Job request: 1075

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher angelwong121 requested one or more actions to be run against real patient data in the Anticoagulant project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

ID Status Action
kbnxalgqazio7hlv succeeded generate_cohort
uyevxqhl3eev3jqu succeeded flowchart_af
cpmmqxt7xiqenuie succeeded flowchart_general_population
gxhvmyjucvlup66a succeeded format_dataset_af_oac
4nauqdjcmmoqcrjm succeeded create_dataset_af_oac
wagu6s5gh2o4vapt succeeded 02ai_exportfile_matching
uu3iwpasx6wdeyfi succeeded 02aii_cr_create_population_af_oac_onscoviddeath
b2vxsr3plzu6stiw succeeded 03_an_checks_af_oac_onscoviddeath
mgquezwmkwyrarm2 succeeded 04_an_descriptive_table_af_oac_onscoviddeath
vfj566dab47hw6n5 succeeded 05a_an_models_af_oac_onscoviddeath
msd4vh4cy22xu43y succeeded 06a_an_models_ethnicity_af_oac_onscoviddeath
3kxc73nsukitphqf succeeded 07_an_model_explore_af_oac_onscoviddeath
oan5jnx3o7fv3foz succeeded 08a_an_model_checks_af_oac_onscoviddeath
sh5ftvl2uy6sbkqb succeeded 09a_an_models_plot_af_oac_onscoviddeath
illrsgosdyumvmjc succeeded 02aii_cr_create_population_af_oac_admitcovid
sr4v35m26glk5rnc succeeded 03_an_checks_af_oac_admitcovid
u6sgat6gszfpcf4o succeeded 05a_an_models_af_oac_admitcovid
rwtbouetj5urtagk succeeded 06a_an_models_ethnicity_af_oac_admitcovid
wg7gm56bypp4wpyq succeeded 07_an_model_explore_af_oac_admitcovid
gzn2ngfvh22lkriz succeeded 08a_an_model_checks_af_oac_admitcovid
ljk5ddlxtfr5p3au succeeded 09a_an_models_plot_af_oac_admitcovid
bjl7n6qz4pcl2hge succeeded 02aii_cr_create_population_af_oac_covidtest
qyy4p4dj4vnrq7wi succeeded 03_an_checks_af_oac_covidtest
czgwsjwkia43ap2o succeeded 05a_an_models_af_oac_covidtest
2nxpk4lyxefinqi4 succeeded 06a_an_models_ethnicity_af_oac_covidtest
f6e77p5dyokj6ykf succeeded 08a_an_model_checks_af_oac_covidtest
4njnkus2nqk3zkq3 succeeded 09a_an_models_plot_af_oac_covidtest
p4675tffz5fqmhxt succeeded 02aii_cr_create_population_af_oac_positivecovidtest
37i4my7ucrmyprfy succeeded 03_an_checks_af_oac_positivecovidtest
oj74zpaayxvapghn succeeded 05a_an_models_af_oac_positivecovidtest
o2j4cjx5gvrr7rr6 succeeded 06a_an_models_ethnicity_af_oac_positivecovidtest
yphcrwg43uiz2q5f succeeded 08a_an_model_checks_af_oac_positivecovidtest
mzicw6eytn7lfxmi succeeded 09a_an_models_plot_af_oac_positivecovidtest
42ialgogr6bn6p5y succeeded format_dataset_af_warfarin
jvimnpfvv3nnk6bk succeeded create_dataset_af_warfarin
qih4txabkby3r6j6 succeeded 02b_cr_create_population_af_warfarin_onscoviddeath
7aapxntnml24m37c succeeded 03_an_checks_af_warfarin_onscoviddeath
ue4xb3ieebnxqotj succeeded 04_an_descriptive_table_af_warfarin_onscoviddeath
gr2fez64yqgur23p succeeded 05b_an_models_af_warfarin_onscoviddeath
sb5xt6u3z353qk45 succeeded 06b_an_models_ethnicity_af_warfarin_onscoviddeath
r26xoxlkfyipfwj2 succeeded 07_an_model_explore_af_warfarin_onscoviddeath
ibchprgmdt3vzgtg succeeded 08b_an_model_checks_af_warfarin_onscoviddeath
bgb74y57jeaay7sf succeeded 09b_an_models_plot_af_warfarin_onscoviddeath
52il6jm5x7okgni3 succeeded 02b_cr_create_population_af_warfarin_admitcovid
anhmryuk6vblqrzm succeeded 03_an_checks_af_warfarin_admitcovid
bsl6mmf44kawapbi succeeded 05b_an_models_af_warfarin_admitcovid
bwxhkwzpkchfgbxj succeeded 06b_an_models_ethnicity_af_warfarin_admitcovid
hktzxk6oc7lld74n succeeded 07_an_model_explore_af_warfarin_admitcovid
fyfvsxnfqtfh7lc3 succeeded 08b_an_model_checks_af_warfarin_admitcovid
f624jx2bcyb6ewfw succeeded 09b_an_models_plot_af_warfarin_admitcovid
bj75teaop7twejml succeeded 02b_cr_create_population_af_warfarin_onsnoncoviddeath
v45iidbydycwijmn succeeded 03_an_checks_af_warfarin_onsnoncoviddeath
kuounvofi7dol4a4 succeeded 05b_an_models_af_warfarin_onsnoncoviddeath
rgtpxqrsbof54awh succeeded 06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
teb6gl24s3wamov5 succeeded 08b_an_model_checks_af_warfarin_onsnoncoviddeath
rrip3vxyyiihbm53 succeeded 09b_an_models_plot_af_warfarin_onsnoncoviddeath
3hmtisqk2icbx2hw succeeded 02b_cr_create_population_af_warfarin_covidtest
xknahx4dfasdu3on succeeded 03_an_checks_af_warfarin_covidtest
fom47ypjjvtzvw3m succeeded 05b_an_models_af_warfarin_covidtest
k75pxgrhis2odwag succeeded 06b_an_models_ethnicity_af_warfarin_covidtest
2tksyoznjkcsdb2w succeeded 08b_an_model_checks_af_warfarin_covidtest
yribac3aimfetuaf succeeded 09b_an_models_plot_af_warfarin_covidtest
q25ai6fiw6ibqlsi succeeded 02b_cr_create_population_af_warfarin_positivecovidtest
n4fxx6j7gklgomhy succeeded 03_an_checks_af_warfarin_positivecovidtest
3uiiutiego2jpkpp succeeded 05b_an_models_af_warfarin_positivecovidtest
bs53hzblpaspyjv3 succeeded 06b_an_models_ethnicity_af_warfarin_positivecovidtest
hjjdvdd3l47tynck succeeded 08b_an_model_checks_af_warfarin_positivecovidtest
sbza76mhcfcmqviz succeeded 09b_an_models_plot_af_warfarin_positivecovidtest
rnaryqv5vxqw4wpw succeeded matching
zlwvqdvgp5p5mndg succeeded format_dataset_af_match
o3ek5hpbtmojp6d6 succeeded create_dataset_af_match
zg633ylgz4thzhyw succeeded 02c_cr_create_population_af_match_onscoviddeath
otzdialminqjvsrg succeeded 03_an_checks_af_match_onscoviddeath
b7eogmoipy34arv3 succeeded 04_an_descriptive_table_af_match_onscoviddeath
hzyb6vgkwjyeulio succeeded 05c_an_models_af_match_onscoviddeath
iaukjfo4fuptlwee succeeded 06c_an_models_ethnicity_af_match_onscoviddeath
h4p6l4vajwuze44m succeeded 07_an_model_explore_af_match_onscoviddeath
wfuatfwtnge7z7nq succeeded 08c_an_model_checks_af_match_onscoviddeath
rtlqkjii7nu5rdfw succeeded 09a_an_models_plot_af_match_onscoviddeath
kdioccfrllhrponp succeeded 02c_cr_create_population_af_match_admitcovid
gwwwqr6fj6fucyuv succeeded 03_an_checks_af_match_admitcovid
oafpd3xmpczqn6a6 succeeded 05c_an_models_af_match_admitcovid
y25ybpuvs6aj6akt succeeded 06c_an_models_ethnicity_af_match_admitcovid
eqsu26vdugto2ibr succeeded 07_an_model_explore_af_match_admitcovid
l2w24uriyokkmqhb succeeded 08c_an_model_checks_af_match_admitcovid
cwlzwnlpt5ljqkcv succeeded 09a_an_models_plot_af_match_admitcovid
ivzwjpubqw3kj5gs succeeded 02c_cr_create_population_af_match_covidtest
zcayt5ebgtxnkcec succeeded 03_an_checks_af_match_covidtest
dat5jdl7jexhdem7 succeeded 05c_an_models_af_match_covidtest
hvbepwfpzueaepi7 succeeded 06c_an_models_ethnicity_af_match_covidtest
agn4zoy4yoicq75w succeeded 08c_an_model_checks_af_match_covidtest
cpkh3ppfy7gun7xm succeeded 09a_an_models_plot_af_match_covidtest
4p5uiivznqvs4lid succeeded 02c_cr_create_population_af_match_positivecovidtest
uu2jbuvmeb5wqjfp succeeded 03_an_checks_af_match_positivecovidtest
lrmjdvv2miu7vuj4 succeeded 05c_an_models_af_match_positivecovidtest
3lxbczhl7pfcfqp2 succeeded 06c_an_models_ethnicity_af_match_positivecovidtest
nuxkrwxvy2s7w2pv succeeded 08c_an_model_checks_af_match_positivecovidtest
y6urf6mb7qn62cte succeeded 09a_an_models_plot_af_match_positivecovidtest
dw3xsraa2uiu6ddw succeeded SA1_02a_cr_create_population_af_oac_onscoviddeath
cph3tueywyq3b6w7 succeeded SA1_05a_an_models_af_oac_onscoviddeath
aj34iyfs25dzaq73 succeeded SA1_06a_an_models_ethnicity_af_oac_onscoviddeath
2amyhqybewyocuu6 succeeded SA1_02a_cr_create_population_af_oac_admitcovid
2sc7u2onvgwz2s26 succeeded SA1_05a_an_models_af_oac_admitcovid
2ti5ic3xvlaf2i7g succeeded SA1_06a_an_models_ethnicity_af_oac_admitcovid
bnal35b3wob2mosw succeeded SA1_02a_cr_create_population_af_oac_covidtest
aevlgvnujs3qogj2 succeeded SA1_05a_an_models_af_oac_covidtest
2ln4osfnznslur4k succeeded SA1_06a_an_models_ethnicity_af_oac_covidtest
aprrbocr5mhifwoj succeeded SA1_02a_cr_create_population_af_oac_positivecovidtest
te3kmpdotqaj6ywd succeeded SA1_05a_an_models_af_oac_positivecovidtest
2ecuc5c7sat4k7bx succeeded SA1_06a_an_models_ethnicity_af_oac_positivecovidtest
blq47mjfczhxyf6q succeeded SA1_02b_cr_create_population_af_warfarin_onscoviddeath
gqokb5why4l2c44u succeeded SA1_05b_an_models_af_warfarin_onscoviddeath
yrjn7lbzjnwklfyw succeeded SA1_06b_an_models_ethnicity_af_warfarin_onscoviddeath
x63s3mbolonozslt succeeded SA1_02b_cr_create_population_af_warfarin_admitcovid
n2otmusjd37ki6nf succeeded SA1_05b_an_models_af_warfarin_admitcovid
us3lika4ex245i5p succeeded SA1_06b_an_models_ethnicity_af_warfarin_admitcovid
ado2bsqnmb2tlcxr succeeded SA1_02b_cr_create_population_af_warfarin_onsnoncoviddeath
3gthlyd4hvddbs63 succeeded SA1_05b_an_models_af_warfarin_onsnoncoviddeath
iar6qsvimdk75kn5 succeeded SA1_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
hov4x7tqdjfzl52h succeeded SA1_02b_cr_create_population_af_warfarin_covidtest
oskee3c7clxulsb2 succeeded SA1_05b_an_models_af_warfarin_covidtest
ldxpnq22we5ohdyq succeeded SA1_06b_an_models_ethnicity_af_warfarin_covidtest
7r2ig7yfgl7lmefq succeeded SA1_02b_cr_create_population_af_warfarin_positivecovidtest
ld6ycsondottvaca succeeded SA1_05b_an_models_af_warfarin_positivecovidtest
6p7lcxq5ureu2oal succeeded SA1_06b_an_models_ethnicity_af_warfarin_positivecovidtest
ujiktzwdxcvelq4u succeeded SA1_02c_cr_create_population_af_match_onscoviddeath
wn7soifh7fgkvmn3 succeeded SA1_05c_an_models_af_match_onscoviddeath
6xzsaqvqrcqxtqi7 succeeded SA1_06c_an_models_ethnicity_af_match_onscoviddeath
o4ax4jgwqkiuj6hn succeeded SA1_02c_cr_create_population_af_match_admitcovid
u2zvvm4zqjxuxh3v succeeded SA1_05c_an_models_af_match_admitcovid
2m4minls7ul5zkdl succeeded SA1_06c_an_models_ethnicity_af_match_admitcovid
u2xbljn77gl7yr6l succeeded SA1_02c_cr_create_population_af_match_covidtest
kbs6c5o5s7hu4dhs succeeded SA1_05c_an_models_af_match_covidtest
iboa6y3lgk4swx57 succeeded SA1_06c_an_models_ethnicity_af_match_covidtest
swh7k3uf4lzqhwgq succeeded SA1_02c_cr_create_population_af_match_positivecovidtest
657sbd5e5odbn2vl succeeded SA1_05c_an_models_af_match_positivecovidtest
gytwssftwtm7fvjr succeeded SA1_06c_an_models_ethnicity_af_match_positivecovidtest
rwav3d42jq7o5j4t succeeded SA2_02a_cr_create_population_af_oac_onscoviddeath
fkkj2xy5h3qpldcj succeeded SA2_05a_an_models_af_oac_onscoviddeath
pb36hdrifrtcj2gj succeeded SA2_06a_an_models_ethnicity_af_oac_onscoviddeath
xkx6ajwjft63rhjk succeeded SA2_02a_cr_create_population_af_oac_admitcovid
kuf7odndzii6svi5 succeeded SA2_05a_an_models_af_oac_admitcovid
zwujihhlatvcxah7 succeeded SA2_06a_an_models_ethnicity_af_oac_admitcovid
prx6y65jwnx4ri7m succeeded SA2_02a_cr_create_population_af_oac_covidtest
uf2kc5sqveeazgsw succeeded SA2_05a_an_models_af_oac_covidtest
7hwtgytqckgbjdzb succeeded SA2_06a_an_models_ethnicity_af_oac_covidtest
7qjfr3hxili74y5m succeeded SA2_02a_cr_create_population_af_oac_positivecovidtest
tff7sktxdjedtsj5 succeeded SA2_05a_an_models_af_oac_positivecovidtest
rokzzztc4px6a664 succeeded SA2_06a_an_models_ethnicity_af_oac_positivecovidtest
iwoaafjvaluzvh4q succeeded SA2_02c_cr_create_population_af_match_onscoviddeath
xldpx77fti4crzbt succeeded SA2_05c_an_models_af_match_onscoviddeath
nnwxgbkjnwmmn7pf succeeded SA2_06c_an_models_ethnicity_af_match_onscoviddeath
dgcs3ktamapk4wur succeeded SA2_02c_cr_create_population_af_match_admitcovid
w5xap2mujuyphnej succeeded SA2_05c_an_models_af_match_admitcovid
oafmlccauqe7cqp6 succeeded SA2_06c_an_models_ethnicity_af_match_admitcovid
pdotvzmz3m2ukfq5 succeeded SA2_02c_cr_create_population_af_match_covidtest
ckcue6tmklyqtavw succeeded SA2_05c_an_models_af_match_covidtest
fnbflu23v6dgw722 succeeded SA2_06c_an_models_ethnicity_af_match_covidtest
4pcqbh4ujzmto3ho succeeded SA2_02c_cr_create_population_af_match_positivecovidtest
4tljvzdqiff5vc3r succeeded SA2_05c_an_models_af_match_positivecovidtest
htczvygasucn2ow4 succeeded SA2_06c_an_models_ethnicity_af_match_positivecovidtest
eoeelecc3t4lr2ep succeeded SA3_02b_cr_create_population_af_warfarin_onscoviddeath
h3i5ir4b6aogqsnp succeeded SA3_05b_an_models_af_warfarin_onscoviddeath
ftlzos6i7cjnfdfy succeeded SA3_06b_an_models_ethnicity_af_warfarin_onscoviddeath
tytrfedf3vsgf63l succeeded SA3_02b_cr_create_population_af_warfarin_admitcovid
kz6r2tbk5cyxmyyx succeeded SA3_05b_an_models_af_warfarin_admitcovid
sgmusqfalhnxgpo6 succeeded SA3_06b_an_models_ethnicity_af_warfarin_admitcovid
tbwntevurbg4d3b5 succeeded SA3_02b_cr_create_population_af_warfarin_onsnoncoviddeath
6zozynfctsrl5g7e succeeded SA3_05b_an_models_af_warfarin_onsnoncoviddeath
evlzsxpvp5gyzzr3 succeeded SA3_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
tzza3l4n4wlsokt6 succeeded SA3_02b_cr_create_population_af_warfarin_covidtest
sueh727o7cauhxk5 succeeded SA3_05b_an_models_af_warfarin_covidtest
rwsb3gn3cnpcosoa succeeded SA3_06b_an_models_ethnicity_af_warfarin_covidtest
hxz2aupxfvwgq36f succeeded SA3_02b_cr_create_population_af_warfarin_positivecovidtest
sox4r4k5pxcjp2g2 succeeded SA3_05b_an_models_af_warfarin_positivecovidtest
j25v3gxnlolxuss3 succeeded SA3_06b_an_models_ethnicity_af_warfarin_positivecovidtest
ko3eool6jrdt6ob6 succeeded SA4_02b_cr_create_population_af_warfarin_onscoviddeath
h734e4kga2wolb6z succeeded SA4_05b_an_models_af_warfarin_onscoviddeath
jdlrwowsidtocozb succeeded SA4_06b_an_models_ethnicity_af_warfarin_onscoviddeath
l2x6ulygntdauipk succeeded SA4_02b_cr_create_population_af_warfarin_admitcovid
22arkqiuv72b6x7o succeeded SA4_05b_an_models_af_warfarin_admitcovid
zzj4baxg4n72xw2y succeeded SA4_06b_an_models_ethnicity_af_warfarin_admitcovid
efxig246z576ew2u succeeded SA4_02b_cr_create_population_af_warfarin_onsnoncoviddeath
syilwby5fpl43cww succeeded SA4_05b_an_models_af_warfarin_onsnoncoviddeath
bcqgsvpmzmft3nfy succeeded SA4_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
auckb6sknbpjzsf6 succeeded SA4_02b_cr_create_population_af_warfarin_covidtest
25ejsjwc6zsxidgc succeeded SA4_05b_an_models_af_warfarin_covidtest
yteakesiidn7aqqo succeeded SA4_06b_an_models_ethnicity_af_warfarin_covidtest
x7kfvdj4gjprmqp7 succeeded SA4_02b_cr_create_population_af_warfarin_positivecovidtest
3rgk4zeba54qjhfv succeeded SA4_05b_an_models_af_warfarin_positivecovidtest
xf44hwpbsebpe3sg succeeded SA4_06b_an_models_ethnicity_af_warfarin_positivecovidtest
w45f36xenpdnuuqi succeeded SA5_02b_cr_create_population_af_warfarin_onscoviddeath
3q4otffrq7bgpo2g succeeded SA5_05b_an_models_af_warfarin_onscoviddeath
mgjisfewbtbvqwkt succeeded SA5_03b_an_checks_onscoviddeath
jzktoohvfq2laiuu succeeded SA5_06b_an_models_ethnicity_af_warfarin_onscoviddeath
oxw2w6m4syd6g6bm succeeded SA5_02b_cr_create_population_af_warfarin_admitcovid
k5nahmljtbcxhv3e succeeded SA5_05b_an_models_af_warfarin_admitcovid
bjdrvanhxetb66r6 succeeded SA5_03b_an_checks_admitcovid
slb3igegiirypuok succeeded SA5_06b_an_models_ethnicity_af_warfarin_admitcovid
pbsuflokav3d2ns2 succeeded SA5_02b_cr_create_population_af_warfarin_onsnoncoviddeath
3p5gethj2fvd4nz2 succeeded SA5_05b_an_models_af_warfarin_onsnoncoviddeath
e4m77qi2tma2uxgd succeeded SA5_03b_an_checks_onsnoncoviddeath
5revajiqw3yb4d2g succeeded SA5_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
kcstetkbclkcanxu succeeded SA5_02b_cr_create_population_af_warfarin_covidtest
iiecb4opb6u2q5nz succeeded SA5_05b_an_models_af_warfarin_covidtest
a3jmxzz7x3luia7k succeeded SA5_03b_an_checks_covidtest
jor2w7i3xjtwife4 succeeded SA5_06b_an_models_ethnicity_af_warfarin_covidtest
dhlql4tnyikgvzcv succeeded SA5_02b_cr_create_population_af_warfarin_positivecovidtest
rirjtsmbhhgklpy6 succeeded SA5_05b_an_models_af_warfarin_positivecovidtest
oj4qzc6cexq3nzdx succeeded SA5_03b_an_checks_positivecovidtest
uy2p24cohuri2uzd succeeded SA5_06b_an_models_ethnicity_af_warfarin_positivecovidtest
7vk7tb3jk7w5bbw5 succeeded 10a_an_models_int_af_oac_positivecovidtest
l5p7is2dz4o5ypnu succeeded 02b_cr_create_population_af_warfarin_mi_ons
ienfatbjupvnve4k succeeded 05b_an_models_af_warfarin_mi_ons
cohua5ksv4iuk5f4 succeeded 06b_an_models_ethnicity_af_warfarin_mi_ons
eqeb2jzy6vbm444x succeeded 02b_cr_create_population_af_warfarin_stroke_ons
4fhlhwh7pdaamtqt succeeded 05b_an_models_af_warfarin_stroke_ons
nnefxskv3f4e37lf succeeded 06b_an_models_ethnicity_af_warfarin_stroke_ons
fbceg7i27zifmrdm succeeded 02b_cr_create_population_af_warfarin_vte_ons
b7upcatiy4q5laol succeeded 05b_an_models_af_warfarin_vte_ons
x4qybw6ybrrp5ttf succeeded 06b_an_models_ethnicity_af_warfarin_vte_ons
cbz5alyidik6agj2 succeeded 02b_cr_create_population_af_warfarin_gi_bleed_ons
jssuhtdx2psghaas succeeded 05b_an_models_af_warfarin_gi_bleed_ons
itnnvxxficri6avw succeeded 06b_an_models_ethnicity_af_warfarin_gi_bleed_ons
4fof4ibkvf2uu26g succeeded 02b_cr_create_population_af_warfarin_intracranial_bleed_ons
4q3zp2cw76nq44n5 succeeded 05b_an_models_af_warfarin_intracranial_bleed_ons
jo5b62pyjc4hybwq succeeded 06b_an_models_ethnicity_af_warfarin_intracranial_bleed_ons

