Job request: 1070

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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
r3jnsotpmifv5kwc failed generate_cohort
3s5mlzmzwoau5hqq failed flowchart_af
oe324dw7qn2di5ky failed flowchart_general_population
724y762h4s46qocy failed format_dataset_af_oac
adcksqm67wyp5ops failed create_dataset_af_oac
kwaku3glhtfvyatk failed 02ai_exportfile_matching
5t52544rfd3oznhf failed 02aii_cr_create_population_af_oac_onscoviddeath
zfhhqfi7yzlefwgm failed 03_an_checks_af_oac_onscoviddeath
d3btdkjr5zy3slzr failed 04_an_descriptive_table_af_oac_onscoviddeath
v4nv33miq2vr7xgp failed 05a_an_models_af_oac_onscoviddeath
lffcpfw4zew2trmd failed 06a_an_models_ethnicity_af_oac_onscoviddeath
ny5wh4txspcylozm failed 07_an_model_explore_af_oac_onscoviddeath
g6uoeldaifj5z2yt failed 08a_an_model_checks_af_oac_onscoviddeath
2q4seqp5vsoizofj failed 09a_an_models_plot_af_oac_onscoviddeath
t6lo7ersrzlpt3xg failed 02aii_cr_create_population_af_oac_admitcovid
cmsxr4skdvy6ab4v failed 03_an_checks_af_oac_admitcovid
rg5ygruqwzpt7nor failed 05a_an_models_af_oac_admitcovid
kex4rruejpuyg6jp failed 06a_an_models_ethnicity_af_oac_admitcovid
d7a5p4vd6uyiscjl failed 07_an_model_explore_af_oac_admitcovid
ak2jmervsebnx4nz failed 08a_an_model_checks_af_oac_admitcovid
55oh5gteocdewmmr failed 09a_an_models_plot_af_oac_admitcovid
53bbmtewdslefcrq failed 02aii_cr_create_population_af_oac_covidtest
tmu2busnfz2fksyd failed 03_an_checks_af_oac_covidtest
pcu6axyfbnrqnn3w failed 05a_an_models_af_oac_covidtest
goepv7nyfial44mm failed 06a_an_models_ethnicity_af_oac_covidtest
wwhorgffhbaqw2jh failed 08a_an_model_checks_af_oac_covidtest
vpshx37rbxzmz4ke failed 09a_an_models_plot_af_oac_covidtest
rcd3tppupc5l25ua failed 02aii_cr_create_population_af_oac_positivecovidtest
id4ise6fm47q7uij failed 03_an_checks_af_oac_positivecovidtest
5acv65yq2s2su3sc failed 05a_an_models_af_oac_positivecovidtest
sex255a52xluo6rm failed 06a_an_models_ethnicity_af_oac_positivecovidtest
6nyo244nb454af7e failed 08a_an_model_checks_af_oac_positivecovidtest
ql77qs2iozkyicx6 failed 09a_an_models_plot_af_oac_positivecovidtest
g5cnlgq7jgetai7r failed format_dataset_af_warfarin
rngoukx26qpaiuat failed create_dataset_af_warfarin
of4m4vejvlte4p4p failed 02b_cr_create_population_af_warfarin_onscoviddeath
jhqu2uenaoacwuty failed 03_an_checks_af_warfarin_onscoviddeath
yu3y5asceqnwwlhy failed 04_an_descriptive_table_af_warfarin_onscoviddeath
mo3slnlzk4hkudyi failed 05b_an_models_af_warfarin_onscoviddeath
iqzgmbgtcmdsv7x3 failed 06b_an_models_ethnicity_af_warfarin_onscoviddeath
r4jikyh3fkwvh6jk failed 07_an_model_explore_af_warfarin_onscoviddeath
b5fvhmgrtc6dnmuu failed 08b_an_model_checks_af_warfarin_onscoviddeath
67h6xwtjxpjouqtg failed 09b_an_models_plot_af_warfarin_onscoviddeath
ihhxbkxaswsejz6n failed 02b_cr_create_population_af_warfarin_admitcovid
4ikkohpwkcinz4dm failed 03_an_checks_af_warfarin_admitcovid
zvz4y3gfod2ldox7 failed 05b_an_models_af_warfarin_admitcovid
cqggfnapri3ewtp2 failed 06b_an_models_ethnicity_af_warfarin_admitcovid
yo46phiji52mdufc failed 07_an_model_explore_af_warfarin_admitcovid
6wqufpvxycpx5rk3 failed 08b_an_model_checks_af_warfarin_admitcovid
