Job request: 16918
- Organisation:
- University of Bristol
- Workspace:
- post-covid-gastrointestinal
- ID:
- wobub4bp4srmejc2
This page shows the technical details of what happened when authorised researcher Marwa Al Arab requested one or more actions to be run against real patient data in the 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
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- Job identifier:
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7ir527ceq2fpjnkr
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- Job identifier:
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peoqnbqjni2fp3f7
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- Job identifier:
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zdjynb3kwqkscysr
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- Job identifier:
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au2upexq44x67qf3
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- Job identifier:
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qcewqs4glzlqbiw4
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- Job identifier:
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jcttzgtdbtixbyi6
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- Job identifier:
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cm6rfv3544wjb6ip
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- Job identifier:
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nhlydhgngcdyixhe
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- Job identifier:
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i3mb5tmucrji3b4e
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- Job identifier:
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4jepgxwpclpy5ago
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- Job identifier:
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bq2epzcnetfeprdo
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- Job identifier:
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bikz2d4gbj6o7cjc
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- Job identifier:
-
s3xtfg3o2uxab4kl
-
- Action:
- make_model_input-cohort_vax-sub_sex_female-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
dlz7odmlrnaf7fuk
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- Job identifier:
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url5jlb2wdlwwmjo
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- Job identifier:
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7yidlivrmlzd6vx5
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- Job identifier:
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r7epp4747bujfoem
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- Job identifier:
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q5277nx43a42tl5k
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- Job identifier:
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i3i7qygig5zkr5oh
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- Job identifier:
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nyiigeqev57seiy5
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- Job identifier:
-
6omuicxaesd7n4ak
-
- Action:
- make_model_input-cohort_prevax-sub_sex_female-nonvariceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
zsaaykgyknu5gui3
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- Job identifier:
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74x3mnimpdftn2qs
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- Job identifier:
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uz4htibtr6sqs4u4
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- Job identifier:
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b3vhpmlrmcpnatvr
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- Job identifier:
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kfba6dfix4zwbsnw
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- Job identifier:
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rpiv3isgr5f2xz5z
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- Job identifier:
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pfpgkktf2qa7apfn
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- Job identifier:
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bz7ntsrpvrngyuht
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- Job identifier:
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jwgl6v3vrrrrx6el
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- Job identifier:
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nedcw3rbpx47d45e
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- Job identifier:
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sf6rzid5qxzuxh6i
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- Job identifier:
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zfhbho66gmd5xos7
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- Job identifier:
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wagr2wa5f5klexoa
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- Job identifier:
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fyk2h7r5jhknqhf4
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- Job identifier:
-
dpfaj6cjxwfywoed
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- Action:
- make_model_input-cohort_unvax-sub_sex_male-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
n5bg7vwbx266lytf
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- Job identifier:
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c5elllba44ruanbc
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- Job identifier:
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le7ri23syjslltcn
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- Job identifier:
