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Merge pull request #11 from opensafely/update_study_definitions
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Update study definitions
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@alexwalkerepi
alexwalkerepi authored Dec 2, 2020
2 parents 79a2fdc + 033c01f commit a184ac2
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Showing 13 changed files with 1,277 additions and 107 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/test_runner.yaml
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Expand Up @@ -39,7 +39,7 @@ jobs:
run: '[[ -z $(git status --porcelain codelists) ]] || (echo "Uncommitted changes to codelists detected, aborting" && exit 1)'

- name: Generate dummy data
run: cohortextractor generate_cohort --expectations-population=100000
run: cohortextractor generate_cohort --expectations-population=10000

- name: Run model
run: docker run --mount source=${{ github.workspace }},dst=/workspace,type=bind docker.opensafely.org/stata-mp analysis/model.do
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199 changes: 186 additions & 13 deletions analysis/000_cr_define_covariates_simple_rates.do
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Expand Up @@ -36,11 +36,28 @@ drop if discharged_expo_date ==.
drop if discharged_expo_date > $dataEndDate

drop if discharged_expo_date < hospitalised_expo_date

* Hospitalised covid/pneumonia is primary dx
gen hospitalised_expo_primary_dx = date(exposure_hosp_primary_dx, "YMD")
format hospitalised_expo_primary_dx %td

gen community_exp = cond(hospitalised_expo_primary_dx !=. , 1, 0)

* Length of stay
gen length_of_stay = discharged_expo_date - hospitalised_expo_date + 1
label var length_of_stay "Length of stay in hospital (days)"
hist length , name(length_of_stay_$group, replace) graphregion(color(white)) col(navy%50) ylab(,angle(h)) lcol(navy%20)
graph export "output/length_of_stay_$group.svg" , as(svg) replace

* Create flag for patients staying in hospital longer than the median length
summ length, detail
gen long_hosp_stay = cond(length_of_stay >= `r(p50)' , 1, 0)

* for matching
gen exposed = 1
gen indexdate= discharged_expo_date
gen indexdate= hospitalised_expo_date
format indexdate %td
gen indexMonth = month(discharged_expo_date)
gen indexMonth = month(hospitalised_expo_date)

gen flag = "$group"

Expand All @@ -50,14 +67,15 @@ gen flag = "$group"
******************************

* To be added: dates related to outcomes
foreach var of varlist dvt_gp ///
pe_gp ///
other_vte_gp ///
dvt_hospital ///
pe_hospital ///
foreach var of varlist af ///
date_icu_admission ///
dvt_gp_* ///
pe_gp_* ///
dvt_hospital_* ///
pe_hospital_* ///
other_vte_hospital ///
stroke_gp ///
stroke_hospital ///
stroke_gp_* ///
stroke_hospital_* ///
died_date_ons ///
bmi_date_measured ///
hypertension ///
Expand Down Expand Up @@ -85,7 +103,7 @@ capture confirm string variable `var'
format `var'_date %td
}


rename date_icu_admission_date icu_admission_date
/* BMI */

* Set implausible BMIs to missing:
Expand Down Expand Up @@ -189,6 +207,7 @@ drop region_string
**************************

/* Age variables */
assert age >= 18 & age <=110

* Create categorised age
recode age 18/39.9999=1 ///
Expand All @@ -197,7 +216,7 @@ recode age 18/39.9999=1 ///
60/69.9999=4 ///
70/79.9999=5 ///
80/max=6, ///
gen(agegroup)
gen(agegroup)

label define agegroup 1 "18-<40" ///
2 "40-<50" ///
Expand Down Expand Up @@ -304,9 +323,153 @@ label define hba1ccat 0 "<6.5%" ///
* Delete unneeded variables
drop hba1c_pct hba1c_percentage_1 hba1c_mmol_per_mol_1

*****************
* History of AF *
*****************

gen hist_of_af = cond(af < hospitalised_expo_date, 1, 0)

***************************
* Hist of anticoagulation *
***************************

gen hist_of_anticoag = .

levelsof indexMonth, local(months)
foreach m of local months {

* Feb
if `m' == 2 {
replace hist_of_anticoag = 1 if (anticoag_rx_jan !=. | ///
anticoag_rx_prev_nov !=. | ///
anticoag_rx_prev_dec !=.) & ///
indexMonth == 2
}
* Mar
if `m' == 3 {
replace hist_of_anticoag = 1 if (anticoag_rx_jan !=. | ///
anticoag_rx_feb !=. | ///
anticoag_rx_prev_dec !=.) & ///
indexMonth == 3
}
* Apr
if `m' == 4 {
replace hist_of_anticoag = 1 if (anticoag_rx_jan !=. | ///
anticoag_rx_feb !=. | ///
anticoag_rx_mar !=.) & ///
indexMonth == 4
}