Pipeline

Show Hide project.yaml
version: "3.0"

expectations:
  population_size: 100000

actions:
  generate_cohort:
    run: cohortextractor:latest generate_cohort 
    outputs:
      highly_sensitive:
        cohort1: output/input_af.csv
        cohort2: output/input_af_population_flow_chart.csv
        cohort3: output/input_general_population.csv
        cohort4: output/input_general_population_flow_chart.csv

  # Flowchart for AF population
  flowchart_af:
    run: stata-mp:latest analysis/flow_chart_af_population.do af_population_flowchart
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        log: output/oac_log/flow_chart_af_population.log
 
  # Flowchart for general population (before matching)
  flowchart_general_population:
    run: stata-mp:latest analysis/flow_chart_general_population.do general_population_flowchart
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        log: output/oac_log/flow_chart_general_population.log

  # Main Analysis 1
  # Objective 1: compare AF treated people with AF non-treated people
  format_dataset_af_oac:
    run: stata-mp:latest analysis/00_cr_create_analysis_dataset.do af_oac input_af
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        log: output/oac_log/00_cr_create_analysis_dataset.log
      highly_sensitive:
        data: "output/oac_tempdata/format_dataset.dta"

  create_dataset_af_oac:
    run: stata-mp:latest analysis/01_cr_create_exposure_outcome_af.do af_oac
    needs: [format_dataset_af_oac]
    outputs:
      moderately_sensitive:
        log: output/oac_log/01_cr_create_exposure_outcome_af.log
      highly_sensitive:
        data: "output/oac_tempdata/cr_dataset_af.dta"

  # Export case dataset for matching
  02ai_exportfile_matching:
    run: stata-mp:latest analysis/02ai_exportfile_matching.do af_oac
    needs: [create_dataset_af_oac]
    outputs:
      moderately_sensitive:
        log: output/oac_log/02ai_exportfile_matching.log
      highly_sensitive:
        data1: "output/input_af_oac.csv"
        data2: "output/input_af_oac.dta"
               
  # Primary Outcomes: ONS COVID-19 death
  02aii_cr_create_population_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/02aii_cr_create_population.do onscoviddeath af_oac
    needs: [create_dataset_af_oac]
    outputs:
      moderately_sensitive:
        log: output/oac_log/02aii_cr_create_population_onscoviddeath.log
      highly_sensitive:
        data1: "output/oac_tempdata/analysis_dataset_onscoviddeath.dta"
        data2: "output/oac_tempdata/analysis_dataset_STSET_onscoviddeath.dta"

  03_an_checks_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/03_an_checks.do onscoviddeath af_oac
    needs: [02aii_cr_create_population_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/03_an_checks_onscoviddeath.log
  
  04_an_descriptive_table_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/04_an_descriptive_table.do onscoviddeath af_oac
    needs: [02aii_cr_create_population_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/04_an_descriptive_table_onscoviddeath.log
        table: "output/oac_tabfig/table1_onscoviddeath.txt"

  05a_an_models_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/05a_an_models.do onscoviddeath af_oac
    needs: [02aii_cr_create_population_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/05a_an_models_onscoviddeath.log
        table: "output/oac_tabfig/table2_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/onscoviddeath_univar.ster"
        data2: "output/oac_tempdata/onscoviddeath_multivar1.ster"
        data3: "output/oac_tempdata/onscoviddeath_multivar2.ster"
        data4: "output/oac_tempdata/onscoviddeath_multivar3.ster"

  06a_an_models_ethnicity_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/06a_an_models_ethnicity.do onscoviddeath af_oac
    needs: [02aii_cr_create_population_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/06a_an_models_ethnicity_onscoviddeath.log
        table: "output/oac_tabfig/table3_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/onscoviddeath_univar_ethn.ster"
        data2: "output/oac_tempdata/onscoviddeath_multivar1_ethn.ster"
        data3: "output/oac_tempdata/onscoviddeath_multivar2_ethn.ster"
        data4: "output/oac_tempdata/onscoviddeath_multivar2_withoutethn.ster"
        data5: "output/oac_tempdata/onscoviddeath_multivar3_ethn.ster"
        data6: "output/oac_tempdata/onscoviddeath_multivar3_withoutethn.ster"

  07_an_model_explore_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/07_an_model_explore.do onscoviddeath af_oac
    needs: [02aii_cr_create_population_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/07_an_model_explore_onscoviddeath.log
        table: "output/oac_tabfig/table4_onscoviddeath.txt"

  08a_an_model_checks_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/08a_an_model_checks.do onscoviddeath af_oac
    needs: [02aii_cr_create_population_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/08a_an_model_checks_onscoviddeath.log
        fig1: "output/oac_tabfig/onscoviddeath_schoenplot1.svg"
        fig2: "output/oac_tabfig/onscoviddeath_schoenplot2.svg"
        fig3: "output/oac_tabfig/onscoviddeath_schoenplot3.svg"
        fig4: "output/oac_tabfig/onscoviddeath_schoenplot4.svg"
        table1: "output/oac_tabfig/table5_onscoviddeath.txt"
        fig5: "output/oac_tabfig/onscoviddeath_schoenplot1_completecase.svg"
        fig6: "output/oac_tabfig/onscoviddeath_schoenplot2_completecase.svg"
        fig7: "output/oac_tabfig/onscoviddeath_schoenplot3_completecase_ethn.svg"
        fig8: "output/oac_tabfig/onscoviddeath_schoenplot3_completecase.svg"
        fig9: "output/oac_tabfig/onscoviddeath_schoenplot4_completecase_ethn.svg"
        fig10: "output/oac_tabfig/onscoviddeath_schoenplot4_completecase.svg"
        table2: "output/oac_tabfig/table6_onscoviddeath.txt"

  09a_an_models_plot_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/09a_an_models_plot.do onscoviddeath af_oac 3 0.5 0.1
    needs: [02aii_cr_create_population_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/09a_an_models_plot_onscoviddeath.log
        fig1: "output/oac_tabfig/adj_curves_onscoviddeath.svg"
        fig2: "output/oac_tabfig/diff_curves_onscoviddeath.svg"

  # Primary Outcomes: COVID-19 hospital admission
  02aii_cr_create_population_af_oac_admitcovid:
    run: stata-mp:latest analysis/02aii_cr_create_population.do admitcovid af_oac
    needs: [create_dataset_af_oac]
    outputs:
      moderately_sensitive:
        log: output/oac_log/02aii_cr_create_population_admitcovid.log
      highly_sensitive:
        data1: "output/oac_tempdata/analysis_dataset_admitcovid.dta"
        data2: "output/oac_tempdata/analysis_dataset_STSET_admitcovid.dta"

  03_an_checks_af_oac_admitcovid:
    run: stata-mp:latest analysis/03_an_checks.do admitcovid af_oac
    needs: [02aii_cr_create_population_af_oac_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_log/03_an_checks_admitcovid.log

  05a_an_models_af_oac_admitcovid:
    run: stata-mp:latest analysis/05a_an_models.do admitcovid af_oac
    needs: [02aii_cr_create_population_af_oac_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_log/05a_an_models_admitcovid.log
        table: "output/oac_tabfig/table2_admitcovid.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/admitcovid_univar.ster"
        data2: "output/oac_tempdata/admitcovid_multivar1.ster"
        data3: "output/oac_tempdata/admitcovid_multivar2.ster"
        data4: "output/oac_tempdata/admitcovid_multivar3.ster"

  06a_an_models_ethnicity_af_oac_admitcovid:
    run: stata-mp:latest analysis/06a_an_models_ethnicity.do admitcovid af_oac
    needs: [02aii_cr_create_population_af_oac_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_log/06a_an_models_ethnicity_admitcovid.log
        table: "output/oac_tabfig/table3_admitcovid.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/admitcovid_univar_ethn.ster"
        data2: "output/oac_tempdata/admitcovid_multivar1_ethn.ster"
        data3: "output/oac_tempdata/admitcovid_multivar2_ethn.ster"
        data4: "output/oac_tempdata/admitcovid_multivar2_withoutethn.ster"
        data5: "output/oac_tempdata/admitcovid_multivar3_ethn.ster"
        data6: "output/oac_tempdata/admitcovid_multivar3_withoutethn.ster"

  07_an_model_explore_af_oac_admitcovid:
    run: stata-mp:latest analysis/07_an_model_explore.do admitcovid af_oac
    needs: [02aii_cr_create_population_af_oac_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_log/07_an_model_explore_admitcovid.log
        table: "output/oac_tabfig/table4_admitcovid.txt"

  08a_an_model_checks_af_oac_admitcovid:
    run: stata-mp:latest analysis/08a_an_model_checks.do admitcovid af_oac
    needs: [02aii_cr_create_population_af_oac_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_log/08a_an_model_checks_admitcovid.log
        fig1: "output/oac_tabfig/admitcovid_schoenplot1.svg"
        fig2: "output/oac_tabfig/admitcovid_schoenplot2.svg"
        fig3: "output/oac_tabfig/admitcovid_schoenplot3.svg"
        fig4: "output/oac_tabfig/admitcovid_schoenplot4.svg"
        table1: "output/oac_tabfig/table5_admitcovid.txt"
        fig5: "output/oac_tabfig/admitcovid_schoenplot1_completecase.svg"
        fig6: "output/oac_tabfig/admitcovid_schoenplot2_completecase.svg"
        fig7: "output/oac_tabfig/admitcovid_schoenplot3_completecase_ethn.svg"
        fig8: "output/oac_tabfig/admitcovid_schoenplot3_completecase.svg"
        fig9: "output/oac_tabfig/admitcovid_schoenplot4_completecase_ethn.svg"
        fig10: "output/oac_tabfig/admitcovid_schoenplot4_completecase.svg"
        table2: "output/oac_tabfig/table6_admitcovid.txt"

  09a_an_models_plot_af_oac_admitcovid:
    run: stata-mp:latest analysis/09a_an_models_plot.do admitcovid af_oac 2 0.5 0.1
    needs: [02aii_cr_create_population_af_oac_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_log/09a_an_models_plot_admitcovid.log
        fig1: "output/oac_tabfig/adj_curves_admitcovid.svg"
        fig2: "output/oac_tabfig/diff_curves_admitcovid.svg"

  # Exploratory Outcomes: COVID-19 test
  02aii_cr_create_population_af_oac_covidtest:
    run: stata-mp:latest analysis/02aii_cr_create_population.do covidtest af_oac
    needs: [create_dataset_af_oac]
    outputs:
      moderately_sensitive:
        log: output/oac_log/02aii_cr_create_population_covidtest.log
      highly_sensitive:
        data1: "output/oac_tempdata/analysis_dataset_covidtest.dta"
        data2: "output/oac_tempdata/analysis_dataset_STSET_covidtest.dta"

  03_an_checks_af_oac_covidtest:
    run: stata-mp:latest analysis/03_an_checks.do covidtest af_oac
    needs: [02aii_cr_create_population_af_oac_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/03_an_checks_covidtest.log

  05a_an_models_af_oac_covidtest:
    run: stata-mp:latest analysis/05a_an_models.do covidtest af_oac
    needs: [02aii_cr_create_population_af_oac_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/05a_an_models_covidtest.log
        table: "output/oac_tabfig/table2_covidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/covidtest_univar.ster"
        data2: "output/oac_tempdata/covidtest_multivar1.ster"
        data3: "output/oac_tempdata/covidtest_multivar2.ster"
        data4: "output/oac_tempdata/covidtest_multivar3.ster"

  06a_an_models_ethnicity_af_oac_covidtest:
    run: stata-mp:latest analysis/06a_an_models_ethnicity.do covidtest af_oac
    needs: [02aii_cr_create_population_af_oac_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/06a_an_models_ethnicity_covidtest.log
        table: "output/oac_tabfig/table3_covidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/covidtest_univar_ethn.ster"
        data2: "output/oac_tempdata/covidtest_multivar1_ethn.ster"
        data3: "output/oac_tempdata/covidtest_multivar2_ethn.ster"
        data4: "output/oac_tempdata/covidtest_multivar2_withoutethn.ster"
        data5: "output/oac_tempdata/covidtest_multivar3_ethn.ster"
        data6: "output/oac_tempdata/covidtest_multivar3_withoutethn.ster"

  08a_an_model_checks_af_oac_covidtest:
    run: stata-mp:latest analysis/08a_an_model_checks.do covidtest af_oac
    needs: [02aii_cr_create_population_af_oac_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/08a_an_model_checks_covidtest.log
        fig1: "output/oac_tabfig/covidtest_schoenplot1.svg"
        fig2: "output/oac_tabfig/covidtest_schoenplot2.svg"
        fig3: "output/oac_tabfig/covidtest_schoenplot3.svg"
        fig4: "output/oac_tabfig/covidtest_schoenplot4.svg"
        table1: "output/oac_tabfig/table5_covidtest.txt"
        fig5: "output/oac_tabfig/covidtest_schoenplot1_completecase.svg"
        fig6: "output/oac_tabfig/covidtest_schoenplot2_completecase.svg"
        fig7: "output/oac_tabfig/covidtest_schoenplot3_completecase_ethn.svg"
        fig8: "output/oac_tabfig/covidtest_schoenplot3_completecase.svg"
        fig9: "output/oac_tabfig/covidtest_schoenplot4_completecase_ethn.svg"
        fig10: "output/oac_tabfig/covidtest_schoenplot4_completecase.svg"
        table2: "output/oac_tabfig/table6_covidtest.txt"

  09a_an_models_plot_af_oac_covidtest:
    run: stata-mp:latest analysis/09a_an_models_plot.do covidtest af_oac 3 20 1
    needs: [02aii_cr_create_population_af_oac_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/09a_an_models_plot_covidtest.log
        fig1: "output/oac_tabfig/adj_curves_covidtest.svg"
        fig2: "output/oac_tabfig/diff_curves_covidtest.svg"

  # Exploratory Outcomes: Positive COVID test
  02aii_cr_create_population_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/02aii_cr_create_population.do positivecovidtest af_oac
    needs: [create_dataset_af_oac]
    outputs:
      moderately_sensitive:
        log: output/oac_log/02aii_cr_create_population_positivecovidtest.log
      highly_sensitive:
        data1: "output/oac_tempdata/analysis_dataset_positivecovidtest.dta"
        data2: "output/oac_tempdata/analysis_dataset_STSET_positivecovidtest.dta"

  03_an_checks_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/03_an_checks.do positivecovidtest af_oac
    needs: [02aii_cr_create_population_af_oac_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/03_an_checks_positivecovidtest.log

  05a_an_models_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/05a_an_models.do positivecovidtest af_oac
    needs: [02aii_cr_create_population_af_oac_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/05a_an_models_positivecovidtest.log
        table: "output/oac_tabfig/table2_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/positivecovidtest_univar.ster"
        data2: "output/oac_tempdata/positivecovidtest_multivar1.ster"
        data3: "output/oac_tempdata/positivecovidtest_multivar2.ster"
        data4: "output/oac_tempdata/positivecovidtest_multivar3.ster"

  06a_an_models_ethnicity_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/06a_an_models_ethnicity.do positivecovidtest af_oac
    needs: [02aii_cr_create_population_af_oac_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/06a_an_models_ethnicity_positivecovidtest.log
        table: "output/oac_tabfig/table3_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/positivecovidtest_univar_ethn.ster"
        data2: "output/oac_tempdata/positivecovidtest_multivar1_ethn.ster"
        data3: "output/oac_tempdata/positivecovidtest_multivar2_ethn.ster"
        data4: "output/oac_tempdata/positivecovidtest_multivar2_withoutethn.ster"
        data5: "output/oac_tempdata/positivecovidtest_multivar3_ethn.ster"
        data6: "output/oac_tempdata/positivecovidtest_multivar3_withoutethn.ster"