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w3wcjdkczikc3e6r
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- Job identifier:
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tr3xbr5yvkpefypm
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- Job identifier:
-
e5l7qsvzna4wzhdp
-
- Action:
- make_model_input-cohort_vax-sub_sex_male-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
wx7bxg4qyssiuwiw
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- Job identifier:
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r667yilvvxwgukaf
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- Job identifier:
-
es6gpilwmmqim5it
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- Job identifier:
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z44qktpsyjizlcy6
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- Job identifier:
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s7f5aimr3ooplin6
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- Job identifier:
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tzhe7x27fegkvlyh
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- Job identifier:
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whdthukqn526a35c
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- Job identifier:
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yuc4uxflz2x543zb
-
- Job identifier:
-
uica6xw267dbh3yc
-
- Job identifier:
-
gzjlpvsryk2mqurb
-
- Action:
- make_model_input-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
wpds4wa5shngk46k
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- Job identifier:
-
dkheksv4s3fpfqkv
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- Job identifier:
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x7qdqc6kyfo6hleu
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- Job identifier:
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o6tv5rq2dcqsjxqa
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- Job identifier:
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xmktfjt7s5yzerqz
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- Job identifier:
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xmgi2dwr5i7czsi5
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- Job identifier:
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l2xvd2ugxwegyciw
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- Job identifier:
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ifaa6r5l647lyq6w
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- Job identifier:
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asrq2a33mcfxr3ey
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- Job identifier:
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6uqdmyrs67fpci77
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- Job identifier:
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sxaxai6feyksrloy
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- Job identifier:
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2mhskbropfzgpatz
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- Job identifier:
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5rit3ekd5m2bdwgu
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- Job identifier:
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maxlipl25ccvabpq
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- Job identifier:
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zzk2ibbuna4cj4xb
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- Job identifier:
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qrd4ofsc3dkzvorv
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- Job identifier:
-
ophnndkifshopg7r
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- Job identifier:
-
fj5z46h6qsoa67sc
-
- Action:
- make_model_input-cohort_prevax-sub_age_80_110-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
zbf3vqv4mbimq7ga
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- Job identifier:
-
4q37b6qrzoyz2uf3
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- Job identifier:
-
qleuu6wzripepn5m
-
- Action:
- make_model_input-cohort_prevax-sub_age_80_110-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
cveqwjt76zgtmbe6
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- Job identifier:
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ziy5is5b7fzl36v6
-
- Job identifier:
-
3lq3efg532xokoiv
-
- Job identifier:
-
aqc4zhba4dmpyidf
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_asian-acute_pancreatitis
- Status:
- Status: Failed
- Job identifier:
-
33wg4nfasgqa5epd
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- Job identifier:
-
lhqnvk2ge7j2ixu4
-
- Job identifier:
-
ynppe5g4i7h7rnoa
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_asian-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
rlk6ydmi74jjcgz2
-
- Job identifier:
-
n32wvvgdhawa3hv5
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_asian-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
ith65i5vszskxzc2
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_asian-nonvariceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
uxabf2payzsb5x2e
-
- Job identifier:
-
sllfdrxvgvd5qmdi
-
- Job identifier:
-
fwwl2i2275pnwnzg
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_black-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
wo44j3plif5deos4
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- Job identifier:
-
s2klhkko4hdpqf7l
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- Job identifier:
-
v7yjfyhywotxwj7n
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- Action:
- make_model_input-cohort_prevax-sub_ethnicity_black-variceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
7rprkhhphjnktozl
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_mixed-acute_pancreatitis
- Status:
- Status: Failed
- Job identifier:
-
3t6z4ilk2glfq2ox
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_mixed-gallstones_disease
- Status:
- Status: Failed
- Job identifier:
-
i7sol7fvikfrym4x
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_mixed-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
oc6bkxvob6vufett
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- Job identifier:
-
2tw3r3ty4fqu6lt2
-
- Job identifier:
-
bjxlwfr5zmu4ixlg
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_mixed-variceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
i2jwkfxreruyz7ts
-
- Job identifier:
-
tjleoi74bz5fw7ub
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_other-gallstones_disease
- Status:
- Status: Failed
- Job identifier:
-
alzmxsxnh4vvc34c
-
- Job identifier:
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5ya566nalpsegtix
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_other-variceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
qqkcs3trsl5qrx7a
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- Job identifier:
-
63efk7iybr6tks72
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_white-gallstones_disease
- Status:
- Status: Failed
- Job identifier:
-
25336ipc2ovq6wrx
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- Job identifier:
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5y2j6xh75jynsqfb
-
- Job identifier:
-
hvf5a37ks57pcvj3
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_white-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
2vi6cjel4tvko6u2
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_white-nonvariceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
hw3z2t7xt5it7x4z
-
- Job identifier:
-
sqov4ctmfznfm5xp
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_white-variceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
o36xjgzu4hjhzefn
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_false-dyspepsia-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
jmginyevcjsko44h
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_false-gallstones_disease-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
3qtytqvx364dyamy
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_false-gastro_oesophageal_reflux_disease-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
priqyjovcjpheztm
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_false-lower_gi_bleeding-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
kbxitzetwhxtmeky
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_false-nonvariceal_gi_bleeding-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
kezyxeauebmxn4qr
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_false-upper_gi_bleeding-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
wevvasgr23zolrus
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_true-dyspepsia-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
p2cjgyqs7lichjcp
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_true-gallstones_disease-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
kike6hhiyqcyutye
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_true-ibs-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
mf5omephsdoitvqx
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_true-lower_gi_bleeding-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
tjfw2daof66xngt2
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_true-nonalcoholic_steatohepatitis-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
ru7pjtiynd6e7wvn
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_true-peptic_ulcer-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
pyrssdq2kizrut7w
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_true-upper_gi_bleeding-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
yi6tlcp4opwpbpm6
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_false-acute_pancreatitis-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
7ohg3xrtijnuvgiz
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_false-appendicitis-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
2ttthgfwbt76tdwu
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_false-ibs-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
b5koixwfioonijij
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_false-lower_gi_bleeding-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
nt2yfd5fkp6se6k4
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_false-nonvariceal_gi_bleeding-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
zxw6ppqfenpeqs77
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_false-peptic_ulcer-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
sqjtatccmva7xpgt
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_false-upper_gi_bleeding-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
q3h6ax2vg4gjucvz
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_true-acute_pancreatitis-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
65avzdte5ffp5rds
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_true-dyspepsia-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
kvkm725zv5f423ey
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_true-gastro_oesophageal_reflux_disease-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
ozqkgcdlbkjfbi4c
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_true-ibs-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
bdd5wls6nigm2aqf
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_true-lower_gi_bleeding-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
doidb47jtbj3pvzc
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_true-nonvariceal_gi_bleeding-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
vmzmlospdz7lf4du
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_true-peptic_ulcer-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