if2lszkisxzdgr6r failed 09b_an_models_plot_af_warfarin_admitcovid
r5jew44gwglprb75 failed 02b_cr_create_population_af_warfarin_onsnoncoviddeath
z4yzyxfj7kvonm7l failed 03_an_checks_af_warfarin_onsnoncoviddeath
a6nwevmrfmlnp5ky failed 05b_an_models_af_warfarin_onsnoncoviddeath
d5aqfjqppdcqfqgn failed 06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
xi3ydoufyrirbzfm failed 08b_an_model_checks_af_warfarin_onsnoncoviddeath
bs5x4gsufsadsa6s failed 09b_an_models_plot_af_warfarin_onsnoncoviddeath
lpbmo2iupa6rzlff failed 02b_cr_create_population_af_warfarin_covidtest
vf7w3q3nxymwqn6o failed 03_an_checks_af_warfarin_covidtest
d2kqh3gg2ljgn5ch failed 05b_an_models_af_warfarin_covidtest
jygtkzke3ajnf732 failed 06b_an_models_ethnicity_af_warfarin_covidtest
owqbahwcwr6cpfnr failed 08b_an_model_checks_af_warfarin_covidtest
3hwfyyvg24d56m2o failed 09b_an_models_plot_af_warfarin_covidtest
o3wdpxb2jodnpgc2 failed 02b_cr_create_population_af_warfarin_positivecovidtest
hzrmnax3jlugxlcx failed 03_an_checks_af_warfarin_positivecovidtest
clfiurovmlxfpnmh failed 05b_an_models_af_warfarin_positivecovidtest
ks4msi7tnj5eyshz failed 06b_an_models_ethnicity_af_warfarin_positivecovidtest
hatxdeqyzzvornl6 failed 08b_an_model_checks_af_warfarin_positivecovidtest
sn5mr2f6hhjwvtyi failed 09b_an_models_plot_af_warfarin_positivecovidtest
6mnuqw5rxdmmmggc failed matching
tzko7oegzktbg4df failed format_dataset_af_match
wbzue3xcqybsygis failed create_dataset_af_match
uo2m6yo47f5j3lzt failed 02c_cr_create_population_af_match_onscoviddeath
anu6mxvymqwr7roo failed 03_an_checks_af_match_onscoviddeath
hwca6dfwibos35ls failed 04_an_descriptive_table_af_match_onscoviddeath
ltwrotaraag32lrr failed 05c_an_models_af_match_onscoviddeath
i3nmw77sf6gsbmgw failed 06c_an_models_ethnicity_af_match_onscoviddeath
gorwxmagmyrq5i62 failed 07_an_model_explore_af_match_onscoviddeath
p3o2qhfipghjkvav failed 08c_an_model_checks_af_match_onscoviddeath
avsqti2c46ppu4wa failed 09a_an_models_plot_af_match_onscoviddeath
xfgpp2557bmdyilw failed 02c_cr_create_population_af_match_admitcovid
tanwq53lwovbvki6 failed 03_an_checks_af_match_admitcovid
gtaf6wgzwrmat365 failed 05c_an_models_af_match_admitcovid
jxkeh2yzk5c6uaoj failed 06c_an_models_ethnicity_af_match_admitcovid
wm4v57xc2juksp4x failed 07_an_model_explore_af_match_admitcovid
fvxwhq4mycqkrpop failed 08c_an_model_checks_af_match_admitcovid
rlizgl3ljragrghh failed 09a_an_models_plot_af_match_admitcovid
weekyu663gwlzria failed 02c_cr_create_population_af_match_covidtest
ushlhugfxssm4zql failed 03_an_checks_af_match_covidtest
5nkxstaiixopie2p failed 05c_an_models_af_match_covidtest
bsrakngik34tgmg2 failed 06c_an_models_ethnicity_af_match_covidtest
d7fci5mxo7uuea43 failed 08c_an_model_checks_af_match_covidtest
mm55mwv6ecvq7t6b failed 09a_an_models_plot_af_match_covidtest
fzleozr2nbjwrz2p failed 02c_cr_create_population_af_match_positivecovidtest
v66irkd63ezay3er failed 03_an_checks_af_match_positivecovidtest
pebujjhbasszwro3 failed 05c_an_models_af_match_positivecovidtest
yzmq6qpxfe3iuq7j failed 06c_an_models_ethnicity_af_match_positivecovidtest
o44blfjsya2fql6u failed 08c_an_model_checks_af_match_positivecovidtest