  08a_an_model_checks_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/08a_an_model_checks.do positivecovidtest af_oac
    needs: [02aii_cr_create_population_af_oac_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/08a_an_model_checks_positivecovidtest.log
        fig1: "output/oac_tabfig/positivecovidtest_schoenplot1.svg"
        fig2: "output/oac_tabfig/positivecovidtest_schoenplot2.svg"
        fig3: "output/oac_tabfig/positivecovidtest_schoenplot3.svg"
        fig4: "output/oac_tabfig/positivecovidtest_schoenplot4.svg"
        table1: "output/oac_tabfig/table5_positivecovidtest.txt"
        fig5: "output/oac_tabfig/positivecovidtest_schoenplot1_completecase.svg"
        fig6: "output/oac_tabfig/positivecovidtest_schoenplot2_completecase.svg"
        fig7: "output/oac_tabfig/positivecovidtest_schoenplot3_completecase_ethn.svg"
        fig8: "output/oac_tabfig/positivecovidtest_schoenplot3_completecase.svg"
        fig9: "output/oac_tabfig/positivecovidtest_schoenplot4_completecase_ethn.svg"
        fig10: "output/oac_tabfig/positivecovidtest_schoenplot4_completecase.svg"
        table2: "output/oac_tabfig/table6_positivecovidtest.txt"

  09a_an_models_plot_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/09a_an_models_plot.do positivecovidtest af_oac 3 2 0.5
    needs: [02aii_cr_create_population_af_oac_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/09a_an_models_plot_positivecovidtest.log
        fig1: "output/oac_tabfig/adj_curves_positivecovidtest.svg"
        fig2: "output/oac_tabfig/diff_curves_positivecovidtest.svg"

  # Main Analysis 2
  # Objective 2: Compare warfarin users and DOAC users
  format_dataset_af_warfarin:
    run: stata-mp:latest analysis/00_cr_create_analysis_dataset.do af_warfarin input_af
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/00_cr_create_analysis_dataset.log
      highly_sensitive:
        data: "output/warfarin_tempdata/format_dataset.dta"

  create_dataset_af_warfarin:
    run: stata-mp:latest analysis/01_cr_create_exposure_outcome_af.do af_warfarin
    needs: [format_dataset_af_warfarin]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/01_cr_create_exposure_outcome_af.log
      highly_sensitive:
        data: "output/warfarin_tempdata/cr_dataset_af.dta"

  # Primary Outcomes: ONS COVID-19 death
  02b_cr_create_population_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/02b_cr_create_population.do onscoviddeath af_warfarin
    needs: [create_dataset_af_warfarin]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/02b_cr_create_population_onscoviddeath.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/analysis_dataset_onscoviddeath.dta"
        data2: "output/warfarin_tempdata/analysis_dataset_STSET_onscoviddeath.dta"

  03_an_checks_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/03_an_checks.do onscoviddeath af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/03_an_checks_onscoviddeath.log
  
  04_an_descriptive_table_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/04_an_descriptive_table.do onscoviddeath af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/04_an_descriptive_table_onscoviddeath.log
        table: "output/warfarin_tabfig/table1_onscoviddeath.txt"

  05b_an_models_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/05b_an_models.do onscoviddeath af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/05b_an_models_onscoviddeath.log
        table: "output/warfarin_tabfig/table2_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/onscoviddeath_univar.ster"
        data2: "output/warfarin_tempdata/onscoviddeath_multivar1.ster"
        data3: "output/warfarin_tempdata/onscoviddeath_multivar2.ster"
        data4: "output/warfarin_tempdata/onscoviddeath_multivar3.ster"

  06b_an_models_ethnicity_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do onscoviddeath af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/06b_an_models_ethnicity_onscoviddeath.log
        table: "output/warfarin_tabfig/table3_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/onscoviddeath_univar_ethn.ster"
        data2: "output/warfarin_tempdata/onscoviddeath_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/onscoviddeath_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/onscoviddeath_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/onscoviddeath_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/onscoviddeath_multivar3_withoutethn.ster"

  07_an_model_explore_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/07_an_model_explore.do onscoviddeath af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/07_an_model_explore_onscoviddeath.log
        table: "output/warfarin_tabfig/table4_onscoviddeath.txt"

  08b_an_model_checks_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/08b_an_model_checks.do onscoviddeath af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/08b_an_model_checks_onscoviddeath.log
        fig1: "output/warfarin_tabfig/onscoviddeath_schoenplot1.svg"
        fig2: "output/warfarin_tabfig/onscoviddeath_schoenplot2.svg"
        fig3: "output/warfarin_tabfig/onscoviddeath_schoenplot3.svg"
        fig4: "output/warfarin_tabfig/onscoviddeath_schoenplot4.svg"
        table1: "output/warfarin_tabfig/table5_onscoviddeath.txt"
        fig5: "output/warfarin_tabfig/onscoviddeath_schoenplot1_completecase.svg"
        fig6: "output/warfarin_tabfig/onscoviddeath_schoenplot2_completecase.svg"
        fig7: "output/warfarin_tabfig/onscoviddeath_schoenplot3_completecase_ethn.svg"
        fig8: "output/warfarin_tabfig/onscoviddeath_schoenplot3_completecase.svg"
        fig9: "output/warfarin_tabfig/onscoviddeath_schoenplot4_completecase_ethn.svg"
        fig10: "output/warfarin_tabfig/onscoviddeath_schoenplot4_completecase.svg"
        table2: "output/warfarin_tabfig/table6_onscoviddeath.txt"

  09b_an_models_plot_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/09b_an_models_plot.do onscoviddeath af_warfarin 2 1 0.1
    needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/09b_an_models_plot_onscoviddeath.log
        fig1: "output/warfarin_tabfig/adj_curves_onscoviddeath.svg"
        fig2: "output/warfarin_tabfig/diff_curves_onscoviddeath.svg"

  # Primary Outcomes: COVID-19 hospital admission
  02b_cr_create_population_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/02b_cr_create_population.do admitcovid af_warfarin
    needs: [create_dataset_af_warfarin]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/02b_cr_create_population_admitcovid.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/analysis_dataset_admitcovid.dta"
        data2: "output/warfarin_tempdata/analysis_dataset_STSET_admitcovid.dta"

  03_an_checks_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/03_an_checks.do admitcovid af_warfarin
    needs: [02b_cr_create_population_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/03_an_checks_admitcovid.log

  05b_an_models_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/05b_an_models.do admitcovid af_warfarin
    needs: [02b_cr_create_population_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/05b_an_models_admitcovid.log
        table: "output/warfarin_tabfig/table2_admitcovid.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/admitcovid_univar.ster"
        data2: "output/warfarin_tempdata/admitcovid_multivar1.ster"
        data3: "output/warfarin_tempdata/admitcovid_multivar2.ster"
        data4: "output/warfarin_tempdata/admitcovid_multivar3.ster"

  06b_an_models_ethnicity_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do admitcovid af_warfarin
    needs: [02b_cr_create_population_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/06b_an_models_ethnicity_admitcovid.log
        table: "output/warfarin_tabfig/table3_admitcovid.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/admitcovid_univar_ethn.ster"
        data2: "output/warfarin_tempdata/admitcovid_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/admitcovid_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/admitcovid_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/admitcovid_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/admitcovid_multivar3_withoutethn.ster"

  07_an_model_explore_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/07_an_model_explore.do admitcovid af_warfarin
    needs: [02b_cr_create_population_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/07_an_model_explore_admitcovid.log
        table: "output/warfarin_tabfig/table4_admitcovid.txt"

  08b_an_model_checks_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/08b_an_model_checks.do admitcovid af_warfarin
    needs: [02b_cr_create_population_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/08b_an_model_checks_admitcovid.log
        fig1: "output/warfarin_tabfig/admitcovid_schoenplot1.svg"
        fig2: "output/warfarin_tabfig/admitcovid_schoenplot2.svg"
        fig3: "output/warfarin_tabfig/admitcovid_schoenplot3.svg"
        fig4: "output/warfarin_tabfig/admitcovid_schoenplot4.svg"
        table1: "output/warfarin_tabfig/table5_admitcovid.txt"
        fig5: "output/warfarin_tabfig/admitcovid_schoenplot1_completecase.svg"
        fig6: "output/warfarin_tabfig/admitcovid_schoenplot2_completecase.svg"
        fig7: "output/warfarin_tabfig/admitcovid_schoenplot3_completecase_ethn.svg"
        fig8: "output/warfarin_tabfig/admitcovid_schoenplot3_completecase.svg"
        fig9: "output/warfarin_tabfig/admitcovid_schoenplot4_completecase_ethn.svg"
        fig10: "output/warfarin_tabfig/admitcovid_schoenplot4_completecase.svg"
        table2: "output/warfarin_tabfig/table6_admitcovid.txt"

  09b_an_models_plot_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/09b_an_models_plot.do admitcovid af_warfarin 2 1 0.1
    needs: [02b_cr_create_population_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/09b_an_models_plot_admitcovid.log
        fig1: "output/warfarin_tabfig/adj_curves_admitcovid.svg"
        fig2: "output/warfarin_tabfig/diff_curves_admitcovid.svg"

    # Exploratory Outcomes: Non-COVID death
  02b_cr_create_population_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/02b_cr_create_population.do onsnoncoviddeath af_warfarin
    needs: [create_dataset_af_warfarin]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/02b_cr_create_population_onsnoncoviddeath.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/analysis_dataset_onsnoncoviddeath.dta"
        data2: "output/warfarin_tempdata/analysis_dataset_STSET_onsnoncoviddeath.dta"

  03_an_checks_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/03_an_checks.do onsnoncoviddeath af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/03_an_checks_onsnoncoviddeath.log

  05b_an_models_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/05b_an_models.do onsnoncoviddeath af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/05b_an_models_onsnoncoviddeath.log
        table: "output/warfarin_tabfig/table2_onsnoncoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/onsnoncoviddeath_univar.ster"
        data2: "output/warfarin_tempdata/onsnoncoviddeath_multivar1.ster"
        data3: "output/warfarin_tempdata/onsnoncoviddeath_multivar2.ster"
        data4: "output/warfarin_tempdata/onsnoncoviddeath_multivar3.ster"

  06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do onsnoncoviddeath af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/06b_an_models_ethnicity_onsnoncoviddeath.log
        table: "output/warfarin_tabfig/table3_onsnoncoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/onsnoncoviddeath_univar_ethn.ster"
        data2: "output/warfarin_tempdata/onsnoncoviddeath_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/onsnoncoviddeath_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/onsnoncoviddeath_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/onsnoncoviddeath_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/onsnoncoviddeath_multivar3_withoutethn.ster"

  08b_an_model_checks_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/08b_an_model_checks.do onsnoncoviddeath af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/08b_an_model_checks_onsnoncoviddeath.log
        fig1: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot1.svg"
        fig2: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot2.svg"
        fig3: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot3.svg"
        fig4: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot4.svg"
        table1: "output/warfarin_tabfig/table5_onsnoncoviddeath.txt"
        fig5: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot1_completecase.svg"
        fig6: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot2_completecase.svg"
        fig7: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot3_completecase_ethn.svg"
        fig8: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot3_completecase.svg"
        fig9: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot4_completecase_ethn.svg"
        fig10: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot4_completecase.svg"
        table2: "output/warfarin_tabfig/table6_onsnoncoviddeath.txt"

  09b_an_models_plot_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/09b_an_models_plot.do onsnoncoviddeath af_warfarin 3 5 1
    needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/09b_an_models_plot_onsnoncoviddeath.log
        fig1: "output/warfarin_tabfig/adj_curves_onsnoncoviddeath.svg"
        fig2: "output/warfarin_tabfig/diff_curves_onsnoncoviddeath.svg"
        
  # Exploratory Outcomes: COVID-19 test
  02b_cr_create_population_af_warfarin_covidtest:
    run: stata-mp:latest analysis/02b_cr_create_population.do covidtest af_warfarin
    needs: [create_dataset_af_warfarin]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/02b_cr_create_population_covidtest.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/analysis_dataset_covidtest.dta"
        data2: "output/warfarin_tempdata/analysis_dataset_STSET_covidtest.dta"

  03_an_checks_af_warfarin_covidtest:
    run: stata-mp:latest analysis/03_an_checks.do covidtest af_warfarin
    needs: [02b_cr_create_population_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/03_an_checks_covidtest.log

  05b_an_models_af_warfarin_covidtest:
    run: stata-mp:latest analysis/05b_an_models.do covidtest af_warfarin
    needs: [02b_cr_create_population_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/05b_an_models_covidtest.log
        table: "output/warfarin_tabfig/table2_covidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/covidtest_univar.ster"
        data2: "output/warfarin_tempdata/covidtest_multivar1.ster"
        data3: "output/warfarin_tempdata/covidtest_multivar2.ster"
        data4: "output/warfarin_tempdata/covidtest_multivar3.ster"

  06b_an_models_ethnicity_af_warfarin_covidtest:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do covidtest af_warfarin
    needs: [02b_cr_create_population_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/06b_an_models_ethnicity_covidtest.log
        table: "output/warfarin_tabfig/table3_covidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/covidtest_univar_ethn.ster"
        data2: "output/warfarin_tempdata/covidtest_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/covidtest_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/covidtest_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/covidtest_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/covidtest_multivar3_withoutethn.ster"

  08b_an_model_checks_af_warfarin_covidtest:
    run: stata-mp:latest analysis/08b_an_model_checks.do covidtest af_warfarin
    needs: [02b_cr_create_population_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/08b_an_model_checks_covidtest.log
        fig1: "output/warfarin_tabfig/covidtest_schoenplot1.svg"
        fig2: "output/warfarin_tabfig/covidtest_schoenplot2.svg"
        fig3: "output/warfarin_tabfig/covidtest_schoenplot3.svg"
        fig4: "output/warfarin_tabfig/covidtest_schoenplot4.svg"
        table1: "output/warfarin_tabfig/table5_covidtest.txt"
        fig5: "output/warfarin_tabfig/covidtest_schoenplot1_completecase.svg"
        fig6: "output/warfarin_tabfig/covidtest_schoenplot2_completecase.svg"
        fig7: "output/warfarin_tabfig/covidtest_schoenplot3_completecase_ethn.svg"
        fig8: "output/warfarin_tabfig/covidtest_schoenplot3_completecase.svg"
        fig9: "output/warfarin_tabfig/covidtest_schoenplot4_completecase_ethn.svg"
        fig10: "output/warfarin_tabfig/covidtest_schoenplot4_completecase.svg"
        table2: "output/warfarin_tabfig/table6_covidtest.txt"

  09b_an_models_plot_af_warfarin_covidtest:
    run: stata-mp:latest analysis/09b_an_models_plot.do covidtest af_warfarin 3 30 1
    needs: [02b_cr_create_population_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/09b_an_models_plot_covidtest.log
        fig1: "output/warfarin_tabfig/adj_curves_covidtest.svg"
        fig2: "output/warfarin_tabfig/diff_curves_covidtest.svg"

  # Exploratory Outcomes: Positive COVID test
  02b_cr_create_population_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/02b_cr_create_population.do positivecovidtest af_warfarin
    needs: [create_dataset_af_warfarin]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/02b_cr_create_population_positivecovidtest.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/analysis_dataset_positivecovidtest.dta"
        data2: "output/warfarin_tempdata/analysis_dataset_STSET_positivecovidtest.dta"

  03_an_checks_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/03_an_checks.do positivecovidtest af_warfarin
    needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/03_an_checks_positivecovidtest.log

  05b_an_models_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/05b_an_models.do positivecovidtest af_warfarin
    needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/05b_an_models_positivecovidtest.log
        table: "output/warfarin_tabfig/table2_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/positivecovidtest_univar.ster"
        data2: "output/warfarin_tempdata/positivecovidtest_multivar1.ster"
        data3: "output/warfarin_tempdata/positivecovidtest_multivar2.ster"
        data4: "output/warfarin_tempdata/positivecovidtest_multivar3.ster"

  06b_an_models_ethnicity_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do positivecovidtest af_warfarin
    needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/06b_an_models_ethnicity_positivecovidtest.log
        table: "output/warfarin_tabfig/table3_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/positivecovidtest_univar_ethn.ster"
        data2: "output/warfarin_tempdata/positivecovidtest_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/positivecovidtest_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/positivecovidtest_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/positivecovidtest_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/positivecovidtest_multivar3_withoutethn.ster"

  08b_an_model_checks_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/08b_an_model_checks.do positivecovidtest af_warfarin
    needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/08b_an_model_checks_positivecovidtest.log
        fig1: "output/warfarin_tabfig/positivecovidtest_schoenplot1.svg"
        fig2: "output/warfarin_tabfig/positivecovidtest_schoenplot2.svg"
        fig3: "output/warfarin_tabfig/positivecovidtest_schoenplot3.svg"
        fig4: "output/warfarin_tabfig/positivecovidtest_schoenplot4.svg"
        table1: "output/warfarin_tabfig/table5_positivecovidtest.txt"
        fig5: "output/warfarin_tabfig/positivecovidtest_schoenplot1_completecase.svg"
        fig6: "output/warfarin_tabfig/positivecovidtest_schoenplot2_completecase.svg"
        fig7: "output/warfarin_tabfig/positivecovidtest_schoenplot3_completecase_ethn.svg"
        fig8: "output/warfarin_tabfig/positivecovidtest_schoenplot3_completecase.svg"
        fig9: "output/warfarin_tabfig/positivecovidtest_schoenplot4_completecase_ethn.svg"
        fig10: "output/warfarin_tabfig/positivecovidtest_schoenplot4_completecase.svg"
        table2: "output/warfarin_tabfig/table6_positivecovidtest.txt"

  09b_an_models_plot_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/09b_an_models_plot.do positivecovidtest af_warfarin 2 1.5 0.1
    needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/09b_an_models_plot_positivecovidtest.log
        fig1: "output/warfarin_tabfig/adj_curves_positivecovidtest.svg"
        fig2: "output/warfarin_tabfig/diff_curves_positivecovidtest.svg"

# Main Analysis 3
# Objective 1: compare AF treated people with general population
  matching:
    run: python:latest python analysis/match_running.py
    needs: [generate_cohort, 02ai_exportfile_matching]
    outputs:
      moderately_sensitive:
        log: output/matching_report_af_gen_pop.txt
      highly_sensitive:
        data1: "output/matched_cases_af_gen_pop.csv"
        data2: "output/matched_matches_af_gen_pop.csv"

  format_dataset_af_match:
    run: stata-mp:latest analysis/00_cr_create_analysis_dataset.do af_match matched_matches_af_gen_pop
    needs: [generate_cohort, matching]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/00_cr_create_analysis_dataset.log
      highly_sensitive:
        data: "output/oac_match_tempdata/format_dataset.dta"

  create_dataset_af_match:
    run: stata-mp:latest analysis/01c_cr_create_exposure_outcome_af_match.do af_match
    needs: [format_dataset_af_match, matching]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/01c_cr_create_exposure_outcome_af_match.log
      highly_sensitive:
        data: "output/oac_match_tempdata/cr_dataset_af.dta"