* May
if `m' == 5 {
replace hist_of_anticoag = 1 if (anticoag_rx_feb !=. | ///
anticoag_rx_mar !=. | ///
anticoag_rx_apr !=.) & ///
indexMonth == 5
}

* Jun
if `m' == 6 {
replace hist_of_anticoag = 1 if (anticoag_rx_mar !=. | ///
anticoag_rx_apr !=. | ///
anticoag_rx_may !=.) & ///
indexMonth == 6
}

* Jul
if `m' == 7 {
replace hist_of_anticoag = 1 if (anticoag_rx_apr !=. | ///
anticoag_rx_may !=. | ///
anticoag_rx_jun !=.) & ///
indexMonth == 7
}

* Aug
if `m' == 8 {
replace hist_of_anticoag = 1 if (anticoag_rx_may !=. | ///
anticoag_rx_jun !=. | ///
anticoag_rx_jul !=.) & ///
indexMonth == 8
}

* Sep
if `m' == 9 {
replace hist_of_anticoag = 1 if (anticoag_rx_jun !=. | ///
anticoag_rx_jul !=. | ///
anticoag_rx_aug !=.) & ///
indexMonth == 9
}

* Oct
if `m' == 10 {
replace hist_of_anticoag = 1 if (anticoag_rx_jul !=. | ///
anticoag_rx_aug !=. | ///
anticoag_rx_sep !=.) & ///
indexMonth == 10
}

}

replace hist_of_anticoag = 0 if hist_of_anticoag == .



******************************************
* Admitted to ICU during hospitalisation *
******************************************

gen icu_admission = cond( icu_admission_date >= hospitalised_expo_date & icu_admission_date <= discharged_expo_date , 1, 0)


**************
* Outcomes *
**************
**************
foreach o in stroke dvt pe {

* Set all dates which are less than the hospitalised date to missing
foreach v in feb mar apr may jun jul aug sep oct {
replace `o'_gp_`v'_date =. if `o'_gp_`v'_date < hospitalised_expo_date
replace `o'_hospital_`v'_date =. if `o'_gp_`v'_date < hospitalised_expo_date
}
* Select the minimum date of the dates as the outcome
gen `o'_gp = min(`o'_gp_feb_date, ///
`o'_gp_mar_date, ///
`o'_gp_apr_date, ///
`o'_gp_may_date, ///
`o'_gp_jun_date, ///
`o'_gp_jul_date, ///
`o'_gp_aug_date, ///
`o'_gp_sep_date, ///
`o'_gp_oct_date)
format `o'_gp %td

gen `o'_hospital = min(`o'_hospital_feb_date, ///
`o'_hospital_mar_date, ///
`o'_hospital_apr_date, ///
`o'_hospital_may_date, ///
`o'_hospital_jun_date, ///
`o'_hospital_jul_date, ///
`o'_hospital_aug_date, ///
`o'_hospital_sep_date, ///
`o'_hospital_oct_date)
format `o'_hospital %td

* For ONS they will be dropped below if they have died before hospitalisation
* This just picks up the min value as this doesn't represent an exact YYYY-MM-DD date
gen `o'_ons = min(`o'_hospital_feb_date, ///
`o'_hospital_mar_date, ///
`o'_hospital_apr_date, ///
`o'_hospital_may_date, ///
`o'_hospital_jun_date, ///
`o'_hospital_jul_date, ///
`o'_hospital_aug_date, ///
`o'_hospital_sep_date, ///
`o'_hospital_oct_date)



}

* Note: There may be deaths recorded after end of our study (08 Oct)
* Set these to missing
replace died_date_ons_date = . if died_date_ons_date>td(01oct2020)
Expand Down Expand Up @@ -368,7 +531,17 @@ foreach out in stroke dvt pe {

}


**** Tidy dataset
keep patient_id died_date_ons_date age ethnicity hospitalised_expo_date ///
discharged_expo_date community_exp long_hosp_stay gender agegroup hist_of_af ///
hist_of_anticoag icu_admission stroke_gp stroke_hospital stroke_ons dvt_gp ///
dvt_hospital dvt_ons pe_gp pe_hospital pe_ons hist_stroke hist_dvt hist_pe ///
stroke_in_hosp stroke_in_hosp_end_date stroke_post_hosp stroke_post_hosp_end_date ///
stroke_post_hosp_gp stroke_post_hosp_gp_end_date dvt_in_hosp dvt_in_hosp_end_date ///
dvt_post_hosp dvt_post_hosp_end_date dvt_post_hosp_gp dvt_post_hosp_gp_end_date ///
pe_in_hosp pe_in_hosp_end_date pe_post_hosp pe_post_hosp_end_date pe_post_hosp_gp ///
pe_post_hosp_gp_end_date

