverse the order (so high is more deprived)
recode imd 5=1 4=2 3=3 2=4 1=5 .=.

label define imd 1 "1 least deprived" 2 "2" 3 "3" 4 "4" 5 "5 most deprived" 
label values imd imd 

noi di "DROPPING IF NO IMD" 
drop if imd>=.





/*  Centred age, sex, IMD, ethnicity (for adjusted KM plots)  */ 

* Centre age (linear)
summ age
gen c_age = age-r(mean)

* "Centre" sex to be coded -1 +1 
recode male 0=-1, gen(c_male)

* "Centre" IMD
gen c_imd = imd - 3

* "Centre" ethnicity
gen c_ethnicity = ethnicity - 3




**************************************************
*  Create binary comorbidity indices from dates  *
**************************************************

* Comorbidities ever before
foreach var of varlist	chronic_respiratory_disease_date 	///
						chronic_cardiac_disease_date 		///
						diabetes 							///
						chronic_liver_disease_date 			///
						stroke_date							///
						dementia_date						///
						other_neuro_date					///
						organ_transplant_date 				///
						aplastic_anaemia_date				///
						hypertension 						///
						dysplenia_date 						///
						sickle_cell_date 					///
						hiv_date							///
						permanent_immunodeficiency_date		///
						temporary_immunodeficiency_date		///
						ra_sle_psoriasis_date dialysis_date {
	local newvar =  substr("`var'", 1, length("`var'") - 5)
	gen `newvar' = (`var'< d(1/9/2020))
	order `newvar', after(`var')
}






***************************
*  Grouped comorbidities  *
***************************


/*  Neurological  */

* Stroke and dementia
egen stroke_dementia = rowmax(stroke dementia)
order stroke_dementia, after(dementia_date)


/*  Spleen  */

* Spleen problems (dysplenia/splenectomy/etc and sickle cell disease)   
egen spleen = rowmax(dysplenia sickle_cell) 
order spleen, after(sickle_cell)



/*  Cancer  */

label define cancer 1 "Never" 2 "Last year" 3 "2-5 years ago" 4 "5+ years"

* Haematological malignancies
gen     cancer_haem_cat = 4 if inrange(haem_cancer_date, d(1/1/1900), d(1/9/2015))
replace cancer_haem_cat = 3 if inrange(haem_cancer_date, d(1/9/2015), d(1/9/2019))
replace cancer_haem_cat = 2 if inrange(haem_cancer_date, d(1/9/2019), d(1/9/2020))
recode  cancer_haem_cat . = 1
label values cancer_haem_cat cancer


* All other cancers
gen     cancer_exhaem_cat = 4 if inrange(lung_cancer_date,  d(1/1/1900), d(1/9/2015)) | ///
								 inrange(other_cancer_date, d(1/1/1900), d(1/9/2015)) 
replace cancer_exhaem_cat = 3 if inrange(lung_cancer_date,  d(1/9/2015), d(1/9/2019)) | ///
								 inrange(other_cancer_date, d(1/9/2015), d(1/9/2019)) 
replace cancer_exhaem_cat = 2 if inrange(lung_cancer_date,  d(1/9/2019), d(1/9/2020)) | ///
								 inrange(other_cancer_date, d(1/9/2019), d(1/9/2020))
recode  cancer_exhaem_cat . = 1
label values cancer_exhaem_cat cancer


* Put variables together
order cancer_exhaem_cat cancer_haem_cat, after(other_cancer_date)



/*  Immunosuppression  */

* Immunosuppressed:
* HIV, permanent immunodeficiency ever, OR 
* temporary immunodeficiency or aplastic anaemia last year
gen temp1  = max(hiv, permanent_immunodeficiency)
gen temp2  = inrange(temporary_immunodeficiency_date, d(1/9/2019), d(1/9/2020))
gen temp3  = inrange(aplastic_anaemia_date, d(1/9/2019), d(1/9/2020))

egen other_immunosuppression = rowmax(temp1 temp2 temp3)
drop temp1 temp2 temp3
order other_immunosuppression, after(temporary_immunodeficiency)




/*  Hypertension  */

gen htdiag_or_highbp = bphigh
recode htdiag_or_highbp 0 = 1 if hypertension==1 




************
*   eGFR   *
************

* Set implausible creatinine values to missing (Note: zero changed to missing)
replace creatinine = . if !inrange(creatinine, 20, 3000) 
	