  # Primary Outcomes: ONS COVID-19 death
  02c_cr_create_population_af_match_onscoviddeath:
    run: stata-mp:latest analysis/02c_cr_create_population.do onscoviddeath af_match matched_cases_af_gen_pop
    needs: [create_dataset_af_match, matching, 02ai_exportfile_matching]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/02c_cr_create_population_onscoviddeath.log
      highly_sensitive:
        data1: "output/oac_match_tempdata/matched_control_onscoviddeath.dta"
        data2: "output/oac_match_tempdata/analysis_dataset_onscoviddeath.dta"
        data3: "output/oac_match_tempdata/analysis_dataset_STSET_onscoviddeath.dta"

  03_an_checks_af_match_onscoviddeath:
    run: stata-mp:latest analysis/03_an_checks.do onscoviddeath af_match
    needs: [02c_cr_create_population_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/03_an_checks_onscoviddeath.log
  
  04_an_descriptive_table_af_match_onscoviddeath:
    run: stata-mp:latest analysis/04_an_descriptive_table.do onscoviddeath af_match
    needs: [02c_cr_create_population_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/04_an_descriptive_table_onscoviddeath.log
        table: "output/oac_match_tabfig/table1_onscoviddeath.txt"

  05c_an_models_af_match_onscoviddeath:
    run: stata-mp:latest analysis/05c_an_models.do onscoviddeath af_match
    needs: [02c_cr_create_population_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/05c_an_models_onscoviddeath.log
        table: "output/oac_match_tabfig/table2_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/onscoviddeath_univar.ster"
        data2: "output/oac_match_tempdata/onscoviddeath_multivar1.ster"
        data3: "output/oac_match_tempdata/onscoviddeath_multivar2.ster"
        data4: "output/oac_match_tempdata/onscoviddeath_multivar3.ster"

  06c_an_models_ethnicity_af_match_onscoviddeath:
    run: stata-mp:latest analysis/06c_an_models_ethnicity.do onscoviddeath af_match
    needs: [02c_cr_create_population_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/06c_an_models_ethnicity_onscoviddeath.log
        table: "output/oac_match_tabfig/table3_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/onscoviddeath_univar_ethn.ster"
        data2: "output/oac_match_tempdata/onscoviddeath_multivar1_ethn.ster"
        data3: "output/oac_match_tempdata/onscoviddeath_multivar2_ethn.ster"
        data4: "output/oac_match_tempdata/onscoviddeath_multivar2_withoutethn.ster"
        data5: "output/oac_match_tempdata/onscoviddeath_multivar3_ethn.ster"
        data6: "output/oac_match_tempdata/onscoviddeath_multivar3_withoutethn.ster"

  07_an_model_explore_af_match_onscoviddeath:
    run: stata-mp:latest analysis/07_an_model_explore.do onscoviddeath af_match
    needs: [02c_cr_create_population_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/07_an_model_explore_onscoviddeath.log
        table: "output/oac_match_tabfig/table4_onscoviddeath.txt"

  08c_an_model_checks_af_match_onscoviddeath:
    run: stata-mp:latest analysis/08c_an_model_checks.do onscoviddeath af_match
    needs: [02c_cr_create_population_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/08c_an_model_checks_onscoviddeath.log
        fig1: "output/oac_match_tabfig/onscoviddeath_schoenplot1.svg"
        fig2: "output/oac_match_tabfig/onscoviddeath_schoenplot2.svg"
        fig3: "output/oac_match_tabfig/onscoviddeath_schoenplot3.svg"
        fig4: "output/oac_match_tabfig/onscoviddeath_schoenplot4.svg"
        table1: "output/oac_match_tabfig/table5_onscoviddeath.txt"
        fig5: "output/oac_match_tabfig/onscoviddeath_schoenplot1_completecase.svg"
        fig6: "output/oac_match_tabfig/onscoviddeath_schoenplot2_completecase.svg"
        fig7: "output/oac_match_tabfig/onscoviddeath_schoenplot3_completecase_ethn.svg"
        fig8: "output/oac_match_tabfig/onscoviddeath_schoenplot3_completecase.svg"
        fig9: "output/oac_match_tabfig/onscoviddeath_schoenplot4_completecase_ethn.svg"
        fig10: "output/oac_match_tabfig/onscoviddeath_schoenplot4_completecase.svg"
        table2: "output/oac_match_tabfig/table6_onscoviddeath.txt"

  09a_an_models_plot_af_match_onscoviddeath:
    run: stata-mp:latest analysis/09a_an_models_plot.do onscoviddeath af_match 1 0.5 0.1
    needs: [02c_cr_create_population_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/09a_an_models_plot_onscoviddeath.log
        fig1: "output/oac_match_tabfig/adj_curves_onscoviddeath.svg"
        fig2: "output/oac_match_tabfig/diff_curves_onscoviddeath.svg"

  # Primary Outcomes: COVID-19 hospital admission
  02c_cr_create_population_af_match_admitcovid:
    run: stata-mp:latest analysis/02c_cr_create_population.do admitcovid af_match matched_cases_af_gen_pop
    needs: [create_dataset_af_match, matching, 02ai_exportfile_matching]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/02c_cr_create_population_admitcovid.log
      highly_sensitive:
        data1: "output/oac_match_tempdata/matched_control_admitcovid.dta"
        data2: "output/oac_match_tempdata/analysis_dataset_admitcovid.dta"
        data3: "output/oac_match_tempdata/analysis_dataset_STSET_admitcovid.dta"

  03_an_checks_af_match_admitcovid:
    run: stata-mp:latest analysis/03_an_checks.do admitcovid af_match
    needs: [02c_cr_create_population_af_match_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/03_an_checks_admitcovid.log

  05c_an_models_af_match_admitcovid:
    run: stata-mp:latest analysis/05c_an_models.do admitcovid af_match
    needs: [02c_cr_create_population_af_match_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/05c_an_models_admitcovid.log
        table: "output/oac_match_tabfig/table2_admitcovid.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/admitcovid_univar.ster"
        data2: "output/oac_match_tempdata/admitcovid_multivar1.ster"
        data3: "output/oac_match_tempdata/admitcovid_multivar2.ster"
        data4: "output/oac_match_tempdata/admitcovid_multivar3.ster"

  06c_an_models_ethnicity_af_match_admitcovid:
    run: stata-mp:latest analysis/06c_an_models_ethnicity.do admitcovid af_match
    needs: [02c_cr_create_population_af_match_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/06c_an_models_ethnicity_admitcovid.log
        table: "output/oac_match_tabfig/table3_admitcovid.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/admitcovid_univar_ethn.ster"
        data2: "output/oac_match_tempdata/admitcovid_multivar1_ethn.ster"
        data3: "output/oac_match_tempdata/admitcovid_multivar2_ethn.ster"
        data4: "output/oac_match_tempdata/admitcovid_multivar2_withoutethn.ster"
        data5: "output/oac_match_tempdata/admitcovid_multivar3_ethn.ster"
        data6: "output/oac_match_tempdata/admitcovid_multivar3_withoutethn.ster"

  07_an_model_explore_af_match_admitcovid:
    run: stata-mp:latest analysis/07_an_model_explore.do admitcovid af_match
    needs: [02c_cr_create_population_af_match_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/07_an_model_explore_admitcovid.log
        table: "output/oac_match_tabfig/table4_admitcovid.txt"

  08c_an_model_checks_af_match_admitcovid:
    run: stata-mp:latest analysis/08c_an_model_checks.do admitcovid af_match
    needs: [02c_cr_create_population_af_match_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/08c_an_model_checks_admitcovid.log
        fig1: "output/oac_match_tabfig/admitcovid_schoenplot1.svg"
        fig2: "output/oac_match_tabfig/admitcovid_schoenplot2.svg"
        fig3: "output/oac_match_tabfig/admitcovid_schoenplot3.svg"
        fig4: "output/oac_match_tabfig/admitcovid_schoenplot4.svg"
        table1: "output/oac_match_tabfig/table5_admitcovid.txt"
        fig5: "output/oac_match_tabfig/admitcovid_schoenplot1_completecase.svg"
        fig6: "output/oac_match_tabfig/admitcovid_schoenplot2_completecase.svg"
        fig7: "output/oac_match_tabfig/admitcovid_schoenplot3_completecase_ethn.svg"
        fig8: "output/oac_match_tabfig/admitcovid_schoenplot3_completecase.svg"
        fig9: "output/oac_match_tabfig/admitcovid_schoenplot4_completecase_ethn.svg"
        fig10: "output/oac_match_tabfig/admitcovid_schoenplot4_completecase.svg"
        table2: "output/oac_match_tabfig/table6_admitcovid.txt"

  09a_an_models_plot_af_match_admitcovid:
    run: stata-mp:latest analysis/09a_an_models_plot.do admitcovid af_match 2 0.5 0.1
    needs: [02c_cr_create_population_af_match_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/09a_an_models_plot_admitcovid.log
        fig1: "output/oac_match_tabfig/adj_curves_admitcovid.svg"
        fig2: "output/oac_match_tabfig/diff_curves_admitcovid.svg"

  # Exploratory Outcomes: COVID-19 test
  02c_cr_create_population_af_match_covidtest:
    run: stata-mp:latest analysis/02c_cr_create_population.do covidtest af_match matched_cases_af_gen_pop
    needs: [create_dataset_af_match, matching, 02ai_exportfile_matching]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/02c_cr_create_population_covidtest.log
      highly_sensitive:
        data1: "output/oac_match_tempdata/matched_control_covidtest.dta"
        data2: "output/oac_match_tempdata/analysis_dataset_covidtest.dta"
        data3: "output/oac_match_tempdata/analysis_dataset_STSET_covidtest.dta"

  03_an_checks_af_match_covidtest:
    run: stata-mp:latest analysis/03_an_checks.do covidtest af_match
    needs: [02c_cr_create_population_af_match_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/03_an_checks_covidtest.log

  05c_an_models_af_match_covidtest:
    run: stata-mp:latest analysis/05c_an_models.do covidtest af_match
    needs: [02c_cr_create_population_af_match_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/05c_an_models_covidtest.log
        table: "output/oac_match_tabfig/table2_covidtest.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/covidtest_univar.ster"
        data2: "output/oac_match_tempdata/covidtest_multivar1.ster"
        data3: "output/oac_match_tempdata/covidtest_multivar2.ster"
        data4: "output/oac_match_tempdata/covidtest_multivar3.ster"

  06c_an_models_ethnicity_af_match_covidtest:
    run: stata-mp:latest analysis/06c_an_models_ethnicity.do covidtest af_match
    needs: [02c_cr_create_population_af_match_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/06c_an_models_ethnicity_covidtest.log
        table: "output/oac_match_tabfig/table3_covidtest.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/covidtest_univar_ethn.ster"
        data2: "output/oac_match_tempdata/covidtest_multivar1_ethn.ster"
        data3: "output/oac_match_tempdata/covidtest_multivar2_ethn.ster"
        data4: "output/oac_match_tempdata/covidtest_multivar2_withoutethn.ster"
        data5: "output/oac_match_tempdata/covidtest_multivar3_ethn.ster"
        data6: "output/oac_match_tempdata/covidtest_multivar3_withoutethn.ster"

  08c_an_model_checks_af_match_covidtest:
    run: stata-mp:latest analysis/08c_an_model_checks.do covidtest af_match
    needs: [02c_cr_create_population_af_match_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/08c_an_model_checks_covidtest.log
        fig1: "output/oac_match_tabfig/covidtest_schoenplot1.svg"
        fig2: "output/oac_match_tabfig/covidtest_schoenplot2.svg"
        fig3: "output/oac_match_tabfig/covidtest_schoenplot3.svg"
        fig4: "output/oac_match_tabfig/covidtest_schoenplot4.svg"
        table1: "output/oac_match_tabfig/table5_covidtest.txt"
        fig5: "output/oac_match_tabfig/covidtest_schoenplot1_completecase.svg"
        fig6: "output/oac_match_tabfig/covidtest_schoenplot2_completecase.svg"
        fig7: "output/oac_match_tabfig/covidtest_schoenplot3_completecase_ethn.svg"
        fig8: "output/oac_match_tabfig/covidtest_schoenplot3_completecase.svg"
        fig9: "output/oac_match_tabfig/covidtest_schoenplot4_completecase_ethn.svg"
        fig10: "output/oac_match_tabfig/covidtest_schoenplot4_completecase.svg"
        table2: "output/oac_match_tabfig/table6_covidtest.txt"

  09a_an_models_plot_af_match_covidtest:
    run: stata-mp:latest analysis/09a_an_models_plot.do covidtest af_match 3 20 1
    needs: [02c_cr_create_population_af_match_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/09a_an_models_plot_covidtest.log
        fig1: "output/oac_match_tabfig/adj_curves_covidtest.svg"
        fig2: "output/oac_match_tabfig/diff_curves_covidtest.svg"

  # Exploratory Outcomes: Positive COVID test
  02c_cr_create_population_af_match_positivecovidtest:
    run: stata-mp:latest analysis/02c_cr_create_population.do positivecovidtest af_match matched_cases_af_gen_pop
    needs: [create_dataset_af_match, matching, 02ai_exportfile_matching]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/02c_cr_create_population_positivecovidtest.log
      highly_sensitive:
        data1: "output/oac_match_tempdata/matched_control_positivecovidtest.dta"
        data2: "output/oac_match_tempdata/analysis_dataset_positivecovidtest.dta"
        data3: "output/oac_match_tempdata/analysis_dataset_STSET_positivecovidtest.dta"

  03_an_checks_af_match_positivecovidtest:
    run: stata-mp:latest analysis/03_an_checks.do positivecovidtest af_match
    needs: [02c_cr_create_population_af_match_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/03_an_checks_positivecovidtest.log

  05c_an_models_af_match_positivecovidtest:
    run: stata-mp:latest analysis/05c_an_models.do positivecovidtest af_match
    needs: [02c_cr_create_population_af_match_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/05c_an_models_positivecovidtest.log
        table: "output/oac_match_tabfig/table2_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/positivecovidtest_univar.ster"
        data2: "output/oac_match_tempdata/positivecovidtest_multivar1.ster"
        data3: "output/oac_match_tempdata/positivecovidtest_multivar2.ster"
        data4: "output/oac_match_tempdata/positivecovidtest_multivar3.ster"

  06c_an_models_ethnicity_af_match_positivecovidtest:
    run: stata-mp:latest analysis/06c_an_models_ethnicity.do positivecovidtest af_match
    needs: [02c_cr_create_population_af_match_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/06c_an_models_ethnicity_positivecovidtest.log
        table: "output/oac_match_tabfig/table3_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/positivecovidtest_univar_ethn.ster"
        data2: "output/oac_match_tempdata/positivecovidtest_multivar1_ethn.ster"
        data3: "output/oac_match_tempdata/positivecovidtest_multivar2_ethn.ster"
        data4: "output/oac_match_tempdata/positivecovidtest_multivar2_withoutethn.ster"
        data5: "output/oac_match_tempdata/positivecovidtest_multivar3_ethn.ster"
        data6: "output/oac_match_tempdata/positivecovidtest_multivar3_withoutethn.ster"

  08c_an_model_checks_af_match_positivecovidtest:
    run: stata-mp:latest analysis/08c_an_model_checks.do positivecovidtest af_match
    needs: [02c_cr_create_population_af_match_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/08c_an_model_checks_positivecovidtest.log
        fig1: "output/oac_match_tabfig/positivecovidtest_schoenplot1.svg"
        fig2: "output/oac_match_tabfig/positivecovidtest_schoenplot2.svg"
        fig3: "output/oac_match_tabfig/positivecovidtest_schoenplot3.svg"
        fig4: "output/oac_match_tabfig/positivecovidtest_schoenplot4.svg"
        table1: "output/oac_match_tabfig/table5_positivecovidtest.txt"
        fig5: "output/oac_match_tabfig/positivecovidtest_schoenplot1_completecase.svg"
        fig6: "output/oac_match_tabfig/positivecovidtest_schoenplot2_completecase.svg"
        fig7: "output/oac_match_tabfig/positivecovidtest_schoenplot3_completecase_ethn.svg"
        fig8: "output/oac_match_tabfig/positivecovidtest_schoenplot3_completecase.svg"
        fig9: "output/oac_match_tabfig/positivecovidtest_schoenplot4_completecase_ethn.svg"
        fig10: "output/oac_match_tabfig/positivecovidtest_schoenplot4_completecase.svg"
        table2: "output/oac_match_tabfig/table6_positivecovidtest.txt"

  09a_an_models_plot_af_match_positivecovidtest:
    run: stata-mp:latest analysis/09a_an_models_plot.do positivecovidtest af_match 4 1 0.1
    needs: [02c_cr_create_population_af_match_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/09a_an_models_plot_positivecovidtest.log
        fig1: "output/oac_match_tabfig/adj_curves_positivecovidtest.svg"
        fig2: "output/oac_match_tabfig/diff_curves_positivecovidtest.svg"

  # Sensitivity Analysis 1
  # Remove people with antiplatelets
  # Objective 1: compare AF treated people with AF non-treated people

  # Primary Outcomes: ONS COVID-19 death
  SA1_02a_cr_create_population_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/SA1_02a_cr_create_population.do onscoviddeath SA1_af_oac
    needs: [02aii_cr_create_population_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_1/SA1_02a_cr_create_population_onscoviddeath.log
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_1/analysis_dataset_onscoviddeath.dta"
        data2: "output/oac_tempdata/sens_analysis_1/analysis_dataset_STSET_onscoviddeath.dta"

  SA1_05a_an_models_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/05a_an_models.do onscoviddeath SA1_af_oac
    needs: [SA1_02a_cr_create_population_af_oac_onscoviddeath, 05a_an_models_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_1/05a_an_models_onscoviddeath.log
        table: "output/oac_tabfig/sens_analysis_1/table2_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_1/onscoviddeath_univar.ster"
        data2: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar1.ster"
        data3: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar2.ster"
        data4: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar3.ster"

  SA1_06a_an_models_ethnicity_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/06a_an_models_ethnicity.do onscoviddeath SA1_af_oac
    needs: [SA1_02a_cr_create_population_af_oac_onscoviddeath, 06a_an_models_ethnicity_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_1/06a_an_models_ethnicity_onscoviddeath.log
        table: "output/oac_tabfig/sens_analysis_1/table3_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_1/onscoviddeath_univar_ethn.ster"
        data2: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar1_ethn.ster"
        data3: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar2_ethn.ster"
        data4: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar2_withoutethn.ster"
        data5: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar3_ethn.ster"
        data6: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar3_withoutethn.ster"

  # Primary Outcomes: COVID-19 hospital admission
  SA1_02a_cr_create_population_af_oac_admitcovid:
    run: stata-mp:latest analysis/SA1_02a_cr_create_population.do admitcovid SA1_af_oac
    needs: [02aii_cr_create_population_af_oac_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_1/SA1_02a_cr_create_population_admitcovid.log
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_1/analysis_dataset_admitcovid.dta"
        data2: "output/oac_tempdata/sens_analysis_1/analysis_dataset_STSET_admitcovid.dta"

  SA1_05a_an_models_af_oac_admitcovid:
    run: stata-mp:latest analysis/05a_an_models.do admitcovid SA1_af_oac
    needs: [SA1_02a_cr_create_population_af_oac_admitcovid, 05a_an_models_af_oac_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_1/05a_an_models_admitcovid.log
        table: "output/oac_tabfig/sens_analysis_1/table2_admitcovid.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_1/admitcovid_univar.ster"
        data2: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar1.ster"
        data3: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar2.ster"
        data4: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar3.ster"