save "data/cohort_rates_$group", replace


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41 changes: 28 additions & 13 deletions analysis/201_cr_simple_rates.do
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
use "data/cohort_rates_$group", replace

tempname measures
postfile `measures' str13(group) str12(outcome) str12(analysis) str20(variable) category personTime numEvents rate lc uc using "data/rates_summary_$group", replace
postfile `measures' str16(group) str20(outcome) str12(analysis) str20(variable) category personTime numEvents rate lc uc using "data/rates_summary_$group", replace


foreach v in stroke dvt pe {
Expand All @@ -35,23 +35,32 @@ foreach v in stroke dvt pe {
* Overall rate
stptime
* Save measure
post `measures' ("$group") ("Overall") ("in_hosp") ("") (0) (`r(ptime)') ///
post `measures' ("$group") ("`v'") ("in_hosp") ("Overall") (0) (`r(ptime)') ///
(`r(failures)') (`r(rate)') ///
(`r(lb)') (`r(ub))')

* Stratified
foreach c in hist_`v' {
* Stratified by history of...
foreach c in hist_`v' agegroup gender ethnicity hist_of_af hist_of_anticoag long_hosp_stay icu_admission {
qui levelsof `c' , local(cats)
di `cats'
foreach l of local cats {
noi di "$group: Calculate rate for variable `c' and level `l'"


qui count if `c' ==`l'
if `r(N)' > 0 {
stptime if `c'==`l'
* Save measures
post `measures' ("$group") ("`v'") ("in_hosp") ("`c'") (`l') (`r(ptime)') ///
(`r(failures)') (`r(rate)') ///
(`r(lb)') (`r(ub))')
(`r(lb)') (`r(ub))')
}
else {
post `measures' ("$group") ("`v'") ("`a'") ("`c'") (`l') (.) ///
(.) (.) ///
(.) (.)
}


}
}

Expand All @@ -64,23 +73,32 @@ foreach v in stroke dvt pe {
* Overall rate
stptime
* Save measure
post `measures' ("$group") ("Overall") ("`a'") ("") (0) (`r(ptime)') ///
post `measures' ("$group") ("`v'") ("`a'") ("Overall") (0) (`r(ptime)') ///
(`r(failures)') (`r(rate)') ///
(`r(lb)') (`r(ub))')

* Stratified
foreach c in hist_`v' {
foreach c in hist_`v' agegroup gender ethnicity hist_of_af hist_of_anticoag long_hosp_stay icu_admission {
qui levelsof `c' , local(cats)
di `cats'
foreach l of local cats {
noi di "$group: Calculate rate for variable `c' and level `l'"

qui count if `c' ==`l'
if `r(N)' > 0 {
stptime if `c'==`l'

* Save measures
post `measures' ("$group") ("`v'") ("`a'") ("`c'") (`l') (`r(ptime)') ///
(`r(failures)') (`r(rate)') ///
(`r(lb)') (`r(ub))')
}

else {
post `measures' ("$group") ("`v'") ("`a'") ("`c'") (`l') (.) ///
(.) (.) ///
(.) (.)
}

}
}
}
Expand All @@ -96,8 +114,5 @@ gen rate_ppm = 100*(rate * 365.25 / 12)
gen lc_ppm = 100*(lc * 365.25 /12)
gen uc_ppm = 100*(uc * 365.25 /12)



* per perso
export delimited using "data/rates_summary_$group.csv", replace
erase "data/rates_summary_$group.dta"

20 changes: 20 additions & 0 deletions analysis/codelists.py
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@@ -1,12 +1,32 @@
from cohortextractor import codelist, codelist_from_csv

af_codes = codelist_from_csv(
"codelists/opensafely-atrial-fibrillation-clinical-finding.csv",
system="ctv3",
column="CTV3Code",
)

ethnicity_codes = codelist_from_csv(
"codelists/opensafely-ethnicity.csv",
system="ctv3",
column="Code",
category_column="Grouping_6",
)


# MEDICATIONS
warfarin_codes = codelist_from_csv(
"codelists/opensafely-warfarin.csv",
system="snomed",
column="id",
)

doac_codes = codelist_from_csv(
"codelists/opensafely-direct-acting-oral-anticoagulants-doac.csv",
system="snomed",
column="id",
)

diabetes_codes = codelist_from_csv(
"codelists/opensafely-diabetes.csv", system="ctv3", column="CTV3ID"
)
Expand Down
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