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cr_create_analysis_dataset.do
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cr_create_analysis_dataset.do
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********************************************************************************
*
* Do-file: cr_create_analysis_dataset.do
*
* Project: Post COVID-admission admissions
*
* Programmed by: Krishnan, Fizz
*
* Data used: Data in memory (from input.csv)
*
* Data created: cr_create_analysis_dataset.dta
*
* Other output: None
*
********************************************************************************
*
* Purpose: This do-file creates the variables required for the
* main analysis and saves into Stata datasets.
*
********************************************************************************
local cpf "`1'"
* Open a log file
cap log close
log using ./analysis/output/cr_create_analysis_dataset_`cpf', replace t
clear
noi di "importing csv"
if "`cpf'"=="COVID" import delimited ./output/input_covdischarged.csv
else if "`cpf'"=="PNEUM" import delimited ./output/input_pneum2019.csv
else if "`cpf'"=="FLU" import delimited ./output/input_flu2017_19.csv
if "`cpf'"=="FLU" local diedsource "1ocare"
else local diedsource "ons"
*correction
cap rename admitted1_dishcargedestination admitted1_dischargedestination
cap rename admitted1_dishchargedestination admitted1_dischargedestination
for num 2/5: cap rename admittedX_dishchargedestination admittedX_dischargedestination
di "STARTING COUNT FROM IMPORT:"
cou
****************************
* Create required cohort *
****************************
/* DROP IF DIED ON/BEFORE DISCHARGE DATE
noi di "DIED ON/BEFORE DISCHARGE DATE :"
drop if date(died_date_ons, "YMD")<=date(discharged1_date, "YMD")
else drop if date(died_date_ons, "YMD")<=d(1/2/2020)
*/
/*
* 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")
/* 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>=.
******************************
* Convert strings to dates *
******************************
capture confirm var died_date_1ocare
if _rc==0 local died_date_1ocare "died_date_1ocare"
* Process variables with exact dates (admissions, deaths)
foreach var of varlist admitted1_date ///
discharged1_date ///
admitted2_date ///
discharged2_date ///
admitted3_date ///
discharged3_date ///
admitted4_date ///
discharged4_date ///
admitted5_date ///
discharged5_date ///
died_date_ons ///
`died_date_1ocare' ///
patient_index_date ///
admitted_*_date {
confirm string variable `var'
rename `var' _tmp
gen `var' = date(_tmp, "YMD")
drop _tmp
format %d `var'
}
* Process variables with nearest month dates only
foreach var of varlist bmi_date_measured ///
creatinine_date ///
bp_sys_date_measured ///
hba1c_mmol_per_mol_date ///
hba1c_percentage_date ///
haem_cancer ///
lung_cancer ///
other_cancer ///
temporary_immunodeficiency ///
aplastic_anaemia {
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_sys_date_measured_date bp_sys_date
rename creatinine_date_date creatinine_date
rename hba1c_percentage_date_date hba1c_percentage_date
rename hba1c_mmol_per_mol_date_date hba1c_mmol_per_mol_date
********* DEFAULT CENSORING IS MAX OUTCOME DATE MINUS 7 **********
summ died_date_ons
global deathcensor = r(max)-7
*******************************
* 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
* 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 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_sys_date)
***************************
* Grouped comorbidities *
***************************
/* 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"
gen fiveybefore = patient_index_date-5*365.25
gen oneybefore = patient_index_date-365.25
* Haematological malignancies
gen cancer_haem_cat = 4 if inrange(haem_cancer_date, d(1/1/1900), fiveybefore)
replace cancer_haem_cat = 3 if inrange(haem_cancer_date, fiveybefore, oneybefore)
replace cancer_haem_cat = 2 if inrange(haem_cancer_date, oneybefore, patient_index_date)
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), fiveybefore) | ///
inrange(other_cancer_date, d(1/1/1900), fiveybefore)
replace cancer_exhaem_cat = 3 if inrange(lung_cancer_date, fiveybefore, oneybefore) | ///
inrange(other_cancer_date, fiveybefore, oneybefore)
replace cancer_exhaem_cat = 2 if inrange(lung_cancer_date, oneybefore, patient_index_date) | ///
inrange(other_cancer_date, oneybefore, patient_index_date)
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, oneybefore, patient_index_date)
gen temp3 = inrange(aplastic_anaemia_date, oneybefore, patient_index_date)
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 = 4 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 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
local fifteenmbefore = `studystart'-15*(365.25/12)
* Only consider measurements in last 15 months
replace hba1c_percentage = . if hba1c_percentage_date < `fifteenmbefore'
replace hba1c_mmol_per_mol = . if hba1c_mmol_per_mol_date < `fifteenmbefore'
/* 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_percentage* hba1c_mmol_per_mol* bmi_date_measured creatinine_date bp_sys_date *cancer_date aplastic_anaemia_date temporary_immunodeficiency_date SCr_adj min max egfr egfr_cat ckd hba1c_pct hba1ccat asthma diabetes ethnicity_16_date reduced_kidney_function_cat bphigh dysplenia sickle_cell permanent_immunodeficiency hiv creatinine
order patient_id region stp imd age agegroup male ethnicity ethnicity_16 bmi bmicat obese4cat smoke_nomiss patient_index_date admitted1_date admitted1_reason discharged1_date admitted2_date admitted2_reason discharged2_date died_date_ons died_cause_ons died_ons_covid_flag