  SA1_06a_an_models_ethnicity_af_oac_admitcovid:
    run: stata-mp:latest analysis/06a_an_models_ethnicity.do admitcovid SA1_af_oac
    needs: [SA1_02a_cr_create_population_af_oac_admitcovid, 06a_an_models_ethnicity_af_oac_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_1/06a_an_models_ethnicity_admitcovid.log
        table: "output/oac_tabfig/sens_analysis_1/table3_admitcovid.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_1/admitcovid_univar_ethn.ster"
        data2: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar1_ethn.ster"
        data3: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar2_ethn.ster"
        data4: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar2_withoutethn.ster"
        data5: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar3_ethn.ster"
        data6: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar3_withoutethn.ster"

  # Exploratory Outcomes: COVID-19 test
  SA1_02a_cr_create_population_af_oac_covidtest:
    run: stata-mp:latest analysis/SA1_02a_cr_create_population.do covidtest SA1_af_oac
    needs: [02aii_cr_create_population_af_oac_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_1/SA1_02a_cr_create_population_covidtest.log
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_1/analysis_dataset_covidtest.dta"
        data2: "output/oac_tempdata/sens_analysis_1/analysis_dataset_STSET_covidtest.dta"

  SA1_05a_an_models_af_oac_covidtest:
    run: stata-mp:latest analysis/05a_an_models.do covidtest SA1_af_oac
    needs: [SA1_02a_cr_create_population_af_oac_covidtest, 05a_an_models_af_oac_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_1/05a_an_models_covidtest.log
        table: "output/oac_tabfig/sens_analysis_1/table2_covidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_1/covidtest_univar.ster"
        data2: "output/oac_tempdata/sens_analysis_1/covidtest_multivar1.ster"
        data3: "output/oac_tempdata/sens_analysis_1/covidtest_multivar2.ster"
        data4: "output/oac_tempdata/sens_analysis_1/covidtest_multivar3.ster"

  SA1_06a_an_models_ethnicity_af_oac_covidtest:
    run: stata-mp:latest analysis/06a_an_models_ethnicity.do covidtest SA1_af_oac
    needs: [SA1_02a_cr_create_population_af_oac_covidtest, 06a_an_models_ethnicity_af_oac_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_1/06a_an_models_ethnicity_covidtest.log
        table: "output/oac_tabfig/sens_analysis_1/table3_covidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_1/covidtest_univar_ethn.ster"
        data2: "output/oac_tempdata/sens_analysis_1/covidtest_multivar1_ethn.ster"
        data3: "output/oac_tempdata/sens_analysis_1/covidtest_multivar2_ethn.ster"
        data4: "output/oac_tempdata/sens_analysis_1/covidtest_multivar2_withoutethn.ster"
        data5: "output/oac_tempdata/sens_analysis_1/covidtest_multivar3_ethn.ster"
        data6: "output/oac_tempdata/sens_analysis_1/covidtest_multivar3_withoutethn.ster"

  # Exploratory Outcomes: Positive COVID test
  SA1_02a_cr_create_population_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/SA1_02a_cr_create_population.do positivecovidtest SA1_af_oac
    needs: [02aii_cr_create_population_af_oac_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_1/SA1_02a_cr_create_population_positivecovidtest.log
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_1/analysis_dataset_positivecovidtest.dta"
        data2: "output/oac_tempdata/sens_analysis_1/analysis_dataset_STSET_positivecovidtest.dta"

  SA1_05a_an_models_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/05a_an_models.do positivecovidtest SA1_af_oac
    needs: [SA1_02a_cr_create_population_af_oac_positivecovidtest, 05a_an_models_af_oac_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_1/05a_an_models_positivecovidtest.log
        table: "output/oac_tabfig/sens_analysis_1/table2_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_1/positivecovidtest_univar.ster"
        data2: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar1.ster"
        data3: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar2.ster"
        data4: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar3.ster"

  SA1_06a_an_models_ethnicity_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/06a_an_models_ethnicity.do positivecovidtest SA1_af_oac
    needs: [SA1_02a_cr_create_population_af_oac_positivecovidtest, 06a_an_models_ethnicity_af_oac_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_1/06a_an_models_ethnicity_positivecovidtest.log
        table: "output/oac_tabfig/sens_analysis_1/table3_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_1/positivecovidtest_univar_ethn.ster"
        data2: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar1_ethn.ster"
        data3: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar2_ethn.ster"
        data4: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar2_withoutethn.ster"
        data5: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar3_ethn.ster"
        data6: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar3_withoutethn.ster"

  # Sensitivity Analysis 1
  # Remove people with antiplatelets
  # Objective 2: Compare warfarin users and DOAC users

  # Primary Outcomes: ONS COVID-19 death
  SA1_02b_cr_create_population_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/SA1_02b_cr_create_population.do onscoviddeath SA1_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/SA1_02b_cr_create_population_onscoviddeath.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_onscoviddeath.dta"
        data2: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_STSET_onscoviddeath.dta"

  SA1_05b_an_models_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/05b_an_models.do onscoviddeath SA1_af_warfarin
    needs: [SA1_02b_cr_create_population_af_warfarin_onscoviddeath, 05b_an_models_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/05b_an_models_onscoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_1/table2_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar3.ster"

  SA1_06b_an_models_ethnicity_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do onscoviddeath SA1_af_warfarin
    needs: [SA1_02b_cr_create_population_af_warfarin_onscoviddeath, 06b_an_models_ethnicity_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/06b_an_models_ethnicity_onscoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_1/table3_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar3_withoutethn.ster"

  # Primary Outcomes: COVID-19 hospital admission
  SA1_02b_cr_create_population_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/SA1_02b_cr_create_population.do admitcovid SA1_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/SA1_02b_cr_create_population_admitcovid.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_admitcovid.dta"
        data2: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_STSET_admitcovid.dta"

  SA1_05b_an_models_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/05b_an_models.do admitcovid SA1_af_warfarin
    needs: [SA1_02b_cr_create_population_af_warfarin_admitcovid, 05b_an_models_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/05b_an_models_admitcovid.log
        table: "output/warfarin_tabfig/sens_analysis_1/table2_admitcovid.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/admitcovid_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar3.ster"

  SA1_06b_an_models_ethnicity_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do admitcovid SA1_af_warfarin
    needs: [SA1_02b_cr_create_population_af_warfarin_admitcovid, 06b_an_models_ethnicity_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/06b_an_models_ethnicity_admitcovid.log
        table: "output/warfarin_tabfig/sens_analysis_1/table3_admitcovid.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/admitcovid_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar3_withoutethn.ster"

    # Exploratory Outcomes: Non-COVID death
  SA1_02b_cr_create_population_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/SA1_02b_cr_create_population.do onsnoncoviddeath SA1_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/SA1_02b_cr_create_population_onsnoncoviddeath.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_onsnoncoviddeath.dta"
        data2: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_STSET_onsnoncoviddeath.dta"

  SA1_05b_an_models_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/05b_an_models.do onsnoncoviddeath SA1_af_warfarin
    needs: [SA1_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 05b_an_models_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/05b_an_models_onsnoncoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_1/table2_onsnoncoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar3.ster"

  SA1_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do onsnoncoviddeath SA1_af_warfarin
    needs: [SA1_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/06b_an_models_ethnicity_onsnoncoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_1/table3_onsnoncoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar3_withoutethn.ster"
        
  # Exploratory Outcomes: COVID-19 test
  SA1_02b_cr_create_population_af_warfarin_covidtest:
    run: stata-mp:latest analysis/SA1_02b_cr_create_population.do covidtest SA1_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/SA1_02b_cr_create_population_covidtest.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_covidtest.dta"
        data2: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_STSET_covidtest.dta"

  SA1_05b_an_models_af_warfarin_covidtest:
    run: stata-mp:latest analysis/05b_an_models.do covidtest SA1_af_warfarin
    needs: [SA1_02b_cr_create_population_af_warfarin_covidtest, 05b_an_models_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/05b_an_models_covidtest.log
        table: "output/warfarin_tabfig/sens_analysis_1/table2_covidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/covidtest_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar3.ster"

  SA1_06b_an_models_ethnicity_af_warfarin_covidtest:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do covidtest SA1_af_warfarin
    needs: [SA1_02b_cr_create_population_af_warfarin_covidtest, 06b_an_models_ethnicity_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/06b_an_models_ethnicity_covidtest.log
        table: "output/warfarin_tabfig/sens_analysis_1/table3_covidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/covidtest_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar3_withoutethn.ster"

  # Exploratory Outcomes: Positive COVID test
  SA1_02b_cr_create_population_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/SA1_02b_cr_create_population.do positivecovidtest SA1_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/SA1_02b_cr_create_population_positivecovidtest.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_positivecovidtest.dta"
        data2: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_STSET_positivecovidtest.dta"

  SA1_05b_an_models_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/05b_an_models.do positivecovidtest SA1_af_warfarin
    needs: [SA1_02b_cr_create_population_af_warfarin_positivecovidtest, 05b_an_models_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/05b_an_models_positivecovidtest.log
        table: "output/warfarin_tabfig/sens_analysis_1/table2_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar3.ster"

  SA1_06b_an_models_ethnicity_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do positivecovidtest SA1_af_warfarin
    needs: [SA1_02b_cr_create_population_af_warfarin_positivecovidtest, 06b_an_models_ethnicity_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_1/06b_an_models_ethnicity_positivecovidtest.log
        table: "output/warfarin_tabfig/sens_analysis_1/table3_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar3_withoutethn.ster"

# Sensitivity Analysis 1
# Remove people with antiplatelets
# Objective 1: compare AF treated people with general population

  # Primary Outcomes: ONS COVID-19 death
  SA1_02c_cr_create_population_af_match_onscoviddeath:
    run: stata-mp:latest analysis/SA1_02c_cr_create_population.do onscoviddeath SA1_af_match matched_cases_af_gen_pop
    needs: [02c_cr_create_population_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_1/SA1_02c_cr_create_population_onscoviddeath.log
      highly_sensitive:
        data2: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_onscoviddeath.dta"
        data3: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_STSET_onscoviddeath.dta"

  SA1_05c_an_models_af_match_onscoviddeath:
    run: stata-mp:latest analysis/05c_an_models.do onscoviddeath SA1_af_match
    needs: [SA1_02c_cr_create_population_af_match_onscoviddeath, 05c_an_models_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_1/05c_an_models_onscoviddeath.log
        table: "output/oac_match_tabfig/sens_analysis_1/table2_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_univar.ster"
        data2: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar1.ster"
        data3: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar2.ster"
        data4: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar3.ster"

  SA1_06c_an_models_ethnicity_af_match_onscoviddeath:
    run: stata-mp:latest analysis/06c_an_models_ethnicity.do onscoviddeath SA1_af_match
    needs: [SA1_02c_cr_create_population_af_match_onscoviddeath, 06c_an_models_ethnicity_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_1/06c_an_models_ethnicity_onscoviddeath.log
        table: "output/oac_match_tabfig/sens_analysis_1/table3_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_univar_ethn.ster"
        data2: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar1_ethn.ster"
        data3: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar2_ethn.ster"
        data4: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar2_withoutethn.ster"
        data5: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar3_ethn.ster"
        data6: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar3_withoutethn.ster"

  # Primary Outcomes: COVID-19 hospital admission
  SA1_02c_cr_create_population_af_match_admitcovid:
    run: stata-mp:latest analysis/SA1_02c_cr_create_population.do admitcovid SA1_af_match matched_cases_af_gen_pop
    needs: [02c_cr_create_population_af_match_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_1/SA1_02c_cr_create_population_admitcovid.log
      highly_sensitive:
        data2: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_admitcovid.dta"
        data3: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_STSET_admitcovid.dta"

  SA1_05c_an_models_af_match_admitcovid:
    run: stata-mp:latest analysis/05c_an_models.do admitcovid SA1_af_match
    needs: [SA1_02c_cr_create_population_af_match_admitcovid, 05c_an_models_af_match_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_1/05c_an_models_admitcovid.log
        table: "output/oac_match_tabfig/sens_analysis_1/table2_admitcovid.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_1/admitcovid_univar.ster"
        data2: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar1.ster"
        data3: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar2.ster"
        data4: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar3.ster"

  SA1_06c_an_models_ethnicity_af_match_admitcovid:
    run: stata-mp:latest analysis/06c_an_models_ethnicity.do admitcovid SA1_af_match
    needs: [SA1_02c_cr_create_population_af_match_admitcovid, 06c_an_models_ethnicity_af_match_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_1/06c_an_models_ethnicity_admitcovid.log
        table: "output/oac_match_tabfig/sens_analysis_1/table3_admitcovid.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_1/admitcovid_univar_ethn.ster"
        data2: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar1_ethn.ster"
        data3: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar2_ethn.ster"
        data4: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar2_withoutethn.ster"
        data5: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar3_ethn.ster"
        data6: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar3_withoutethn.ster"

  # Exploratory Outcomes: COVID-19 test
  SA1_02c_cr_create_population_af_match_covidtest:
    run: stata-mp:latest analysis/SA1_02c_cr_create_population.do covidtest SA1_af_match matched_cases_af_gen_pop
    needs: [02c_cr_create_population_af_match_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_1/SA1_02c_cr_create_population_covidtest.log
      highly_sensitive:
        data2: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_covidtest.dta"
        data3: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_STSET_covidtest.dta"

  SA1_05c_an_models_af_match_covidtest:
    run: stata-mp:latest analysis/05c_an_models.do covidtest SA1_af_match
    needs: [SA1_02c_cr_create_population_af_match_covidtest, 05c_an_models_af_match_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_1/05c_an_models_covidtest.log
        table: "output/oac_match_tabfig/sens_analysis_1/table2_covidtest.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_1/covidtest_univar.ster"
        data2: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar1.ster"
        data3: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar2.ster"
        data4: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar3.ster"

  SA1_06c_an_models_ethnicity_af_match_covidtest:
    run: stata-mp:latest analysis/06c_an_models_ethnicity.do covidtest SA1_af_match
    needs: [SA1_02c_cr_create_population_af_match_covidtest, 06c_an_models_ethnicity_af_match_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_1/06c_an_models_ethnicity_covidtest.log
        table: "output/oac_match_tabfig/sens_analysis_1/table3_covidtest.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_1/covidtest_univar_ethn.ster"
        data2: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar1_ethn.ster"
        data3: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar2_ethn.ster"
        data4: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar2_withoutethn.ster"
        data5: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar3_ethn.ster"
        data6: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar3_withoutethn.ster"

  # Exploratory Outcomes: Positive COVID test
  SA1_02c_cr_create_population_af_match_positivecovidtest:
    run: stata-mp:latest analysis/SA1_02c_cr_create_population.do positivecovidtest SA1_af_match matched_cases_af_gen_pop
    needs: [02c_cr_create_population_af_match_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_1/SA1_02c_cr_create_population_positivecovidtest.log
      highly_sensitive:
        data2: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_positivecovidtest.dta"
        data3: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_STSET_positivecovidtest.dta"

  SA1_05c_an_models_af_match_positivecovidtest:
    run: stata-mp:latest analysis/05c_an_models.do positivecovidtest SA1_af_match
    needs: [SA1_02c_cr_create_population_af_match_positivecovidtest, 05c_an_models_af_match_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_1/05c_an_models_positivecovidtest.log
        table: "output/oac_match_tabfig/sens_analysis_1/table2_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_univar.ster"
        data2: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar1.ster"
        data3: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar2.ster"
        data4: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar3.ster"

  SA1_06c_an_models_ethnicity_af_match_positivecovidtest:
    run: stata-mp:latest analysis/06c_an_models_ethnicity.do positivecovidtest SA1_af_match
    needs: [SA1_02c_cr_create_population_af_match_positivecovidtest, 06c_an_models_ethnicity_af_match_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_1/06c_an_models_ethnicity_positivecovidtest.log
        table: "output/oac_match_tabfig/sens_analysis_1/table3_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_univar_ethn.ster"
        data2: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar1_ethn.ster"
        data3: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar2_ethn.ster"
        data4: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar2_withoutethn.ster"
        data5: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar3_ethn.ster"
        data6: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar3_withoutethn.ster"

 # Sensitivity Analysis 2
  # limit the study cohort to people who aged 55 
  # Objective 1: compare AF treated people with AF non-treated people

  # Primary Outcomes: ONS COVID-19 death
  SA2_02a_cr_create_population_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/SA2_02a_cr_create_population.do onscoviddeath SA2_af_oac
    needs: [02aii_cr_create_population_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_2/SA2_02a_cr_create_population_onscoviddeath.log
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_2/analysis_dataset_onscoviddeath.dta"
        data2: "output/oac_tempdata/sens_analysis_2/analysis_dataset_STSET_onscoviddeath.dta"

  SA2_05a_an_models_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/05a_an_models.do onscoviddeath SA2_af_oac
    needs: [SA2_02a_cr_create_population_af_oac_onscoviddeath, 05a_an_models_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_2/05a_an_models_onscoviddeath.log
        table: "output/oac_tabfig/sens_analysis_2/table2_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_2/onscoviddeath_univar.ster"
        data2: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar1.ster"
        data3: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar2.ster"
        data4: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar3.ster"

  SA2_06a_an_models_ethnicity_af_oac_onscoviddeath:
    run: stata-mp:latest analysis/06a_an_models_ethnicity.do onscoviddeath SA2_af_oac
    needs: [SA2_02a_cr_create_population_af_oac_onscoviddeath, 06a_an_models_ethnicity_af_oac_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_2/06a_an_models_ethnicity_onscoviddeath.log
        table: "output/oac_tabfig/sens_analysis_2/table3_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_2/onscoviddeath_univar_ethn.ster"
        data2: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar1_ethn.ster"
        data3: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar2_ethn.ster"
        data4: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar2_withoutethn.ster"
        data5: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar3_ethn.ster"
        data6: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar3_withoutethn.ster"

  # Primary Outcomes: COVID-19 hospital admission
  SA2_02a_cr_create_population_af_oac_admitcovid:
    run: stata-mp:latest analysis/SA2_02a_cr_create_population.do admitcovid SA2_af_oac
    needs: [02aii_cr_create_population_af_oac_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_2/SA2_02a_cr_create_population_admitcovid.log
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_2/analysis_dataset_admitcovid.dta"
        data2: "output/oac_tempdata/sens_analysis_2/analysis_dataset_STSET_admitcovid.dta"

  SA2_05a_an_models_af_oac_admitcovid:
    run: stata-mp:latest analysis/05a_an_models.do admitcovid SA2_af_oac
    needs: [SA2_02a_cr_create_population_af_oac_admitcovid, 05a_an_models_af_oac_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_2/05a_an_models_admitcovid.log
        table: "output/oac_tabfig/sens_analysis_2/table2_admitcovid.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_2/admitcovid_univar.ster"
        data2: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar1.ster"
        data3: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar2.ster"
        data4: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar3.ster"