bdweh7dfh5nk6vyj failed 09a_an_models_plot_af_match_positivecovidtest
ys52pxbtva6recwy failed SA1_02a_cr_create_population_af_oac_onscoviddeath
j3bkfpeyh5dw2nnu failed SA1_05a_an_models_af_oac_onscoviddeath
v7li7epdrwwn7q57 failed SA1_06a_an_models_ethnicity_af_oac_onscoviddeath
sgsjfhremor37chg failed SA1_02a_cr_create_population_af_oac_admitcovid
ci5flrv6tmt7e5fa failed SA1_05a_an_models_af_oac_admitcovid
ty65kb6d3phygypr failed SA1_06a_an_models_ethnicity_af_oac_admitcovid
r2wq2e7lnjk4rkr4 failed SA1_02a_cr_create_population_af_oac_covidtest
ypye637whtlgvv55 failed SA1_05a_an_models_af_oac_covidtest
ih7ii6rypzkg3u6s failed SA1_06a_an_models_ethnicity_af_oac_covidtest
m4fzdkeigiyeqqmf failed SA1_02a_cr_create_population_af_oac_positivecovidtest
iqt4iao5jvj3xg3u failed SA1_05a_an_models_af_oac_positivecovidtest
4add7yqlt7xt6vqn failed SA1_06a_an_models_ethnicity_af_oac_positivecovidtest
z4gfh4t3sltn6xrz failed SA1_02b_cr_create_population_af_warfarin_onscoviddeath
ofxbd7jkjcnnwie3 failed SA1_05b_an_models_af_warfarin_onscoviddeath
5kfx4npbnb2bqhin failed SA1_06b_an_models_ethnicity_af_warfarin_onscoviddeath
4mt5drdaznqxl6hk failed SA1_02b_cr_create_population_af_warfarin_admitcovid
53cxstqr4z4j2eqd failed SA1_05b_an_models_af_warfarin_admitcovid
nlhmm5x2ul6dfba5 failed SA1_06b_an_models_ethnicity_af_warfarin_admitcovid
3nmaqe4rehjzsuo5 failed SA1_02b_cr_create_population_af_warfarin_onsnoncoviddeath
et46xdzaqtpjesnq failed SA1_05b_an_models_af_warfarin_onsnoncoviddeath
yoawdg2jjygl4xj2 failed SA1_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
sipe2f4asrgi2f63 failed SA1_02b_cr_create_population_af_warfarin_covidtest
vyaygthewkoe42m4 failed SA1_05b_an_models_af_warfarin_covidtest
ysufto3yhpamdw2h failed SA1_06b_an_models_ethnicity_af_warfarin_covidtest
7vxrskldzptlrncq failed SA1_02b_cr_create_population_af_warfarin_positivecovidtest
yy662mi5u3c3dyws failed SA1_05b_an_models_af_warfarin_positivecovidtest
og3yozwi2bvjrnwd failed SA1_06b_an_models_ethnicity_af_warfarin_positivecovidtest
v2s2ohrsb4sg7gss failed SA1_02c_cr_create_population_af_match_onscoviddeath
wjaqv4k7w7cu2coc failed SA1_05c_an_models_af_match_onscoviddeath
plopnipfaj5ax2qj failed SA1_06c_an_models_ethnicity_af_match_onscoviddeath
zex3cslwnrrasl5j failed SA1_02c_cr_create_population_af_match_admitcovid
rmtontaw4eakzfq2 failed SA1_05c_an_models_af_match_admitcovid
btot76j254e2q7an failed SA1_06c_an_models_ethnicity_af_match_admitcovid
m6e6ulzjmwtdal5y failed SA1_02c_cr_create_population_af_match_covidtest
kyynrh3qgkeacwn5 failed SA1_05c_an_models_af_match_covidtest
7vmghybftq6lsyhd failed SA1_06c_an_models_ethnicity_af_match_covidtest
clwqq3ommobt5cev failed SA1_02c_cr_create_population_af_match_positivecovidtest
whl6beuvyjck6own failed SA1_05c_an_models_af_match_positivecovidtest
rjdpzjtwickv65ju failed SA1_06c_an_models_ethnicity_af_match_positivecovidtest
glko4zskn7sm33vg failed SA2_02a_cr_create_population_af_oac_onscoviddeath
en5morrsu3xysjyl failed SA2_05a_an_models_af_oac_onscoviddeath
ph7x7ydseehgydrz failed SA2_06a_an_models_ethnicity_af_oac_onscoviddeath
ychgbx6rvvhkote2 failed SA2_02a_cr_create_population_af_oac_admitcovid