y2phrlppe42scy66
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_true-variceal_gi_bleeding-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
yt22jz45yzznya3k
-
- Job identifier:
-
mzt7h5hbdc6h2npx
-
- Job identifier:
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brjbiwttmihf2f3r
-
- Job identifier:
-
3ram5vo5z77lzn2x
-
- Job identifier:
-
z3gikhmtfhyz6rx7
-
- Action:
- make_model_input-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
aoha6abc44ytgkig
-
- Job identifier:
-
645fjsby57gz527c
-
- Action:
- make_model_input-cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
pmh3rfb4ambo3e5l
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_asian-variceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
ymdflin7nc5gmeto
-
- Job identifier:
-
i7k5onmmhwezyxh2
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_true-gallstones_disease-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
ozzqj3ixy7s3wgyu
-
- Job identifier:
-
awwgl6u2x6zqc5rh
-
- Job identifier:
-
s24slxlgr5wigz3f
-
- Job identifier:
-
2tk6u4sagqutflfx
-
- Job identifier:
-
wv76i5edu7xl65xs
-
- Action:
- make_model_input-cohort_prevax-sub_sex_male-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
v4cp7thlvwhhzafn
-
- Action:
- make_model_input-cohort_vax-sub_sex_male-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
bebsadd2lq43tup7
-
- Action:
- make_model_input-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
yx233fvij4ueadsc
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_asian-gallstones_disease
- Status:
- Status: Failed
- Job identifier:
-
hmfndjj2yyegxadt
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_black-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
w25y2zt74wiub4dl
-
- Job identifier:
-
jjrvn7rdrovigqzd
-
- Job identifier:
-
c5x2d4t3v22oktwx
-
- Job identifier:
-
ln7n3q63dwk2c6zo
-
- Job identifier:
-
2xq75ojeuzs7fnpe
-
- Job identifier:
-
snwxcxnksfwr6y4e
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_mixed-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
qgczbghglkkbq4p3
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_other-nonvariceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
ddrkhptedlar2v3l
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_false-dyspepsia-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
feiokj7u6yyr2zlr
-
- Job identifier:
-
h7pdrhimij7kiykm
-
- Job identifier:
-
vdc3jmff6c7b2gph
-
- Job identifier:
-
liri6xpw3kbxcatg
-
- Job identifier:
-
nj3jzwqqnkrvyrfu
-
- Job identifier:
-
7rdioqyr5tnsa5lk
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_other-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
3wjupnn4u4lrtl6i
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_black-acute_pancreatitis
- Status:
- Status: Failed
- Job identifier:
-
zs3x4uiioytuie27
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_white-acute_pancreatitis
- Status:
- Status: Failed
- Job identifier:
-
moqkpdmnikb7zzmr
-
- Job identifier:
-
etsrg2g4glqr5ruc
-
- Action:
- make_model_input-cohort_prevax-sub_sex_female-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
hzdnwsd2nr6itpey
-
- Action:
- make_model_input-cohort_prevax-sub_sex_female-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
w46spnfvu5zzseeu
-
- Action:
- make_model_input-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
cdxxfrbwj7vcxlgw
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_false-variceal_gi_bleeding-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
o747yma7myyolita
-
- Job identifier:
-
t5kukggyetcp3glk
-
- Action:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
y66ds7dyupgutkrn
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_false-gastro_oesophageal_reflux_disease-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
wvo3gd2cbjxxblnb
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_mixed-nonvariceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
likduuwgyjzta6vq
-
- Action:
- make_model_input-cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
ldogerzmynv44uda
-
- Job identifier:
-
jjf2ja3spyjtzesy
-
- Job identifier:
-
3mxyjaondo27an7g
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_false-nonalcoholic_steatohepatitis-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
wjj4743mt4zoqj5o
-
- Action:
- make_model_input-cohort_unvax-sub_sex_female-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
lejzynymffexbliz
-
- Job identifier:
-
cwkkc5svo4p2a27p
-
- Action:
- make_model_input-cohort_prevax-sub_age_60_79-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
bdwspd5abz26wqoq
-
- Action:
- make_model_input-cohort_vax-sub_sex_female-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
na2emepmrtkqzpkt
-
- Job identifier:
-
aw2s52hmgzatfukw
-
- Action:
- make_model_input-cohort_prevax-sub_age_60_79-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
vsspf2uh3gp2iqzi
-
- Job identifier:
-
e6zp5vmtkjsjaks3
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_black-gallstones_disease
- Status:
- Status: Failed
- Job identifier:
-
nly7xl2sbvoaczau
-
- Job identifier:
-
r7cufzshxii43ond
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_other-acute_pancreatitis
- Status:
- Status: Failed
- Job identifier:
-
zczlxukpjugufhia
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_true-nonvariceal_gi_bleeding-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
wlyqx32buijrh5iv
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_true-variceal_gi_bleeding-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
nnyjajj5xt5nrbca
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_false-gallstones_disease-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
umlazxjzp3isn7ma
-
- Job identifier:
-
5ee6h5mz6cfwvdr5
-
- Job identifier:
-
mgoca23am7ex74wa