* Divide by 88.4 (to convert umol/l to mg/dl)
gen SCr_adj = creatinine/88.4

gen min=.
replace min = SCr_adj/0.7 if male==0
replace min = SCr_adj/0.9 if male==1
replace min = min^-0.329  if male==0
replace min = min^-0.411  if male==1
replace min = 1 if min<1

gen max=.
replace max=SCr_adj/0.7 if male==0
replace max=SCr_adj/0.9 if male==1
replace max=max^-1.209
replace max=1 if max>1

gen egfr=min*max*141
replace egfr=egfr*(0.993^age)
replace egfr=egfr*1.018 if male==0
label var egfr "egfr calculated using CKD-EPI formula with no eth"

* Categorise into ckd stages
egen egfr_cat = cut(egfr), at(0, 15, 30, 45, 60, 5000)
recode egfr_cat 0=5 15=4 30=3 45=2 60=0, generate(ckd)
* 0 = "No CKD" 	2 "stage 3a" 3 "stage 3b" 4 "stage 4" 5 "stage 5"
label define ckd 0 "No CKD" 1 "CKD"
label values ckd ckd
label var ckd "CKD stage calc without eth"

* Convert into CKD group
*recode ckd 2/5=1, gen(chronic_kidney_disease)
*replace chronic_kidney_disease = 0 if creatinine==. 

recode ckd 0=1 2/3=2 4/5=3, gen(reduced_kidney_function_cat)
replace reduced_kidney_function_cat = 1 if creatinine==. 
label define reduced_kidney_function_catlab ///
	1 "None" 2 "Stage 3a/3b egfr 30-60	" 3 "Stage 4/5 egfr<30"
label values reduced_kidney_function_cat reduced_kidney_function_catlab 

*More detailed version incorporating stage 5 or dialysis as a separate category	
recode ckd 0=1 2/3=2 4=3 5=4, gen(reduced_kidney_function_cat2)
replace reduced_kidney_function_cat2 = 1 if creatinine==. 
replace reduced_kidney_function_cat2 = 5 if dialysis==1 

label define reduced_kidney_function_cat2lab ///
	1 "None" 2 "Stage 3a/3b egfr 30-60	" 3 "Stage 4 egfr 15-<30" 4 "Stage 4 egfr <15-<30" 5 "Stage 5 egfr <15 or dialysis"
label values reduced_kidney_function_cat2 reduced_kidney_function_cat2lab 
 
	
************
*   Hba1c  *
************
	

/*  Diabetes severity  */

* Set zero or negative to missing
replace hba1c_percentage   = . if hba1c_percentage<=0
replace hba1c_mmol_per_mol = . if hba1c_mmol_per_mol<=0


* Only consider measurements in last 15 months
replace hba1c_percentage   = . if hba1c_percentage_date   < d(1/6/2019)
replace hba1c_mmol_per_mol = . if hba1c_mmol_per_mol_date < d(1/6/2019)



/* Express  HbA1c as percentage  */ 

* Express all values as perecentage 
noi summ hba1c_percentage hba1c_mmol_per_mol 
gen 	hba1c_pct = hba1c_percentage 
replace hba1c_pct = (hba1c_mmol_per_mol/10.929)+2.15 if hba1c_mmol_per_mol<. 

* Valid % range between 0-20  
replace hba1c_pct = . if !inrange(hba1c_pct, 0, 20) 
replace hba1c_pct = round(hba1c_pct, 0.1)


/* Categorise hba1c and diabetes  */

* Group hba1c
gen 	hba1ccat = 0 if hba1c_pct <  6.5
replace hba1ccat = 1 if hba1c_pct >= 6.5  & hba1c_pct < 7.5
replace hba1ccat = 2 if hba1c_pct >= 7.5  & hba1c_pct < 8
replace hba1ccat = 3 if hba1c_pct >= 8    & hba1c_pct < 9
replace hba1ccat = 4 if hba1c_pct >= 9    & hba1c_pct !=.
label define hba1ccat 0 "<6.5%" 1">=6.5-7.4" 2">=7.5-7.9" 3">=8-8.9" 4">=9"
label values hba1ccat hba1ccat
tab hba1ccat

* Create diabetes, split by control/not
gen     diabcat = 1 if diabetes==0
replace diabcat = 2 if diabetes==1 & inlist(hba1ccat, 0, 1)
replace diabcat = 3 if diabetes==1 & inlist(hba1ccat, 2, 3, 4)
replace diabcat = 4 if diabetes==1 & !inlist(hba1ccat, 0, 1, 2, 3, 4)

label define diabcat 	1 "No diabetes" 			///
						2 "Controlled diabetes"		///
						3 "Uncontrolled diabetes" 	///
						4 "Diabetes, no hba1c measure"
label values diabcat diabcat

* Delete unneeded variables
drop hba1c_pct hba1c_percentage hba1c_mmol_per_mol


********************************
*  Outcomes and survival time  *
********************************

/*  Cohort entry and censor dates  */

* Date of cohort entry, 1 Sep 2020
gen enter_date = date("01/09/2020", "DMY")
format %d enter_date

/*   Outcomes   */
* Binary indicators for CPNS, primary care death outcome
gen cpnsdeath 		= (died_date_cpns		< .)
gen primarycaredeath = (died_date_1ocare < .)