  SA2_06a_an_models_ethnicity_af_oac_admitcovid:
    run: stata-mp:latest analysis/06a_an_models_ethnicity.do admitcovid SA2_af_oac
    needs: [SA2_02a_cr_create_population_af_oac_admitcovid, 06a_an_models_ethnicity_af_oac_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_2/06a_an_models_ethnicity_admitcovid.log
        table: "output/oac_tabfig/sens_analysis_2/table3_admitcovid.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_2/admitcovid_univar_ethn.ster"
        data2: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar1_ethn.ster"
        data3: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar2_ethn.ster"
        data4: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar2_withoutethn.ster"
        data5: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar3_ethn.ster"
        data6: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar3_withoutethn.ster"

  # Exploratory Outcomes: COVID-19 test
  SA2_02a_cr_create_population_af_oac_covidtest:
    run: stata-mp:latest analysis/SA2_02a_cr_create_population.do covidtest SA2_af_oac
    needs: [02aii_cr_create_population_af_oac_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_2/SA2_02a_cr_create_population_covidtest.log
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_2/analysis_dataset_covidtest.dta"
        data2: "output/oac_tempdata/sens_analysis_2/analysis_dataset_STSET_covidtest.dta"

  SA2_05a_an_models_af_oac_covidtest:
    run: stata-mp:latest analysis/05a_an_models.do covidtest SA2_af_oac
    needs: [SA2_02a_cr_create_population_af_oac_covidtest, 05a_an_models_af_oac_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_2/05a_an_models_covidtest.log
        table: "output/oac_tabfig/sens_analysis_2/table2_covidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_2/covidtest_univar.ster"
        data2: "output/oac_tempdata/sens_analysis_2/covidtest_multivar1.ster"
        data3: "output/oac_tempdata/sens_analysis_2/covidtest_multivar2.ster"
        data4: "output/oac_tempdata/sens_analysis_2/covidtest_multivar3.ster"

  SA2_06a_an_models_ethnicity_af_oac_covidtest:
    run: stata-mp:latest analysis/06a_an_models_ethnicity.do covidtest SA2_af_oac
    needs: [SA2_02a_cr_create_population_af_oac_covidtest, 06a_an_models_ethnicity_af_oac_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_2/06a_an_models_ethnicity_covidtest.log
        table: "output/oac_tabfig/sens_analysis_2/table3_covidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_2/covidtest_univar_ethn.ster"
        data2: "output/oac_tempdata/sens_analysis_2/covidtest_multivar1_ethn.ster"
        data3: "output/oac_tempdata/sens_analysis_2/covidtest_multivar2_ethn.ster"
        data4: "output/oac_tempdata/sens_analysis_2/covidtest_multivar2_withoutethn.ster"
        data5: "output/oac_tempdata/sens_analysis_2/covidtest_multivar3_ethn.ster"
        data6: "output/oac_tempdata/sens_analysis_2/covidtest_multivar3_withoutethn.ster"

  # Exploratory Outcomes: Positive COVID test
  SA2_02a_cr_create_population_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/SA2_02a_cr_create_population.do positivecovidtest SA2_af_oac
    needs: [02aii_cr_create_population_af_oac_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_2/SA2_02a_cr_create_population_positivecovidtest.log
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_2/analysis_dataset_positivecovidtest.dta"
        data2: "output/oac_tempdata/sens_analysis_2/analysis_dataset_STSET_positivecovidtest.dta"

  SA2_05a_an_models_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/05a_an_models.do positivecovidtest SA2_af_oac
    needs: [SA2_02a_cr_create_population_af_oac_positivecovidtest, 05a_an_models_af_oac_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_2/05a_an_models_positivecovidtest.log
        table: "output/oac_tabfig/sens_analysis_2/table2_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_2/positivecovidtest_univar.ster"
        data2: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar1.ster"
        data3: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar2.ster"
        data4: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar3.ster"

  SA2_06a_an_models_ethnicity_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/06a_an_models_ethnicity.do positivecovidtest SA2_af_oac
    needs: [SA2_02a_cr_create_population_af_oac_positivecovidtest, 06a_an_models_ethnicity_af_oac_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/sens_analysis_2/06a_an_models_ethnicity_positivecovidtest.log
        table: "output/oac_tabfig/sens_analysis_2/table3_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/sens_analysis_2/positivecovidtest_univar_ethn.ster"
        data2: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar1_ethn.ster"
        data3: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar2_ethn.ster"
        data4: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar2_withoutethn.ster"
        data5: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar3_ethn.ster"
        data6: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar3_withoutethn.ster"

# Sensitivity Analysis 2
# limit the study cohort to people who aged 55 
# Objective 1: compare AF treated people with general population

  # Primary Outcomes: ONS COVID-19 death
  SA2_02c_cr_create_population_af_match_onscoviddeath:
    run: stata-mp:latest analysis/SA2_02c_cr_create_population.do onscoviddeath SA2_af_match matched_cases_af_gen_pop
    needs: [02c_cr_create_population_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_2/SA2_02c_cr_create_population_onscoviddeath.log
      highly_sensitive:
        data2: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_onscoviddeath.dta"
        data3: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_STSET_onscoviddeath.dta"

  SA2_05c_an_models_af_match_onscoviddeath:
    run: stata-mp:latest analysis/05c_an_models.do onscoviddeath SA2_af_match
    needs: [SA2_02c_cr_create_population_af_match_onscoviddeath, 05c_an_models_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_2/05c_an_models_onscoviddeath.log
        table: "output/oac_match_tabfig/sens_analysis_2/table2_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_univar.ster"
        data2: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar1.ster"
        data3: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar2.ster"
        data4: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar3.ster"

  SA2_06c_an_models_ethnicity_af_match_onscoviddeath:
    run: stata-mp:latest analysis/06c_an_models_ethnicity.do onscoviddeath SA2_af_match
    needs: [SA2_02c_cr_create_population_af_match_onscoviddeath, 06c_an_models_ethnicity_af_match_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_2/06c_an_models_ethnicity_onscoviddeath.log
        table: "output/oac_match_tabfig/sens_analysis_2/table3_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_univar_ethn.ster"
        data2: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar1_ethn.ster"
        data3: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar2_ethn.ster"
        data4: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar2_withoutethn.ster"
        data5: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar3_ethn.ster"
        data6: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar3_withoutethn.ster"

  # Primary Outcomes: COVID-19 hospital admission
  SA2_02c_cr_create_population_af_match_admitcovid:
    run: stata-mp:latest analysis/SA2_02c_cr_create_population.do admitcovid SA2_af_match 
    needs: [02c_cr_create_population_af_match_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_2/SA2_02c_cr_create_population_admitcovid.log
      highly_sensitive:
        data2: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_admitcovid.dta"
        data3: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_STSET_admitcovid.dta"

  SA2_05c_an_models_af_match_admitcovid:
    run: stata-mp:latest analysis/05c_an_models.do admitcovid SA2_af_match
    needs: [SA2_02c_cr_create_population_af_match_admitcovid, 05c_an_models_af_match_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_2/05c_an_models_admitcovid.log
        table: "output/oac_match_tabfig/sens_analysis_2/table2_admitcovid.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_2/admitcovid_univar.ster"
        data2: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar1.ster"
        data3: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar2.ster"
        data4: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar3.ster"

  SA2_06c_an_models_ethnicity_af_match_admitcovid:
    run: stata-mp:latest analysis/06c_an_models_ethnicity.do admitcovid SA2_af_match
    needs: [SA2_02c_cr_create_population_af_match_admitcovid, 06c_an_models_ethnicity_af_match_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_2/06c_an_models_ethnicity_admitcovid.log
        table: "output/oac_match_tabfig/sens_analysis_2/table3_admitcovid.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_2/admitcovid_univar_ethn.ster"
        data2: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar1_ethn.ster"
        data3: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar2_ethn.ster"
        data4: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar2_withoutethn.ster"
        data5: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar3_ethn.ster"
        data6: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar3_withoutethn.ster"

  # Exploratory Outcomes: COVID-19 test
  SA2_02c_cr_create_population_af_match_covidtest:
    run: stata-mp:latest analysis/SA2_02c_cr_create_population.do covidtest SA2_af_match
    needs: [02c_cr_create_population_af_match_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_2/SA2_02c_cr_create_population_covidtest.log
      highly_sensitive:
        data2: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_covidtest.dta"
        data3: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_STSET_covidtest.dta"

  SA2_05c_an_models_af_match_covidtest:
    run: stata-mp:latest analysis/05c_an_models.do covidtest SA2_af_match
    needs: [SA2_02c_cr_create_population_af_match_covidtest, 05c_an_models_af_match_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_2/05c_an_models_covidtest.log
        table: "output/oac_match_tabfig/sens_analysis_2/table2_covidtest.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_2/covidtest_univar.ster"
        data2: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar1.ster"
        data3: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar2.ster"
        data4: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar3.ster"

  SA2_06c_an_models_ethnicity_af_match_covidtest:
    run: stata-mp:latest analysis/06c_an_models_ethnicity.do covidtest SA2_af_match
    needs: [SA2_02c_cr_create_population_af_match_covidtest, 06c_an_models_ethnicity_af_match_covidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_2/06c_an_models_ethnicity_covidtest.log
        table: "output/oac_match_tabfig/sens_analysis_2/table3_covidtest.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_2/covidtest_univar_ethn.ster"
        data2: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar1_ethn.ster"
        data3: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar2_ethn.ster"
        data4: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar2_withoutethn.ster"
        data5: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar3_ethn.ster"
        data6: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar3_withoutethn.ster"

  # Exploratory Outcomes: Positive COVID test
  SA2_02c_cr_create_population_af_match_positivecovidtest:
    run: stata-mp:latest analysis/SA2_02c_cr_create_population.do positivecovidtest SA2_af_match
    needs: [02c_cr_create_population_af_match_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_2/SA2_02c_cr_create_population_positivecovidtest.log
      highly_sensitive:
        data2: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_positivecovidtest.dta"
        data3: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_STSET_positivecovidtest.dta"

  SA2_05c_an_models_af_match_positivecovidtest:
    run: stata-mp:latest analysis/05c_an_models.do positivecovidtest SA2_af_match
    needs: [SA2_02c_cr_create_population_af_match_positivecovidtest, 05c_an_models_af_match_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_2/05c_an_models_positivecovidtest.log
        table: "output/oac_match_tabfig/sens_analysis_2/table2_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_univar.ster"
        data2: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar1.ster"
        data3: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar2.ster"
        data4: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar3.ster"

  SA2_06c_an_models_ethnicity_af_match_positivecovidtest:
    run: stata-mp:latest analysis/06c_an_models_ethnicity.do positivecovidtest SA2_af_match
    needs: [SA2_02c_cr_create_population_af_match_positivecovidtest, 06c_an_models_ethnicity_af_match_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_match_log/sens_analysis_2/06c_an_models_ethnicity_positivecovidtest.log
        table: "output/oac_match_tabfig/sens_analysis_2/table3_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_univar_ethn.ster"
        data2: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar1_ethn.ster"
        data3: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar2_ethn.ster"
        data4: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar2_withoutethn.ster"
        data5: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar3_ethn.ster"
        data6: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar3_withoutethn.ster"

  # Sensitivity Analysis 3
  # Exclude people who were prescribed both warfarin and DOACs on the same day as the latest OAC prescription
  # Objective 2: Compare warfarin users and DOAC users

  # Primary Outcomes: ONS COVID-19 death
  SA3_02b_cr_create_population_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/SA3_02b_cr_create_population.do onscoviddeath SA3_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/SA3_02b_cr_create_population_onscoviddeath.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_onscoviddeath.dta"
        data2: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_STSET_onscoviddeath.dta"

  SA3_05b_an_models_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/05b_an_models.do onscoviddeath SA3_af_warfarin
    needs: [SA3_02b_cr_create_population_af_warfarin_onscoviddeath, 05b_an_models_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/05b_an_models_onscoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_3/table2_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar3.ster"

  SA3_06b_an_models_ethnicity_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do onscoviddeath SA3_af_warfarin
    needs: [SA3_02b_cr_create_population_af_warfarin_onscoviddeath, 06b_an_models_ethnicity_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/06b_an_models_ethnicity_onscoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_3/table3_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar3_withoutethn.ster"

  # Primary Outcomes: COVID-19 hospital admission
  SA3_02b_cr_create_population_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/SA3_02b_cr_create_population.do admitcovid SA3_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/SA3_02b_cr_create_population_admitcovid.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_admitcovid.dta"
        data2: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_STSET_admitcovid.dta"

  SA3_05b_an_models_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/05b_an_models.do admitcovid SA3_af_warfarin
    needs: [SA3_02b_cr_create_population_af_warfarin_admitcovid, 05b_an_models_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/05b_an_models_admitcovid.log
        table: "output/warfarin_tabfig/sens_analysis_3/table2_admitcovid.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/admitcovid_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar3.ster"

  SA3_06b_an_models_ethnicity_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do admitcovid SA3_af_warfarin
    needs: [SA3_02b_cr_create_population_af_warfarin_admitcovid, 06b_an_models_ethnicity_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/06b_an_models_ethnicity_admitcovid.log
        table: "output/warfarin_tabfig/sens_analysis_3/table3_admitcovid.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/admitcovid_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar3_withoutethn.ster"

    # Exploratory Outcomes: Non-COVID death
  SA3_02b_cr_create_population_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/SA3_02b_cr_create_population.do onsnoncoviddeath SA3_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/SA3_02b_cr_create_population_onsnoncoviddeath.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_onsnoncoviddeath.dta"
        data2: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_STSET_onsnoncoviddeath.dta"

  SA3_05b_an_models_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/05b_an_models.do onsnoncoviddeath SA3_af_warfarin
    needs: [SA3_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 05b_an_models_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/05b_an_models_onsnoncoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_3/table2_onsnoncoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar3.ster"

  SA3_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do onsnoncoviddeath SA3_af_warfarin
    needs: [SA3_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/06b_an_models_ethnicity_onsnoncoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_3/table3_onsnoncoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar3_withoutethn.ster"
        
  # Exploratory Outcomes: COVID-19 test
  SA3_02b_cr_create_population_af_warfarin_covidtest:
    run: stata-mp:latest analysis/SA3_02b_cr_create_population.do covidtest SA3_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/SA3_02b_cr_create_population_covidtest.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_covidtest.dta"
        data2: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_STSET_covidtest.dta"

  SA3_05b_an_models_af_warfarin_covidtest:
    run: stata-mp:latest analysis/05b_an_models.do covidtest SA3_af_warfarin
    needs: [SA3_02b_cr_create_population_af_warfarin_covidtest, 05b_an_models_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/05b_an_models_covidtest.log
        table: "output/warfarin_tabfig/sens_analysis_3/table2_covidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/covidtest_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar3.ster"

  SA3_06b_an_models_ethnicity_af_warfarin_covidtest:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do covidtest SA3_af_warfarin
    needs: [SA3_02b_cr_create_population_af_warfarin_covidtest, 06b_an_models_ethnicity_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/06b_an_models_ethnicity_covidtest.log
        table: "output/warfarin_tabfig/sens_analysis_3/table3_covidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/covidtest_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar3_withoutethn.ster"

  # Exploratory Outcomes: Positive COVID test
  SA3_02b_cr_create_population_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/SA3_02b_cr_create_population.do positivecovidtest SA3_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/SA3_02b_cr_create_population_positivecovidtest.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_positivecovidtest.dta"
        data2: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_STSET_positivecovidtest.dta"

  SA3_05b_an_models_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/05b_an_models.do positivecovidtest SA3_af_warfarin
    needs: [SA3_02b_cr_create_population_af_warfarin_positivecovidtest, 05b_an_models_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/05b_an_models_positivecovidtest.log
        table: "output/warfarin_tabfig/sens_analysis_3/table2_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar3.ster"

  SA3_06b_an_models_ethnicity_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do positivecovidtest SA3_af_warfarin
    needs: [SA3_02b_cr_create_population_af_warfarin_positivecovidtest, 06b_an_models_ethnicity_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_3/06b_an_models_ethnicity_positivecovidtest.log
        table: "output/warfarin_tabfig/sens_analysis_3/table3_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar3_withoutethn.ster"

  # Sensitivity Analysis 4
  # Exclude people who ever had warfarin prescription 4 months before cohort entry in the DOAC group
  # Objective 2: Compare warfarin users and DOAC users

  # Primary Outcomes: ONS COVID-19 death
  SA4_02b_cr_create_population_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/SA4_02b_cr_create_population.do onscoviddeath SA4_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/SA4_02b_cr_create_population_onscoviddeath.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_onscoviddeath.dta"
        data2: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_STSET_onscoviddeath.dta"

  SA4_05b_an_models_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/05b_an_models.do onscoviddeath SA4_af_warfarin
    needs: [SA4_02b_cr_create_population_af_warfarin_onscoviddeath, 05b_an_models_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/05b_an_models_onscoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_4/table2_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar3.ster"

  SA4_06b_an_models_ethnicity_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do onscoviddeath SA4_af_warfarin
    needs: [SA4_02b_cr_create_population_af_warfarin_onscoviddeath, 06b_an_models_ethnicity_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/06b_an_models_ethnicity_onscoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_4/table3_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar3_withoutethn.ster"

  # Primary Outcomes: COVID-19 hospital admission
  SA4_02b_cr_create_population_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/SA4_02b_cr_create_population.do admitcovid SA4_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/SA4_02b_cr_create_population_admitcovid.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_admitcovid.dta"
        data2: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_STSET_admitcovid.dta"

  SA4_05b_an_models_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/05b_an_models.do admitcovid SA4_af_warfarin
    needs: [SA4_02b_cr_create_population_af_warfarin_admitcovid, 05b_an_models_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/05b_an_models_admitcovid.log
        table: "output/warfarin_tabfig/sens_analysis_4/table2_admitcovid.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/admitcovid_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar3.ster"

  SA4_06b_an_models_ethnicity_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do admitcovid SA4_af_warfarin
    needs: [SA4_02b_cr_create_population_af_warfarin_admitcovid, 06b_an_models_ethnicity_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/06b_an_models_ethnicity_admitcovid.log
        table: "output/warfarin_tabfig/sens_analysis_4/table3_admitcovid.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/admitcovid_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar3_withoutethn.ster"

    # Exploratory Outcomes: Non-COVID death
  SA4_02b_cr_create_population_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/SA4_02b_cr_create_population.do onsnoncoviddeath SA4_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/SA4_02b_cr_create_population_onsnoncoviddeath.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_onsnoncoviddeath.dta"
        data2: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_STSET_onsnoncoviddeath.dta"

  SA4_05b_an_models_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/05b_an_models.do onsnoncoviddeath SA4_af_warfarin
    needs: [SA4_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 05b_an_models_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/05b_an_models_onsnoncoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_4/table2_onsnoncoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar3.ster"

  SA4_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do onsnoncoviddeath SA4_af_warfarin
    needs: [SA4_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/06b_an_models_ethnicity_onsnoncoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_4/table3_onsnoncoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar3_withoutethn.ster"
        
  # Exploratory Outcomes: COVID-19 test
  SA4_02b_cr_create_population_af_warfarin_covidtest:
    run: stata-mp:latest analysis/SA4_02b_cr_create_population.do covidtest SA4_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/SA4_02b_cr_create_population_covidtest.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_covidtest.dta"
        data2: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_STSET_covidtest.dta"