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_other-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
m3l5tihxmq4lvveu
-
- Job identifier:
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i2vor25iysncuv2y
-
- Job identifier:
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2yuwr3zk5yd6melj
-
- Job identifier:
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zzidwz5ofg37xqjl
-
- Job identifier:
-
sic7n2spt72xujkm
-
- Action:
- cox_ipw-cohort_prevax-sub_sex_female-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
tq5ot6gxo4htt2ks
-
- Job identifier:
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pfzsxaj24vesyqjk
-
- Job identifier:
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g2oq7go7ufaellud
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- Job identifier:
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nlspjjzzqvxoi3nn
-
- Job identifier:
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nrot26lflk4dutmj
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- Job identifier:
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cegrmi6worelyfxt
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- Job identifier:
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rd56rqc26burztmv
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- Job identifier:
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mvt4klizhjqwvw2u
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- Job identifier:
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m5nxzxdolcnqyfnc
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- Job identifier:
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3yqlcudzkahk46x2
-
- Job identifier:
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v7mgsj7tu5nrwbcz
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_white-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
jywf37dynyuffgig
-
- Job identifier:
-
cp4xamodogntwmqo
-
- Action:
- cox_ipw-cohort_unvax-sub_sex_female-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
gko2hq7l6ucibvjx
-
- Job identifier:
-
bpk2kzjrplblyzep
-
- Job identifier:
-
lbemywnidyrujg5h
-
- Action:
- make_model_input-cohort_unvax-sub_sex_female-nonalcoholic_steatohepatitis
- Status:
- Status: Failed
- Job identifier:
-
y7nvzrc2yfhw4iqz
-
- Job identifier:
-
dgqufwx4h5yovahd
-
- Job identifier:
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pncz6mi47dplz474
-
- Job identifier:
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hcalo2ummxwuqeaj
-
- Job identifier:
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m3soj446fwiccg2g
-
- Job identifier:
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opgjzcsdmlctwpag
-
- Job identifier:
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qyq5xlze2t4sljca
-
- Job identifier:
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mcr4xpybv6juwwmo
-
- Job identifier:
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kurii7k7kzawcjkw
-
- Job identifier:
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yzp4bfsmvjjpbolw
-
- Job identifier:
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g6iwpcwganhexvtu
-
- Job identifier:
-
d5dn7j5yx43iwh44
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_false-acute_pancreatitis-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
d2xhmw7vaqfy42ia
-
- Job identifier:
-
ewumitfcbysxc6xm
-
- Job identifier:
-
gwesc3zvi5powxh2
-
- Job identifier:
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nbwwlf4bmokco4qj
-
- Job identifier:
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fiyxo2igssout7e2
-
- Job identifier:
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dfrusban76mhgcuy
-
- Job identifier:
-
xba2onugln644keh
-
- Job identifier:
-
vdvhzqiklbjqgz5b
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_false-appendicitis-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
uzhzzav24zv4fi44
-
- Job identifier:
-
dbrjprvucyiptaji
-
- Job identifier:
-
ix3xxzcaqan2wjs4
-
- Job identifier:
-
argi5euzq2wp5pxf
-
- Job identifier:
-
nh2cklcnl6z3j4yr
-
- Action:
- make_model_input-cohort_prevax-sub_sex_male-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
pmc4bikelxlrcfpe
-
- Job identifier:
-
dywvjmm6rd46dqqh
-
- Job identifier:
-
rhjc45j65ysqbr2e
-
- Job identifier:
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mfjsqt2xgoa4a3eb
-
- Job identifier:
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iznz7b66etjii45o
-
- Job identifier:
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s63grvozgqy36ewl
-
- Job identifier:
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dfzymse3rqflexts
-
- Job identifier:
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cdt5g2vknmlybbqf
-
- Job identifier:
-
wovoo32rp6srue2i
-
- Job identifier:
-
o3rch4apka6xz6ne
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_false-ibs-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
g2htxvls7fdgyqpy
-
- Job identifier:
-
7bwgcbheaofdzcpj
-
- Action:
- make_model_input-cohort_unvax-sub_sex_male-gastro_oesophageal_reflux_disease
- Status:
- Status: Failed
- Job identifier:
-
33cmlbxx7ohcgr5g
-
- Job identifier:
-
srd5x7cu25ocrqs7
-
- Job identifier:
-
thiuu3s25mk4ex2e
-
- Job identifier:
-
gxtihp6o4lrrzlny
-
- Job identifier:
-
ofpxgu5wvr6sxmkm
-
- Job identifier:
-
rrt33hnaysw2vrxn
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_false-peptic_ulcer-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
u7dg5ymfwds42omy
-
- Job identifier:
-
hn2rpvwct5sweimr
-
- Job identifier:
-
smeyudg2whhmuw26
-
- Job identifier:
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rcigzbfilte6ntpw
-
- Job identifier:
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usxhn2qol3c6abfr
-
- Job identifier:
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a7v5duqc3m7mcwr7
-
- Job identifier:
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vfumbr3g7llqlpok
-
- Job identifier:
-
o3dgu65bowj7xlug
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_true-acute_pancreatitis-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
g22mq26ttqmv4xje
-
- Job identifier:
-
lh6bqrhvyiyrdbwo
-
- Job identifier:
-
2umiqo5eefpvpbdq
-
- Job identifier:
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blvyzki5zi3d3kah
-
- Job identifier:
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zwgq7qjogpip5qew
-
- Job identifier:
-
7s3twn6jlf7cbeol
-
- Job identifier:
-
2iienmbledlhhacl
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_true-appendicitis-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
cy752ywakx2mooy5
-
- Action:
- make_model_input-cohort_prevax-sub_priorhistory_true-gastro_oesophageal_reflux_disease-cov_bin_overall_gi_and_symptoms
- Status:
- Status: Failed
- Job identifier:
-
dpodwtlruflp34qi
-
- Job identifier:
-
nkmrmntiphxnfrvc
-
- Job identifier:
-
ycptxgumtyejedvr
-
- Job identifier:
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jogsll5sh4rlmmrc
-
- Job identifier:
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5wxb4kyxxcrwwxpp
-
- Job identifier:
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qlbf7twi2kshw65b
-
- Job identifier:
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-
- Job identifier:
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j4bdgu3ivfemeyh5
-
- Job identifier:
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fvdsc4jo27dqae4c
-
- Job identifier:
-
76hsodpby32gfyqg
-
- Job identifier:
-
h3bdfndubmejrev6
-
- Action:
- make_model_input-cohort_prevax-sub_age_80_110-nonvariceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
uipjvd3w6fm2jl26
-
- Action:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
jwteye4uyimon3cd
-
- Job identifier:
-
y454pilbkb5jizvl
-
- Job identifier:
-
kf25jgqxqi4zh26g
-
- Job identifier:
-
7t6jwbofbktpgrl6
-
- Job identifier:
-
d2dvmn6pkahwg2cu
-
- Job identifier:
-
ti22stsngegobckp
-
- Action:
- make_model_input-cohort_prevax-sub_ethnicity_black-nonvariceal_gi_bleeding
- Status:
- Status: Failed
- Job identifier:
-
s4f74cpp3sdnz3kh
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_false-nonalcoholic_steatohepatitis-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
h54cvqt45r7fuaon
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_false-variceal_gi_bleeding-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
mof4hmhh3jk2keca
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_true-appendicitis-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
p2y6lkswprwhglxh
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_true-nonalcoholic_steatohepatitis-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
gziu5eyami4jolte
-
- Job identifier:
-
j5eq7knxrptt5i5o
-
- Action:
- make_model_input-cohort_prevax-sub_prioroperations_true-upper_gi_bleeding-cov_bin_gi_operations
- Status:
- Status: Failed
- Job identifier:
-
arske2cagtqdhgal
-
- Job identifier:
-
vgicstop5vbo7m7j
-
- Job identifier:
-
qxw75kwkok4ngd4k
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 200000
actions:
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create_project_actions.R
## Edit and run create_project_actions.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## Generate vaccination eligibility information
vax_eligibility_inputs:
run: r:latest analysis/metadates.R
outputs:
highly_sensitive:
study_dates_json: output/study_dates.json
vax_jcvi_groups: output/vax_jcvi_groups.csv.gz
vax_eligible_dates: output/vax_eligible_dates.csv.gz
## Generate prelim study_definition
generate_study_population_prelim:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prelim
--output-format csv.gz
needs:
- vax_eligibility_inputs
outputs:
highly_sensitive:
cohort: output/input_prelim.csv.gz
## Generate dates for all study cohorts
generate_index_dates:
run: r:latest analysis/prelim.R
needs:
- vax_eligibility_inputs
- generate_study_population_prelim
outputs:
highly_sensitive:
index_dates: output/index_dates.csv.gz
## Generate study population - prevax
generate_study_population_prevax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_prevax.csv.gz
## Generate study population - unvax
generate_study_population_unvax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_unvax.csv.gz
## Generate study population - vax
generate_study_population_vax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_vax.csv.gz
## Preprocess data - prevax
preprocess_data_prevax:
run: r:latest analysis/preprocess/preprocess_data.R prevax
needs:
- generate_index_dates
- generate_study_population_prevax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_prevax_stage0.txt
describe_venn: output/not-for-review/describe_venn_prevax.txt
highly_sensitive:
cohort: output/input_prevax.rds
venn: output/venn_prevax.rds
## Preprocess data - unvax
preprocess_data_unvax:
run: r:latest analysis/preprocess/preprocess_data.R unvax
needs:
- generate_index_dates
- generate_study_population_unvax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_unvax_stage0.txt
describe_venn: output/not-for-review/describe_venn_unvax.txt
highly_sensitive:
cohort: output/input_unvax.rds
venn: output/venn_unvax.rds
## Preprocess data - vax
preprocess_data_vax:
run: r:latest analysis/preprocess/preprocess_data.R vax
needs:
- generate_index_dates
- generate_study_population_vax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_vax_stage0.txt
describe_venn: output/not-for-review/describe_venn_vax.txt
highly_sensitive:
cohort: output/input_vax.rds
venn: output/venn_vax.rds
count_study_def_variables:
run: r:latest analysis/descriptives/intitial_input_counts.R
needs:
- generate_study_population_prevax
- generate_study_population_unvax
- generate_study_population_vax
- preprocess_data_prevax