* Date of Covid death in ONS
gen died_date_onscovid = died_date_ons if died_ons_covid_flag_any==1

*Classify ONS deaths
datacheck died_cause_ons!="" if died_date_ons<., nol
datacheck died_date_ons<. if died_cause_ons!="", nol

gen _causechapter = substr(died_cause,1,1)
gen _causenumber = real(substr(died_cause,2,2))
gen onsdeath = 1 if _causechapter=="U" & _causenumber==07
replace onsdeath = 2 if _causechapter=="C" /*& !(_causenumber>=81 & _causenumber<=96)
replace onsdeath = 3 if _causechapter=="C" & (_causenumber>=81 & _causenumber<=96)*/
replace onsdeath = 3 if _causechapter=="I"
replace onsdeath = 4 if (_causechapter=="F" & (_causenumber==0|_causenumber==1|_causenumber==3))|(_causechapter=="G" & (_causenumber==30))
replace onsdeath = 5 if _causechapter=="J" /*& (_causenumber>=9 & _causenumber<=22)
replace onsdeath = 7 if _causechapter=="J" & (_causenumber>=23)*/
replace onsdeath = 6 if _causechapter!="" & onsdeath==.
label define onsdeathlab 1 covid 2 cancer 3 cvd 4 dem_alz 5 respiratory 6 other
label values onsdeath onsdeathlab 


/*  Create survival times  */
* For looping later, name must be stime_binary_outcome_name

* Survival time = last followup date (first: end study, death, or that outcome)
gen stime_cpnsdeath  	= min($cpnsdeathcensor, died_date_cpns, died_date_ons)
gen stime_onsdeath 		= min($onsdeathcensor, died_date_ons)
gen stime_primarycaredeath 		= min($primarycaredeathcensor, died_date_1ocare)

* If outcome was after censoring occurred, set to zero
replace cpnsdeath 		= 0 if (died_date_cpns > $cpnsdeathcensor) 
replace onsdeath 		= 0 if (died_date_ons > $onsdeathcensor) 
replace primarycaredeath = 0 if (died_date_1ocare > $primarycaredeathcensor)

* Format date variables
format stime* %td 
format	stime* 				///
		died_date_onscovid 	///
		died_date_ons 		///
		died_date_cpns %td 

*********************
*  Label variables  *
*********************

* Demographics
label var patient_id					"Patient ID"
label var age 							"Age (years)"
label var agegroup						"Grouped age"
label var age70 						"70 years and older"
label var male 							"Male"
label var bmi 							"Body Mass Index (BMI, kg/m2)"
label var bmicat 						"Grouped BMI"
label var bmi_date  					"Body Mass Index (BMI, kg/m2), date measured"
label var obese4cat						"Evidence of obesity (4 categories)"
label var smoke		 					"Smoking status"
label var smoke_nomiss	 				"Smoking status (missing set to non)"
label var imd 							"Index of Multiple Deprivation (IMD)"
label var ethnicity						"Ethnicity"
label var ethnicity_16					"Ethnicity in 16 categories"
label var ethnicity_16_combinemixed		"Ethnicity detailed with mixed groups combined"
label var stp 							"Sustainability and Transformation Partnership"
label var region 						"Geographical region"

label var hba1ccat						"Categorised hba1c"
label var egfr_cat						"Calculated eGFR"
	
label var bp_sys 						"Systolic blood pressure"
label var bp_sys_date 					"Systolic blood pressure, date"
label var bp_dias 						"Diastolic blood pressure"
label var bp_dias_date 					"Diastolic blood pressure, date"
label var bpcat 						"Grouped blood pressure"
label var bphigh						"Binary high (stage 1/2) blood pressure"
label var htdiag_or_highbp				"Diagnosed hypertension or high blood pressure"

label var age1 							"Age spline 1"
label var age2 							"Age spline 2"
label var age3 							"Age spline 3"
label var c_age							"Centred age"
label var c_male 						"Centred sex (code: -1/+1)"
label var c_imd							"Centred Index of Multiple Deprivation (values: -2/+2)"
label var c_ethnicity					"Centred ethnicity (values: -2/+2)"