bh52dcln3jf34rmo failed SA2_05a_an_models_af_oac_admitcovid
zot3efemnv7bhx6d failed SA2_06a_an_models_ethnicity_af_oac_admitcovid
d5oitsik5zmalt4a failed SA2_02a_cr_create_population_af_oac_covidtest
ryxq4cevqsya6gzf failed SA2_05a_an_models_af_oac_covidtest
odcxu7usa4zajx2y failed SA2_06a_an_models_ethnicity_af_oac_covidtest
qs5z7orsawbszpeb failed SA2_02a_cr_create_population_af_oac_positivecovidtest
c4jeiqucvjvai6d4 failed SA2_05a_an_models_af_oac_positivecovidtest
ulq7ahbxfzefgz2z failed SA2_06a_an_models_ethnicity_af_oac_positivecovidtest
4h4sen6kja46ivwl failed SA2_02c_cr_create_population_af_match_onscoviddeath
7dffylkwzvwhkn5k failed SA2_05c_an_models_af_match_onscoviddeath
6mm45jbd4sq73mub failed SA2_06c_an_models_ethnicity_af_match_onscoviddeath
wksp6rnbwuv524jo failed SA2_02c_cr_create_population_af_match_admitcovid
ifofieqcfvuamj3h failed SA2_05c_an_models_af_match_admitcovid
b4shepgz5j32wgpn failed SA2_06c_an_models_ethnicity_af_match_admitcovid
zrv2bdz7x7pdlkgg failed SA2_02c_cr_create_population_af_match_covidtest
r7ohjip5ey4ikcrg failed SA2_05c_an_models_af_match_covidtest
ppr7a3yoq3biwrny failed SA2_06c_an_models_ethnicity_af_match_covidtest
fazycknyez4xz62e failed SA2_02c_cr_create_population_af_match_positivecovidtest
3i72crbeso2kadhm failed SA2_05c_an_models_af_match_positivecovidtest
k7kvnztp6vu54z2w failed SA2_06c_an_models_ethnicity_af_match_positivecovidtest
fr5j4hnw4atgiiei failed SA3_02b_cr_create_population_af_warfarin_onscoviddeath
o33ry43nf3vgwewm failed SA3_05b_an_models_af_warfarin_onscoviddeath
ay4kmcgkonzjp7eq failed SA3_06b_an_models_ethnicity_af_warfarin_onscoviddeath
qbppjvy7njriqkfd failed SA3_02b_cr_create_population_af_warfarin_admitcovid
5zou2y6aq5e7ivx2 failed SA3_05b_an_models_af_warfarin_admitcovid
txckyt3lxpfi4qcd failed SA3_06b_an_models_ethnicity_af_warfarin_admitcovid
i64a56yp2pbi7kpc failed SA3_02b_cr_create_population_af_warfarin_onsnoncoviddeath
idp67os6vexeiykr failed SA3_05b_an_models_af_warfarin_onsnoncoviddeath
v3ehl3z7cakyc35e failed SA3_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
6clvs42igstiw5gk failed SA3_02b_cr_create_population_af_warfarin_covidtest
bgkjleaqnundecyy failed SA3_05b_an_models_af_warfarin_covidtest
m4tk775tfk7mthsw failed SA3_06b_an_models_ethnicity_af_warfarin_covidtest
grpcjm7fgh5xdcia failed SA3_02b_cr_create_population_af_warfarin_positivecovidtest
ku2qvpx7ebbpjwra failed SA3_05b_an_models_af_warfarin_positivecovidtest
kxmz7y4ugea5h3ml failed SA3_06b_an_models_ethnicity_af_warfarin_positivecovidtest
adygbxxxlqc3v6zn failed SA4_02b_cr_create_population_af_warfarin_onscoviddeath
6ed25vzdepjyuabh failed SA4_05b_an_models_af_warfarin_onscoviddeath
ri4pirllqhi3dn7p failed SA4_06b_an_models_ethnicity_af_warfarin_onscoviddeath
dhrej3hy5jqp6mk7 failed SA4_02b_cr_create_population_af_warfarin_admitcovid
7darmc3rf6hu36bt failed SA4_05b_an_models_af_warfarin_admitcovid
brb7mgh74nw26l5x failed SA4_06b_an_models_ethnicity_af_warfarin_admitcovid
jhfzommix6k76faz failed SA4_02b_cr_create_population_af_warfarin_onsnoncoviddeath
bnymqcjg6cwvvor5 failed SA4_05b_an_models_af_warfarin_onsnoncoviddeath