*FURTHER EXCLUSIONS AND DATE PROCESSING:
*drop if initial admission/discharge are on the same day
drop if admitted1_date==discharged1_date
*tie together admissions that are within 1 week of previous discharge
gen finaldischargedate = discharged1_date
gen finaldischargedest = admitted1_dischargedestination
replace finaldischargedate = discharged2_date if admitted2_date<=(discharged1_date+7)
replace finaldischargedest = admitted2_dischargedestination if admitted2_date<=(discharged1_date+7)
replace finaldischargedate = discharged3_date if admitted2_date<=(discharged1_date+7) & admitted3_date<=(discharged2_date+7)
replace finaldischargedest = admitted3_dischargedestination if admitted2_date<=(discharged1_date+7) & admitted3_date<=(discharged2_date+7)
replace finaldischargedate = discharged4_date if admitted2_date<=(discharged1_date+7) & admitted3_date<=(discharged2_date+7) & admitted4_date<=(discharged3_date+7)
replace finaldischargedest = admitted4_dischargedestination if admitted2_date<=(discharged1_date+7) & admitted3_date<=(discharged2_date+7) & admitted4_date<=(discharged3_date+7)
format %d finaldischargedate
*drop if there is a single day admission in the chain of admissions, as cannot then get f-up:
drop if finaldischargedate==discharged4_date & discharged4_date == admitted4_date
*drop if we get to the 5th readmission with all short gaps
drop if admitted2_date<=(discharged1_date+7) & admitted3_date<=(discharged2_date+7) & admitted4_date<=(discharged3_date+7) & admitted5_date<=(discharged4_date+7)
*drop if the final discharge destination is to hospital transfer, or to hospice
drop if finaldischargedest==30|(finaldischargedest>=48 & finaldischargedest<=53)|finaldischargedest==84|finaldischargedest==87 /*hospital transfers*/
drop if finaldischargedest==88 /*hospice*/
gen dischargedtocarehome = finaldischargedest if (finaldischargedest==54|finaldischargedest==85|finaldischargedest==65)
recode dischargedtocarehome 54=1 85=1 65=2
label define dischargedtocarehomelab 1 carehome 2 la_care
label values dischargedtocarehome dischargedtocarehomelab
gen entrydate = finaldischargedate+8
format %d entrydate
*get total days in critical care, and binary flag
generate totaldayscriticalcare = admitted1_dayscritical
replace totaldayscriticalcare = totaldayscriticalcare + admitted2_dayscritical if discharged2_date<=finaldischargedate
replace totaldayscriticalcare = totaldayscriticalcare + admitted3_dayscritical if discharged3_date<=finaldischargedate
replace totaldayscriticalcare = totaldayscriticalcare + admitted4_dayscritical if discharged4_date<=finaldischargedate
gen byte anycriticalcare = totaldayscriticalcare>0 & totaldayscriticalcare<.
*drop if died date on/before discharge date
cou if died_date_`diedsource'==finaldischargedate
cou if died_date_`diedsource'<finaldischargedate
cou if died_date_`diedsource'<=finaldischargedate|finaldischargedest==79
cou if died_date_`diedsource'>finaldischargedate & died_date_`diedsource'<entrydate
drop if died_date_`diedsource'<entrydate|finaldischargedest==79
cou
*drop if later than 60d before latest sus data
summ discharged1_date, f d
scalar censordate = r(max) - 60
drop if entrydate>=censordate
if ("`cpf'"=="PNEUM"|"`cpf'"=="FLU") drop if entrydate>d(1/11/2019)
*Only keep if COVID/FLU was the primary reason for hospitalisation
if ("`cpf'"=="COVID") keep if admitted1_reason=="U071"|admitted1_reason=="U072"
if ("`cpf'"=="FLU") keep if (admitted1_reason=="J090"|admitted1_reason=="J100"|admitted1_reason=="J101"|admitted1_reason=="J108"|admitted1_reason=="J110"|admitted1_reason=="J111"|admitted1_reason=="J118")
*get readmission date
gen readmission_date = admitted2_date if finaldischargedate==discharged1_date
gen readmission_reason = admitted2_reason if finaldischargedate==discharged1_date
replace readmission_date = admitted3_date if finaldischargedate==discharged2_date
replace readmission_reason = admitted3_reason if finaldischargedate==discharged2_date
replace readmission_date = admitted4_date if finaldischargedate==discharged3_date
replace readmission_reason = admitted4_reason if finaldischargedate==discharged3_date
replace readmission_date = admitted5_date if finaldischargedate==discharged4_date
replace readmission_reason = admitted5_reason if finaldischargedate==discharged4_date
format %d readmission_date
*get exit dates
summ readmission_date, f d
if "`cpf'"=="COVID" scalar censordate = r(max)-60
else if "`cpf'"=="PNEUM" scalar censordate = r(max)-60-365
else if "`cpf'"=="FLU" {
gen _overallcensor = r(max)-60-365
gen _latestfupdate = finaldischargedate + r(max)-60 - d(1/2/2020)
gen censordate = min(_overallcensor, _latestfupdate)
}
gen exitdate = readmission_date if readmission_date<=censordate
gen readmission = (exitdate<.)
replace exitdate = died_date_`diedsource' if died_date_`diedsource'<. & died_date_`diedsource'<=exitdate & died_date_`diedsource'<=censordate
format %d exitdate
if "`cpf'"=="FLU" assert died_date_1ocare<. if readmission ==0 & exitdate<.
else assert died_date_ons<. if readmission ==0 & exitdate<.
replace readmission = 3 if readmission ==0 & exitdate<.
replace exitdate = censordate if exitdate==.
replace readmission = 2 if readmission==1 & (readmission_reason!="U071"&readmission_reason!="U072")
replace exitdate = exitdate+0.5 if exitdate==entrydate
***************
* Save data *
***************
sort patient_id
save ./analysis/cr_create_analysis_dataset_`cpf', replace
log close