* Comorbidities
label var chronic_respiratory_disease	"Respiratory disease (excl. asthma)"
label var asthmacat						"Asthma, grouped by severity (OCS use)"
label var asthma						"Asthma"
label var chronic_cardiac_disease		"Heart disease"
label var diabetes						"Diabetes"
label var diabcat						"Diabetes, grouped"
label var cancer_exhaem_cat				"Cancer (exc. haematological), grouped by time since diagnosis"
label var cancer_haem_cat				"Haematological malignancy, grouped by time since diagnosis"
label var chronic_liver_disease			"Chronic liver disease"
label var stroke_dementia				"Stroke or dementia"
label var other_neuro					"Neuro condition other than stroke/dementia"	
label var reduced_kidney_function_cat	"Reduced kidney function" 
label var organ_transplant 				"Organ transplant recipient"
label var dysplenia						"Dysplenia (splenectomy, other, not sickle cell)"
label var sickle_cell 					"Sickle cell"
label var spleen						"Spleen problems (dysplenia, sickle cell)"
label var ra_sle_psoriasis				"RA, SLE, Psoriasis (autoimmune disease)"
label var aplastic_anaemia				"Aplastic anaemia"
label var hiv 							"HIV"
label var permanent_immunodeficiency 	"Permanent immunodeficiency"
label var temporary_immunodeficiency 	"Temporary immunosuppression"
label var other_immunosuppression		"Immunosuppressed (combination algorithm)"
label var chronic_respiratory_disease_date	"Respiratory disease (excl. asthma), date"
label var chronic_cardiac_disease_date	"Heart disease, date"
label var diabetes_date					"Diabetes, date"
label var lung_cancer_date				"Lung cancer, date"
label var haem_cancer_date				"Haem. cancer, date"
label var other_cancer_date				"Any cancer, date"
label var chronic_liver_disease_date	"Liver, date"
label var stroke_date					"Stroke, date"
label var dementia_date					"Dementia, date"
label var other_neuro_date				"Neuro condition other than stroke/dementia, date"	
label var organ_transplant_date			"Organ transplant recipient, date"
label var dysplenia_date				"Splenectomy etc, date"
label var sickle_cell_date 				"Sickle cell, date"
label var ra_sle_psoriasis_date			"RA, SLE, Psoriasis (autoimmune disease), date"
label var aplastic_anaemia_date			"Aplastic anaemia, date"
label var hiv_date 						"HIV, date"
label var permanent_immunodeficiency_date "Permanent immunodeficiency, date"
label var temporary_immunodeficiency_date "Temporary immunosuppression, date"
label var dialysis						"Dialysis"
	
* Outcomes and follow-up
label var enter_date					"Date of study entry"

label var cpnsdeath						"Failure/censoring indicator for outcome: CPNS covid death"
label var onsdeath						"Failure/censoring indicator for outcome: ONS death (1 = covid death 2 = other death)"

* Survival times
label var  stime_cpnsdeath 				"Survival time (date); outcome CPNS covid death"
label var  stime_onsdeath 				"Survival time (date); outcome ONS covid death"


***************
*  Tidy data  *
***************

* REDUCE DATASET SIZE TO VARIABLES NEEDED
keep patient_id imd stp region enter_date  									///
	cpnsdeath died_date_cpns  stime_cpnsdeath								///
	onsdeath died_date_ons died_date_onscovid died_cause_ons				///
	died_ons_covid_flag_any died_ons_covidconf_flag_underly 				/// 
	stime_onsdeath															///
	primarycaredeath died_date_1ocare stime_primarycaredeath				///
	age agegroup age70 age1 age2 age3 male bmi smoke   						///
	smoke smoke_nomiss bmicat bpcat_nomiss obese4cat ethnicity ethnicity_16	///
	ethnicity_16_combinemixed bpcat bphigh htdiag_or_highbp hypertension 	///
	chronic_respiratory_disease asthma asthmacat chronic_cardiac_disease 	///
	diabetes diabcat hba1ccat cancer_exhaem_cat cancer_haem_cat 			///
	chronic_liver_disease organ_transplant spleen ra_sle_psoriasis 			///
	reduced_kidney_function_cat* stroke dementia stroke_dementia 			///
	other_neuro other_immunosuppression  hiv*								///
	creatinine egfr egfr_cat ckd dialysis 


***************
*  Save data  *
***************

sort patient_id
label data "covid vs noncovid from sept 2020"
*save ./analysis/cr_create_analysis_dataset_sept2020.dta, replace

stset stime_onsdeath, fail(onsdeath) id(patient_id) enter(enter_date) origin(enter_date)
save ./analysis/cr_create_analysis_dataset_sept2020_STSET_ONSCSDEATH.dta, replace

log close