nyhw7hbk6z5petd2 failed SA4_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
iuvk55ykjj2mbqmy failed SA4_02b_cr_create_population_af_warfarin_covidtest
cvuoitqdjr7slvwq failed SA4_05b_an_models_af_warfarin_covidtest
3rulrss5sqb3dywv failed SA4_06b_an_models_ethnicity_af_warfarin_covidtest
ihpek7ofk6r64j4h failed SA4_02b_cr_create_population_af_warfarin_positivecovidtest
zdw5c4auwrommm57 failed SA4_05b_an_models_af_warfarin_positivecovidtest
wk5kl7ixuwh4a6x3 failed SA4_06b_an_models_ethnicity_af_warfarin_positivecovidtest
yc3bfatwtxtqp77b failed SA5_02b_cr_create_population_af_warfarin_onscoviddeath
cpf6kytpr6527qma failed SA5_05b_an_models_af_warfarin_onscoviddeath
7nbrp7uxbyxz424y failed SA5_03b_an_checks_onscoviddeath
bh5cgwry7bstiraw failed SA5_06b_an_models_ethnicity_af_warfarin_onscoviddeath
jqoemz2zur7nnexr failed SA5_02b_cr_create_population_af_warfarin_admitcovid
lv2hkgjuzams6mgf failed SA5_05b_an_models_af_warfarin_admitcovid
bgb3ruw34mbk4wo5 failed SA5_03b_an_checks_admitcovid
pf7usurxojd2ftgb failed SA5_06b_an_models_ethnicity_af_warfarin_admitcovid
jtufx437kvw4hq4o failed SA5_02b_cr_create_population_af_warfarin_onsnoncoviddeath
ho62fhjljwi7pbf3 failed SA5_05b_an_models_af_warfarin_onsnoncoviddeath
kuuxwqtuuxm4ccfa failed SA5_03b_an_checks_onsnoncoviddeath
dftbgr7jfhwt7iut failed SA5_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath
dtamh4ne56mcxxf5 failed SA5_02b_cr_create_population_af_warfarin_covidtest
clligyutiu3c63cv failed SA5_05b_an_models_af_warfarin_covidtest
h4xctrn7ydkh6iwa failed SA5_03b_an_checks_covidtest
cqhq56ugjvaavn7a failed SA5_06b_an_models_ethnicity_af_warfarin_covidtest
xlj6gthjkxcdaezz failed SA5_02b_cr_create_population_af_warfarin_positivecovidtest
scbw2ld7el7gvwxq failed SA5_05b_an_models_af_warfarin_positivecovidtest
pn6mmundbzpfu2bb failed SA5_03b_an_checks_positivecovidtest
cgbu4cussdenvwix failed SA5_06b_an_models_ethnicity_af_warfarin_positivecovidtest
5gy7lk54tawahjiz failed 10a_an_models_int_af_oac_positivecovidtest
xww6ibxtzqkrnytx failed 02b_cr_create_population_af_warfarin_mi_ons
w6wfcywewpvdaxfg failed 05b_an_models_af_warfarin_mi_ons
6ej2iipn63bck5yd failed 06b_an_models_ethnicity_af_warfarin_mi_ons
t4d4lebnnubs4tr6 failed 02b_cr_create_population_af_warfarin_stroke_ons
ycvzviv7ix5weurh failed 05b_an_models_af_warfarin_stroke_ons
sqvh66z5545tmc6w failed 06b_an_models_ethnicity_af_warfarin_stroke_ons
rgubrr3quy3274wx failed 02b_cr_create_population_af_warfarin_vte_ons
nxyzn2nu5kqxep6i failed 05b_an_models_af_warfarin_vte_ons
bnz6dupacwzlvb5c failed 06b_an_models_ethnicity_af_warfarin_vte_ons
uguyylx3op6b2vfd failed 02b_cr_create_population_af_warfarin_gi_bleed_ons
tzi4d76lkckn7iu7 failed 05b_an_models_af_warfarin_gi_bleed_ons
bphz4ucqatgmwemw failed 06b_an_models_ethnicity_af_warfarin_gi_bleed_ons
s5ki4cztzorbjdkz failed 02b_cr_create_population_af_warfarin_intracranial_bleed_ons
hijsig2ujlqnd6hy failed 05b_an_models_af_warfarin_intracranial_bleed_ons
v3if5djtfihyhor3 failed 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: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:00:45

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