  SA4_05b_an_models_af_warfarin_covidtest:
    run: stata-mp:latest analysis/05b_an_models.do covidtest SA4_af_warfarin
    needs: [SA4_02b_cr_create_population_af_warfarin_covidtest, 05b_an_models_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/05b_an_models_covidtest.log
        table: "output/warfarin_tabfig/sens_analysis_4/table2_covidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/covidtest_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar3.ster"

  SA4_06b_an_models_ethnicity_af_warfarin_covidtest:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do covidtest SA4_af_warfarin
    needs: [SA4_02b_cr_create_population_af_warfarin_covidtest, 06b_an_models_ethnicity_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/06b_an_models_ethnicity_covidtest.log
        table: "output/warfarin_tabfig/sens_analysis_4/table3_covidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/covidtest_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar3_withoutethn.ster"

  # Exploratory Outcomes: Positive COVID test
  SA4_02b_cr_create_population_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/SA4_02b_cr_create_population.do positivecovidtest SA4_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/SA4_02b_cr_create_population_positivecovidtest.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_positivecovidtest.dta"
        data2: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_STSET_positivecovidtest.dta"

  SA4_05b_an_models_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/05b_an_models.do positivecovidtest SA4_af_warfarin
    needs: [SA4_02b_cr_create_population_af_warfarin_positivecovidtest, 05b_an_models_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/05b_an_models_positivecovidtest.log
        table: "output/warfarin_tabfig/sens_analysis_4/table2_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar3.ster"

  SA4_06b_an_models_ethnicity_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do positivecovidtest SA4_af_warfarin
    needs: [SA4_02b_cr_create_population_af_warfarin_positivecovidtest, 06b_an_models_ethnicity_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_4/06b_an_models_ethnicity_positivecovidtest.log
        table: "output/warfarin_tabfig/sens_analysis_4/table3_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar3_withoutethn.ster"

  # Sensitivity Analysis 5
  # Use time-updated exposure variable (warfarin/DOACs) 
  # Objective 2: Compare warfarin users and DOAC users

  # Primary Outcomes: ONS COVID-19 death
  SA5_02b_cr_create_population_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/SA5_02b_cr_create_population.do onscoviddeath SA5_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/SA5_02b_cr_create_population_onscoviddeath.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/last_date_onscoviddeath.dta"
        data2: "output/warfarin_tempdata/sens_analysis_5/warfarin_rx_onscoviddeath.dta"
        data3: "output/warfarin_tempdata/sens_analysis_5/doac_rx_onscoviddeath.dta"
        data4: "output/warfarin_tempdata/sens_analysis_5/oac_rx_onscoviddeath.dta"
        data5: "output/warfarin_tempdata/sens_analysis_5/analysis_dataset_STSET_onscoviddeath.dta"

  SA5_03b_an_checks_onscoviddeath:
    run: stata-mp:latest analysis/SA5_03b_an_checks.do SA5_af_warfarin onscoviddeath
    needs: [SA5_02b_cr_create_population_af_warfarin_onscoviddeath, SA5_05b_an_models_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/SA5_03b_an_checks_onscoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_5/time_updated_onscoviddeath.txt"

  SA5_05b_an_models_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/05b_an_models.do onscoviddeath SA5_af_warfarin
    needs: [SA5_02b_cr_create_population_af_warfarin_onscoviddeath, 05b_an_models_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/05b_an_models_onscoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_5/table2_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar3.ster"

  SA5_06b_an_models_ethnicity_af_warfarin_onscoviddeath:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do onscoviddeath SA5_af_warfarin
    needs: [SA5_02b_cr_create_population_af_warfarin_onscoviddeath, 06b_an_models_ethnicity_af_warfarin_onscoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/06b_an_models_ethnicity_onscoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_5/table3_onscoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar3_withoutethn.ster"

  # Primary Outcomes: COVID-19 hospital admission
  SA5_02b_cr_create_population_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/SA5_02b_cr_create_population.do admitcovid SA5_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/SA5_02b_cr_create_population_admitcovid.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/last_date_admitcovid.dta"
        data2: "output/warfarin_tempdata/sens_analysis_5/warfarin_rx_admitcovid.dta"
        data3: "output/warfarin_tempdata/sens_analysis_5/doac_rx_admitcovid.dta"
        data4: "output/warfarin_tempdata/sens_analysis_5/oac_rx_admitcovid.dta"
        data5: "output/warfarin_tempdata/sens_analysis_5/analysis_dataset_STSET_admitcovid.dta"

  SA5_03b_an_checks_admitcovid:
    run: stata-mp:latest analysis/SA5_03b_an_checks.do SA5_af_warfarin admitcovid
    needs: [SA5_02b_cr_create_population_af_warfarin_admitcovid, SA5_05b_an_models_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/SA5_03b_an_checks_admitcovid.log
        table: "output/warfarin_tabfig/sens_analysis_5/time_updated_admitcovid.txt"

  SA5_05b_an_models_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/05b_an_models.do admitcovid SA5_af_warfarin
    needs: [SA5_02b_cr_create_population_af_warfarin_admitcovid, 05b_an_models_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/05b_an_models_admitcovid.log
        table: "output/warfarin_tabfig/sens_analysis_5/table2_admitcovid.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/admitcovid_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar3.ster"

  SA5_06b_an_models_ethnicity_af_warfarin_admitcovid:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do admitcovid SA5_af_warfarin
    needs: [SA5_02b_cr_create_population_af_warfarin_admitcovid, 06b_an_models_ethnicity_af_warfarin_admitcovid]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/06b_an_models_ethnicity_admitcovid.log
        table: "output/warfarin_tabfig/sens_analysis_5/table3_admitcovid.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/admitcovid_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar3_withoutethn.ster"

    # Exploratory Outcomes: Non-COVID death
  SA5_02b_cr_create_population_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/SA5_02b_cr_create_population.do onsnoncoviddeath SA5_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/SA5_02b_cr_create_population_onsnoncoviddeath.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/last_date_onsnoncoviddeath.dta"
        data2: "output/warfarin_tempdata/sens_analysis_5/warfarin_rx_onsnoncoviddeath.dta"
        data3: "output/warfarin_tempdata/sens_analysis_5/doac_rx_onsnoncoviddeath.dta"
        data4: "output/warfarin_tempdata/sens_analysis_5/oac_rx_onsnoncoviddeath.dta"
        data5: "output/warfarin_tempdata/sens_analysis_5/analysis_dataset_STSET_onsnoncoviddeath.dta"

  SA5_03b_an_checks_onsnoncoviddeath:
    run: stata-mp:latest analysis/SA5_03b_an_checks.do SA5_af_warfarin onsnoncoviddeath
    needs: [SA5_02b_cr_create_population_af_warfarin_onsnoncoviddeath, SA5_05b_an_models_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/SA5_03b_an_checks_onsnoncoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_5/time_updated_onsnoncoviddeath.txt"

  SA5_05b_an_models_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/05b_an_models.do onsnoncoviddeath SA5_af_warfarin
    needs: [SA5_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 05b_an_models_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/05b_an_models_onsnoncoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_5/table2_onsnoncoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar3.ster"

  SA5_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do onsnoncoviddeath SA5_af_warfarin
    needs: [SA5_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/06b_an_models_ethnicity_onsnoncoviddeath.log
        table: "output/warfarin_tabfig/sens_analysis_5/table3_onsnoncoviddeath.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar3_withoutethn.ster"
        
  # Exploratory Outcomes: COVID-19 test
  SA5_02b_cr_create_population_af_warfarin_covidtest:
    run: stata-mp:latest analysis/SA5_02b_cr_create_population.do covidtest SA5_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/SA5_02b_cr_create_population_covidtest.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/last_date_covidtest.dta"
        data2: "output/warfarin_tempdata/sens_analysis_5/warfarin_rx_covidtest.dta"
        data3: "output/warfarin_tempdata/sens_analysis_5/doac_rx_covidtest.dta"
        data4: "output/warfarin_tempdata/sens_analysis_5/oac_rx_covidtest.dta"
        data5: "output/warfarin_tempdata/sens_analysis_5/analysis_dataset_STSET_covidtest.dta"

  SA5_03b_an_checks_covidtest:
    run: stata-mp:latest analysis/SA5_03b_an_checks.do SA5_af_warfarin covidtest
    needs: [SA5_02b_cr_create_population_af_warfarin_covidtest, SA5_05b_an_models_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/SA5_03b_an_checks_covidtest.log
        table: "output/warfarin_tabfig/sens_analysis_5/time_updated_covidtest.txt"

  SA5_05b_an_models_af_warfarin_covidtest:
    run: stata-mp:latest analysis/05b_an_models.do covidtest SA5_af_warfarin
    needs: [SA5_02b_cr_create_population_af_warfarin_covidtest, 05b_an_models_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/05b_an_models_covidtest.log
        table: "output/warfarin_tabfig/sens_analysis_5/table2_covidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/covidtest_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar3.ster"

  SA5_06b_an_models_ethnicity_af_warfarin_covidtest:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do covidtest SA5_af_warfarin
    needs: [SA5_02b_cr_create_population_af_warfarin_covidtest, 06b_an_models_ethnicity_af_warfarin_covidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/06b_an_models_ethnicity_covidtest.log
        table: "output/warfarin_tabfig/sens_analysis_5/table3_covidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/covidtest_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar3_withoutethn.ster"

  # Exploratory Outcomes: Positive COVID test
  SA5_02b_cr_create_population_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/SA5_02b_cr_create_population.do positivecovidtest SA5_af_warfarin
    needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/SA5_02b_cr_create_population_positivecovidtest.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/last_date_positivecovidtest.dta"
        data2: "output/warfarin_tempdata/sens_analysis_5/warfarin_rx_positivecovidtest.dta"
        data3: "output/warfarin_tempdata/sens_analysis_5/doac_rx_positivecovidtest.dta"
        data4: "output/warfarin_tempdata/sens_analysis_5/oac_rx_positivecovidtest.dta"
        data5: "output/warfarin_tempdata/sens_analysis_5/analysis_dataset_STSET_positivecovidtest.dta"

  SA5_03b_an_checks_positivecovidtest:
    run: stata-mp:latest analysis/SA5_03b_an_checks.do SA5_af_warfarin positivecovidtest
    needs: [SA5_02b_cr_create_population_af_warfarin_positivecovidtest, SA5_05b_an_models_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/SA5_03b_an_checks_positivecovidtest.log
        table: "output/warfarin_tabfig/sens_analysis_5/time_updated_positivecovidtest.txt"

  SA5_05b_an_models_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/05b_an_models.do positivecovidtest SA5_af_warfarin
    needs: [SA5_02b_cr_create_population_af_warfarin_positivecovidtest, 05b_an_models_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/05b_an_models_positivecovidtest.log
        table: "output/warfarin_tabfig/sens_analysis_5/table2_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_univar.ster"
        data2: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar1.ster"
        data3: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar2.ster"
        data4: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar3.ster"

  SA5_06b_an_models_ethnicity_af_warfarin_positivecovidtest:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do positivecovidtest SA5_af_warfarin
    needs: [SA5_02b_cr_create_population_af_warfarin_positivecovidtest, 06b_an_models_ethnicity_af_warfarin_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/sens_analysis_5/06b_an_models_ethnicity_positivecovidtest.log
        table: "output/warfarin_tabfig/sens_analysis_5/table3_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_univar_ethn.ster"
        data2: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar3_withoutethn.ster"

# Post-hoc Analysis 1
# Compare AF treated people with general population
# where general population was identified without exclusion criteria of no GP visit 1 year before entry
  generate_cohort_wo_GP:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_general_population_wo_exclusion_GP_visit
    outputs:
      highly_sensitive:
        cohort: output/input_general_population_wo_exclusion_GP_visit.csv

  generate_cohort_wo_GP_flowchart:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_general_population_wo_exclusion_GP_visit_flow_chart
    outputs:
      highly_sensitive:
        cohort: output/input_general_population_wo_exclusion_GP_visit_flow_chart.csv

  matching_second:
    run: python:latest python analysis/match_running_second.py
    needs: [generate_cohort, generate_cohort_wo_GP, 02ai_exportfile_matching]
    outputs:
      moderately_sensitive:
        log: output/matching_report_af_gen_pop_second.txt
      highly_sensitive:
        data1: "output/matched_cases_af_gen_pop_second.csv"
        data2: "output/matched_matches_af_gen_pop_second.csv"

  format_dataset_af_match_second:
    run: stata-mp:latest analysis/00_cr_create_analysis_dataset.do posthoc_1_af_match matched_matches_af_gen_pop_second
    needs: [generate_cohort, generate_cohort_wo_GP, matching_second]
    outputs:
      moderately_sensitive:
        log: output/post_hoc_1_oac_match_log/00_cr_create_analysis_dataset.log
      highly_sensitive:
        data: "output/post_hoc_1_oac_match_tempdata/format_dataset.dta"

  create_dataset_af_match_second:
    run: stata-mp:latest analysis/01c_cr_create_exposure_outcome_af_match.do posthoc_1_af_match
    needs: [format_dataset_af_match_second, matching_second]
    outputs:
      moderately_sensitive:
        log: output/post_hoc_1_oac_match_log/01c_cr_create_exposure_outcome_af_match.log
      highly_sensitive:
        data: "output/post_hoc_1_oac_match_tempdata/cr_dataset_af.dta"

  # Primary Outcomes: ONS COVID-19 death
  02c_cr_create_population_af_match_onscoviddeath_second:
    run: stata-mp:latest analysis/02c_cr_create_population.do onscoviddeath posthoc_1_af_match matched_cases_af_gen_pop_second
    needs: [create_dataset_af_match_second, matching_second, 02ai_exportfile_matching]
    outputs:
      moderately_sensitive:
        log: output/post_hoc_1_oac_match_log/02c_cr_create_population_onscoviddeath.log
      highly_sensitive:
        data1: "output/post_hoc_1_oac_match_tempdata/matched_control_onscoviddeath.dta"
        data2: "output/post_hoc_1_oac_match_tempdata/analysis_dataset_onscoviddeath.dta"
        data3: "output/post_hoc_1_oac_match_tempdata/analysis_dataset_STSET_onscoviddeath.dta"

  04_an_descriptive_table_af_match_onscoviddeath_second:
    run: stata-mp:latest analysis/04_an_descriptive_table.do onscoviddeath posthoc_1_af_match
    needs: [02c_cr_create_population_af_match_onscoviddeath_second]
    outputs:
      moderately_sensitive:
        log: output/post_hoc_1_oac_match_log/04_an_descriptive_table_onscoviddeath.log
        table: "output/post_hoc_1_oac_match_tabfig/table1_onscoviddeath.txt"

# Post-hoc Analysis 2
# Compare AF treated people with general population
# Interaction with care home residence

  10a_an_models_int_af_oac_positivecovidtest:
    run: stata-mp:latest analysis/10a_an_models_interact.do positivecovidtest af_oac
    needs: [02aii_cr_create_population_af_oac_positivecovidtest]
    outputs:
      moderately_sensitive:
        log: output/oac_log/10a_an_models_interact_positivecovidtest.log
        table: "output/oac_tabfig/table7_positivecovidtest.txt"
      highly_sensitive:
        data1: "output/oac_tempdata/positivecovidtest_univar_int.ster"
        data2: "output/oac_tempdata/positivecovidtest_multivar1_int.ster"
        data3: "output/oac_tempdata/positivecovidtest_multivar2_int.ster"
        data4: "output/oac_tempdata/positivecovidtest_multivar3_int.ster"

  # Post-hoc analyses for different causes of death outcomes
  # ONS Myocardial infarction death
  02b_cr_create_population_af_warfarin_mi_ons:
    run: stata-mp:latest analysis/02b_cr_create_population.do mi_ons af_warfarin
    needs: [create_dataset_af_warfarin]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/02b_cr_create_population_mi_ons.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/analysis_dataset_mi_ons.dta"
        data2: "output/warfarin_tempdata/analysis_dataset_STSET_mi_ons.dta"

  05b_an_models_af_warfarin_mi_ons:
    run: stata-mp:latest analysis/05b_an_models.do mi_ons af_warfarin
    needs: [02b_cr_create_population_af_warfarin_mi_ons]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/05b_an_models_mi_ons.log
        table: "output/warfarin_tabfig/table2_mi_ons.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/mi_ons_univar.ster"
        data2: "output/warfarin_tempdata/mi_ons_multivar1.ster"
        data3: "output/warfarin_tempdata/mi_ons_multivar2.ster"
        data4: "output/warfarin_tempdata/mi_ons_multivar3.ster"

  06b_an_models_ethnicity_af_warfarin_mi_ons:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do mi_ons af_warfarin
    needs: [02b_cr_create_population_af_warfarin_mi_ons]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/06b_an_models_ethnicity_mi_ons.log
        table: "output/warfarin_tabfig/table3_mi_ons.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/mi_ons_univar_ethn.ster"
        data2: "output/warfarin_tempdata/mi_ons_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/mi_ons_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/mi_ons_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/mi_ons_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/mi_ons_multivar3_withoutethn.ster"

  # ONS Ischaemic stroke death
  02b_cr_create_population_af_warfarin_stroke_ons:
    run: stata-mp:latest analysis/02b_cr_create_population.do stroke_ons af_warfarin
    needs: [create_dataset_af_warfarin]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/02b_cr_create_population_stroke_ons.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/analysis_dataset_stroke_ons.dta"
        data2: "output/warfarin_tempdata/analysis_dataset_STSET_stroke_ons.dta"

  05b_an_models_af_warfarin_stroke_ons:
    run: stata-mp:latest analysis/05b_an_models.do stroke_ons af_warfarin
    needs: [02b_cr_create_population_af_warfarin_stroke_ons]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/05b_an_models_stroke_ons.log
        table: "output/warfarin_tabfig/table2_stroke_ons.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/stroke_ons_univar.ster"
        data2: "output/warfarin_tempdata/stroke_ons_multivar1.ster"
        data3: "output/warfarin_tempdata/stroke_ons_multivar2.ster"
        data4: "output/warfarin_tempdata/stroke_ons_multivar3.ster"

  06b_an_models_ethnicity_af_warfarin_stroke_ons:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do stroke_ons af_warfarin
    needs: [02b_cr_create_population_af_warfarin_stroke_ons]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/06b_an_models_ethnicity_stroke_ons.log
        table: "output/warfarin_tabfig/table3_stroke_ons.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/stroke_ons_univar_ethn.ster"
        data2: "output/warfarin_tempdata/stroke_ons_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/stroke_ons_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/stroke_ons_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/stroke_ons_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/stroke_ons_multivar3_withoutethn.ster"

  # ONS VTE death
  02b_cr_create_population_af_warfarin_vte_ons:
    run: stata-mp:latest analysis/02b_cr_create_population.do vte_ons af_warfarin
    needs: [create_dataset_af_warfarin]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/02b_cr_create_population_vte_ons.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/analysis_dataset_vte_ons.dta"
        data2: "output/warfarin_tempdata/analysis_dataset_STSET_vte_ons.dta"

  05b_an_models_af_warfarin_vte_ons:
    run: stata-mp:latest analysis/05b_an_models.do vte_ons af_warfarin
    needs: [02b_cr_create_population_af_warfarin_vte_ons]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/05b_an_models_vte_ons.log
        table: "output/warfarin_tabfig/table2_vte_ons.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/vte_ons_univar.ster"
        data2: "output/warfarin_tempdata/vte_ons_multivar1.ster"
        data3: "output/warfarin_tempdata/vte_ons_multivar2.ster"
        data4: "output/warfarin_tempdata/vte_ons_multivar3.ster"

  06b_an_models_ethnicity_af_warfarin_vte_ons:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do vte_ons af_warfarin
    needs: [02b_cr_create_population_af_warfarin_vte_ons]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/06b_an_models_ethnicity_vte_ons.log
        table: "output/warfarin_tabfig/table3_vte_ons.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/vte_ons_univar_ethn.ster"
        data2: "output/warfarin_tempdata/vte_ons_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/vte_ons_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/vte_ons_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/vte_ons_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/vte_ons_multivar3_withoutethn.ster"

  # ONS GI bleed death
  02b_cr_create_population_af_warfarin_gi_bleed_ons:
    run: stata-mp:latest analysis/02b_cr_create_population.do gi_bleed_ons af_warfarin
    needs: [create_dataset_af_warfarin]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/02b_cr_create_population_gi_bleed_ons.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/analysis_dataset_gi_bleed_ons.dta"
        data2: "output/warfarin_tempdata/analysis_dataset_STSET_gi_bleed_ons.dta"

  05b_an_models_af_warfarin_gi_bleed_ons:
    run: stata-mp:latest analysis/05b_an_models.do gi_bleed_ons af_warfarin
    needs: [02b_cr_create_population_af_warfarin_gi_bleed_ons]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/05b_an_models_gi_bleed_ons.log
        table: "output/warfarin_tabfig/table2_gi_bleed_ons.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/gi_bleed_ons_univar.ster"
        data2: "output/warfarin_tempdata/gi_bleed_ons_multivar1.ster"
        data3: "output/warfarin_tempdata/gi_bleed_ons_multivar2.ster"
        data4: "output/warfarin_tempdata/gi_bleed_ons_multivar3.ster"

  06b_an_models_ethnicity_af_warfarin_gi_bleed_ons:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do gi_bleed_ons af_warfarin
    needs: [02b_cr_create_population_af_warfarin_gi_bleed_ons]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/06b_an_models_ethnicity_gi_bleed_ons.log
        table: "output/warfarin_tabfig/table3_gi_bleed_ons.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/gi_bleed_ons_univar_ethn.ster"
        data2: "output/warfarin_tempdata/gi_bleed_ons_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/gi_bleed_ons_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/gi_bleed_ons_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/gi_bleed_ons_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/gi_bleed_ons_multivar3_withoutethn.ster"
        
  # ONS Intracranial bleed death
  02b_cr_create_population_af_warfarin_intracranial_bleed_ons:
    run: stata-mp:latest analysis/02b_cr_create_population.do intracranial_bleed_ons af_warfarin
    needs: [create_dataset_af_warfarin]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/02b_cr_create_population_intracranial_bleed_ons.log
      highly_sensitive:
        data1: "output/warfarin_tempdata/analysis_dataset_intracranial_bleed_ons.dta"
        data2: "output/warfarin_tempdata/analysis_dataset_STSET_intracranial_bleed_ons.dta"

  05b_an_models_af_warfarin_intracranial_bleed_ons:
    run: stata-mp:latest analysis/05b_an_models.do intracranial_bleed_ons af_warfarin
    needs: [02b_cr_create_population_af_warfarin_intracranial_bleed_ons]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/05b_an_models_intracranial_bleed_ons.log
        table: "output/warfarin_tabfig/table2_intracranial_bleed_ons.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/intracranial_bleed_ons_univar.ster"
        data2: "output/warfarin_tempdata/intracranial_bleed_ons_multivar1.ster"
        data3: "output/warfarin_tempdata/intracranial_bleed_ons_multivar2.ster"
        data4: "output/warfarin_tempdata/intracranial_bleed_ons_multivar3.ster"

  06b_an_models_ethnicity_af_warfarin_intracranial_bleed_ons:
    run: stata-mp:latest analysis/06b_an_models_ethnicity.do intracranial_bleed_ons af_warfarin
    needs: [02b_cr_create_population_af_warfarin_intracranial_bleed_ons]
    outputs:
      moderately_sensitive:
        log: output/warfarin_log/06b_an_models_ethnicity_intracranial_bleed_ons.log
        table: "output/warfarin_tabfig/table3_intracranial_bleed_ons.txt"
      highly_sensitive:
        data1: "output/warfarin_tempdata/intracranial_bleed_ons_univar_ethn.ster"
        data2: "output/warfarin_tempdata/intracranial_bleed_ons_multivar1_ethn.ster"
        data3: "output/warfarin_tempdata/intracranial_bleed_ons_multivar2_ethn.ster"
        data4: "output/warfarin_tempdata/intracranial_bleed_ons_multivar2_withoutethn.ster"
        data5: "output/warfarin_tempdata/intracranial_bleed_ons_multivar3_ethn.ster"
        data6: "output/warfarin_tempdata/intracranial_bleed_ons_multivar3_withoutethn.ster"

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 44:30:10

Config

  • Backend:
    TPP
  • Workspace:
    anticoagulant-third-run
  • Branch:
    master
  • Creator:
    angelwong121
  • Force run dependencies:
    True
  • Git Commit Hash:
    c0f1328
  • Requested actions:
    • generate_cohort
    • flowchart_af
    • flowchart_general_population
    • format_dataset_af_oac
    • create_dataset_af_oac
    • 02ai_exportfile_matching
    • 02aii_cr_create_population_af_oac_onscoviddeath
    • 03_an_checks_af_oac_onscoviddeath
    • 04_an_descriptive_table_af_oac_onscoviddeath
    • 05a_an_models_af_oac_onscoviddeath
    • 06a_an_models_ethnicity_af_oac_onscoviddeath
    • 07_an_model_explore_af_oac_onscoviddeath
    • 08a_an_model_checks_af_oac_onscoviddeath
    • 09a_an_models_plot_af_oac_onscoviddeath
    • 02aii_cr_create_population_af_oac_admitcovid
    • 03_an_checks_af_oac_admitcovid
    • 05a_an_models_af_oac_admitcovid
    • 06a_an_models_ethnicity_af_oac_admitcovid
    • 07_an_model_explore_af_oac_admitcovid
    • 08a_an_model_checks_af_oac_admitcovid
    • 09a_an_models_plot_af_oac_admitcovid
    • 02aii_cr_create_population_af_oac_covidtest
    • 03_an_checks_af_oac_covidtest
    • 05a_an_models_af_oac_covidtest
    • 06a_an_models_ethnicity_af_oac_covidtest
    • 08a_an_model_checks_af_oac_covidtest
    • 09a_an_models_plot_af_oac_covidtest
    • 02aii_cr_create_population_af_oac_positivecovidtest
    • 03_an_checks_af_oac_positivecovidtest
    • 05a_an_models_af_oac_positivecovidtest
    • 06a_an_models_ethnicity_af_oac_positivecovidtest
    • 08a_an_model_checks_af_oac_positivecovidtest
    • 09a_an_models_plot_af_oac_positivecovidtest
    • format_dataset_af_warfarin
    • create_dataset_af_warfarin
    • 02b_cr_create_population_af_warfarin_onscoviddeath
    • 03_an_checks_af_warfarin_onscoviddeath
    • 04_an_descriptive_table_af_warfarin_onscoviddeath
    • 05b_an_models_af_warfarin_onscoviddeath
    • 06b_an_models_ethnicity_af_warfarin_onscoviddeath
    • 07_an_model_explore_af_warfarin_onscoviddeath
    • 08b_an_model_checks_af_warfarin_onscoviddeath
    • 09b_an_models_plot_af_warfarin_onscoviddeath
    • 02b_cr_create_population_af_warfarin_admitcovid
    • 03_an_checks_af_warfarin_admitcovid
    • 05b_an_models_af_warfarin_admitcovid
    • 06b_an_models_ethnicity_af_warfarin_admitcovid
    • 07_an_model_explore_af_warfarin_admitcovid
    • 08b_an_model_checks_af_warfarin_admitcovid
    • 09b_an_models_plot_af_warfarin_admitcovid
    • 02b_cr_create_population_af_warfarin_onsnoncoviddeath
    • 03_an_checks_af_warfarin_onsnoncoviddeath
    • 05b_an_models_af_warfarin_onsnoncoviddeath
    • 06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
    • 08b_an_model_checks_af_warfarin_onsnoncoviddeath
    • 09b_an_models_plot_af_warfarin_onsnoncoviddeath
    • 02b_cr_create_population_af_warfarin_covidtest
    • 03_an_checks_af_warfarin_covidtest
    • 05b_an_models_af_warfarin_covidtest
    • 06b_an_models_ethnicity_af_warfarin_covidtest
    • 08b_an_model_checks_af_warfarin_covidtest
    • 09b_an_models_plot_af_warfarin_covidtest
    • 02b_cr_create_population_af_warfarin_positivecovidtest
    • 03_an_checks_af_warfarin_positivecovidtest
    • 05b_an_models_af_warfarin_positivecovidtest
    • 06b_an_models_ethnicity_af_warfarin_positivecovidtest
    • 08b_an_model_checks_af_warfarin_positivecovidtest
    • 09b_an_models_plot_af_warfarin_positivecovidtest
    • matching
    • format_dataset_af_match
    • create_dataset_af_match
    • 02c_cr_create_population_af_match_onscoviddeath
    • 03_an_checks_af_match_onscoviddeath
    • 04_an_descriptive_table_af_match_onscoviddeath
    • 05c_an_models_af_match_onscoviddeath
    • 06c_an_models_ethnicity_af_match_onscoviddeath
    • 07_an_model_explore_af_match_onscoviddeath
    • 08c_an_model_checks_af_match_onscoviddeath
    • 09a_an_models_plot_af_match_onscoviddeath
    • 02c_cr_create_population_af_match_admitcovid
    • 03_an_checks_af_match_admitcovid
    • 05c_an_models_af_match_admitcovid
    • 06c_an_models_ethnicity_af_match_admitcovid
    • 07_an_model_explore_af_match_admitcovid
    • 08c_an_model_checks_af_match_admitcovid
    • 09a_an_models_plot_af_match_admitcovid
    • 02c_cr_create_population_af_match_covidtest
    • 03_an_checks_af_match_covidtest
    • 05c_an_models_af_match_covidtest
    • 06c_an_models_ethnicity_af_match_covidtest
    • 08c_an_model_checks_af_match_covidtest
    • 09a_an_models_plot_af_match_covidtest
    • 02c_cr_create_population_af_match_positivecovidtest
    • 03_an_checks_af_match_positivecovidtest
    • 05c_an_models_af_match_positivecovidtest
    • 06c_an_models_ethnicity_af_match_positivecovidtest
    • 08c_an_model_checks_af_match_positivecovidtest
    • 09a_an_models_plot_af_match_positivecovidtest
    • SA1_02a_cr_create_population_af_oac_onscoviddeath
    • SA1_05a_an_models_af_oac_onscoviddeath
    • SA1_06a_an_models_ethnicity_af_oac_onscoviddeath
    • SA1_02a_cr_create_population_af_oac_admitcovid
    • SA1_05a_an_models_af_oac_admitcovid
    • SA1_06a_an_models_ethnicity_af_oac_admitcovid
    • SA1_02a_cr_create_population_af_oac_covidtest
    • SA1_05a_an_models_af_oac_covidtest
    • SA1_06a_an_models_ethnicity_af_oac_covidtest
    • SA1_02a_cr_create_population_af_oac_positivecovidtest
    • SA1_05a_an_models_af_oac_positivecovidtest
    • SA1_06a_an_models_ethnicity_af_oac_positivecovidtest
    • SA1_02b_cr_create_population_af_warfarin_onscoviddeath
    • SA1_05b_an_models_af_warfarin_onscoviddeath
    • SA1_06b_an_models_ethnicity_af_warfarin_onscoviddeath
    • SA1_02b_cr_create_population_af_warfarin_admitcovid
    • SA1_05b_an_models_af_warfarin_admitcovid
    • SA1_06b_an_models_ethnicity_af_warfarin_admitcovid
    • SA1_02b_cr_create_population_af_warfarin_onsnoncoviddeath
    • SA1_05b_an_models_af_warfarin_onsnoncoviddeath
    • SA1_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
    • SA1_02b_cr_create_population_af_warfarin_covidtest
    • SA1_05b_an_models_af_warfarin_covidtest
    • SA1_06b_an_models_ethnicity_af_warfarin_covidtest
    • SA1_02b_cr_create_population_af_warfarin_positivecovidtest
    • SA1_05b_an_models_af_warfarin_positivecovidtest
    • SA1_06b_an_models_ethnicity_af_warfarin_positivecovidtest
    • SA1_02c_cr_create_population_af_match_onscoviddeath
    • SA1_05c_an_models_af_match_onscoviddeath
    • SA1_06c_an_models_ethnicity_af_match_onscoviddeath
    • SA1_02c_cr_create_population_af_match_admitcovid
    • SA1_05c_an_models_af_match_admitcovid
    • SA1_06c_an_models_ethnicity_af_match_admitcovid
    • SA1_02c_cr_create_population_af_match_covidtest
    • SA1_05c_an_models_af_match_covidtest
    • SA1_06c_an_models_ethnicity_af_match_covidtest
    • SA1_02c_cr_create_population_af_match_positivecovidtest
    • SA1_05c_an_models_af_match_positivecovidtest
    • SA1_06c_an_models_ethnicity_af_match_positivecovidtest
    • SA2_02a_cr_create_population_af_oac_onscoviddeath
    • SA2_05a_an_models_af_oac_onscoviddeath
    • SA2_06a_an_models_ethnicity_af_oac_onscoviddeath
    • SA2_02a_cr_create_population_af_oac_admitcovid
    • SA2_05a_an_models_af_oac_admitcovid
    • SA2_06a_an_models_ethnicity_af_oac_admitcovid
    • SA2_02a_cr_create_population_af_oac_covidtest
    • SA2_05a_an_models_af_oac_covidtest
    • SA2_06a_an_models_ethnicity_af_oac_covidtest
    • SA2_02a_cr_create_population_af_oac_positivecovidtest
    • SA2_05a_an_models_af_oac_positivecovidtest
    • SA2_06a_an_models_ethnicity_af_oac_positivecovidtest
    • SA2_02c_cr_create_population_af_match_onscoviddeath
    • SA2_05c_an_models_af_match_onscoviddeath
    • SA2_06c_an_models_ethnicity_af_match_onscoviddeath
    • SA2_02c_cr_create_population_af_match_admitcovid
    • SA2_05c_an_models_af_match_admitcovid
    • SA2_06c_an_models_ethnicity_af_match_admitcovid
    • SA2_02c_cr_create_population_af_match_covidtest
    • SA2_05c_an_models_af_match_covidtest
    • SA2_06c_an_models_ethnicity_af_match_covidtest
    • SA2_02c_cr_create_population_af_match_positivecovidtest
    • SA2_05c_an_models_af_match_positivecovidtest
    • SA2_06c_an_models_ethnicity_af_match_positivecovidtest
    • SA3_02b_cr_create_population_af_warfarin_onscoviddeath
    • SA3_05b_an_models_af_warfarin_onscoviddeath
    • SA3_06b_an_models_ethnicity_af_warfarin_onscoviddeath
    • SA3_02b_cr_create_population_af_warfarin_admitcovid
    • SA3_05b_an_models_af_warfarin_admitcovid
    • SA3_06b_an_models_ethnicity_af_warfarin_admitcovid
    • SA3_02b_cr_create_population_af_warfarin_onsnoncoviddeath
    • SA3_05b_an_models_af_warfarin_onsnoncoviddeath
    • SA3_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
    • SA3_02b_cr_create_population_af_warfarin_covidtest
    • SA3_05b_an_models_af_warfarin_covidtest
    • SA3_06b_an_models_ethnicity_af_warfarin_covidtest
    • SA3_02b_cr_create_population_af_warfarin_positivecovidtest
    • SA3_05b_an_models_af_warfarin_positivecovidtest
    • SA3_06b_an_models_ethnicity_af_warfarin_positivecovidtest
    • SA4_02b_cr_create_population_af_warfarin_onscoviddeath
    • SA4_05b_an_models_af_warfarin_onscoviddeath
    • SA4_06b_an_models_ethnicity_af_warfarin_onscoviddeath
    • SA4_02b_cr_create_population_af_warfarin_admitcovid
    • SA4_05b_an_models_af_warfarin_admitcovid
    • SA4_06b_an_models_ethnicity_af_warfarin_admitcovid
    • SA4_02b_cr_create_population_af_warfarin_onsnoncoviddeath
    • SA4_05b_an_models_af_warfarin_onsnoncoviddeath
    • SA4_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
    • SA4_02b_cr_create_population_af_warfarin_covidtest
    • SA4_05b_an_models_af_warfarin_covidtest
    • SA4_06b_an_models_ethnicity_af_warfarin_covidtest
    • SA4_02b_cr_create_population_af_warfarin_positivecovidtest
    • SA4_05b_an_models_af_warfarin_positivecovidtest
    • SA4_06b_an_models_ethnicity_af_warfarin_positivecovidtest
    • SA5_02b_cr_create_population_af_warfarin_onscoviddeath
    • SA5_03b_an_checks_onscoviddeath
    • SA5_05b_an_models_af_warfarin_onscoviddeath
    • SA5_06b_an_models_ethnicity_af_warfarin_onscoviddeath
    • SA5_02b_cr_create_population_af_warfarin_admitcovid
    • SA5_03b_an_checks_admitcovid
    • SA5_05b_an_models_af_warfarin_admitcovid
    • SA5_06b_an_models_ethnicity_af_warfarin_admitcovid
    • SA5_02b_cr_create_population_af_warfarin_onsnoncoviddeath
    • SA5_03b_an_checks_onsnoncoviddeath
    • SA5_05b_an_models_af_warfarin_onsnoncoviddeath
    • SA5_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
    • SA5_02b_cr_create_population_af_warfarin_covidtest
    • SA5_03b_an_checks_covidtest
    • SA5_05b_an_models_af_warfarin_covidtest
    • SA5_06b_an_models_ethnicity_af_warfarin_covidtest
    • SA5_02b_cr_create_population_af_warfarin_positivecovidtest
    • SA5_03b_an_checks_positivecovidtest
    • SA5_05b_an_models_af_warfarin_positivecovidtest
    • SA5_06b_an_models_ethnicity_af_warfarin_positivecovidtest
    • 10a_an_models_int_af_oac_positivecovidtest
    • 02b_cr_create_population_af_warfarin_mi_ons
    • 05b_an_models_af_warfarin_mi_ons
    • 06b_an_models_ethnicity_af_warfarin_mi_ons
    • 02b_cr_create_population_af_warfarin_stroke_ons
    • 05b_an_models_af_warfarin_stroke_ons
    • 06b_an_models_ethnicity_af_warfarin_stroke_ons
    • 02b_cr_create_population_af_warfarin_vte_ons
    • 05b_an_models_af_warfarin_vte_ons
    • 06b_an_models_ethnicity_af_warfarin_vte_ons
    • 02b_cr_create_population_af_warfarin_gi_bleed_ons
    • 05b_an_models_af_warfarin_gi_bleed_ons
    • 06b_an_models_ethnicity_af_warfarin_gi_bleed_ons
    • 02b_cr_create_population_af_warfarin_intracranial_bleed_ons
    • 05b_an_models_af_warfarin_intracranial_bleed_ons
    • 06b_an_models_ethnicity_af_warfarin_intracranial_bleed_ons