- preprocess_data_unvax
- preprocess_data_vax
outputs:
moderately_sensitive:
counts: output/study_counts_prepro.txt
vax_summary: output/describe_prepro_vax.txt
prevax_summary: output/describe_prepro_prevax.txt
unvax_summary: output/describe_prepro_unvax.txt
## Stage 1 - data cleaning - prevax
stage1_data_cleaning_prevax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R prevax
needs:
- vax_eligibility_inputs
- preprocess_data_prevax
outputs:
moderately_sensitive:
consort: output/consort_prevax.csv
consort_rounded: output/consort_prevax_rounded.csv
highly_sensitive:
cohort: output/input_prevax_stage1.rds
## Stage 1 - data cleaning - unvax
stage1_data_cleaning_unvax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R unvax
needs:
- vax_eligibility_inputs
- preprocess_data_unvax
outputs:
moderately_sensitive:
consort: output/consort_unvax.csv
consort_rounded: output/consort_unvax_rounded.csv
highly_sensitive:
cohort: output/input_unvax_stage1.rds
## Stage 1 - data cleaning - vax
stage1_data_cleaning_vax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R vax
needs:
- vax_eligibility_inputs
- preprocess_data_vax
outputs:
moderately_sensitive:
consort: output/consort_vax.csv
consort_rounded: output/consort_vax_rounded.csv
highly_sensitive:
cohort: output/input_vax_stage1.rds
## Run models
make_model_input-cohort_prevax-main-acute_pancreatitis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-acute_pancreatitis
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-acute_pancreatitis.rds
cox_ipw-cohort_prevax-main-acute_pancreatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-acute_pancreatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-acute_pancreatitis.csv
needs:
- make_model_input-cohort_prevax-main-acute_pancreatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-acute_pancreatitis.csv
make_model_input-cohort_prevax-main-appendicitis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-appendicitis
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-appendicitis.rds
cox_ipw-cohort_prevax-main-appendicitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-appendicitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-appendicitis.csv
needs:
- make_model_input-cohort_prevax-main-appendicitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-appendicitis.csv
make_model_input-cohort_prevax-main-dyspepsia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-dyspepsia
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-dyspepsia.rds
cox_ipw-cohort_prevax-main-dyspepsia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-dyspepsia.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-dyspepsia.csv
needs:
- make_model_input-cohort_prevax-main-dyspepsia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-dyspepsia.csv
make_model_input-cohort_prevax-main-gallstones_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-gallstones_disease
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-gallstones_disease.rds
cox_ipw-cohort_prevax-main-gallstones_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-gallstones_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-gallstones_disease.csv
needs:
- make_model_input-cohort_prevax-main-gallstones_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-gallstones_disease.csv
make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-gastro_oesophageal_reflux_disease
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease.rds
cox_ipw-cohort_prevax-main-gastro_oesophageal_reflux_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-gastro_oesophageal_reflux_disease.csv
needs:
- make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-gastro_oesophageal_reflux_disease.csv
make_model_input-cohort_prevax-main-ibs:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-ibs
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-ibs.rds
cox_ipw-cohort_prevax-main-ibs:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-ibs.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-ibs.csv
needs:
- make_model_input-cohort_prevax-main-ibs
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-ibs.csv
make_model_input-cohort_prevax-main-lower_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-lower_gi_bleeding
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-lower_gi_bleeding.rds
cox_ipw-cohort_prevax-main-lower_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-lower_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-lower_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-main-lower_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-lower_gi_bleeding.csv
make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-nonalcoholic_steatohepatitis
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-nonalcoholic_steatohepatitis.rds
cox_ipw-cohort_prevax-main-nonalcoholic_steatohepatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-nonalcoholic_steatohepatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-nonalcoholic_steatohepatitis.csv
needs:
- make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-nonalcoholic_steatohepatitis.csv
make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-nonvariceal_gi_bleeding
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-nonvariceal_gi_bleeding.rds
cox_ipw-cohort_prevax-main-nonvariceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-nonvariceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-nonvariceal_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-nonvariceal_gi_bleeding.csv
make_model_input-cohort_prevax-main-peptic_ulcer:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-peptic_ulcer
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-peptic_ulcer.rds
cox_ipw-cohort_prevax-main-peptic_ulcer:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-peptic_ulcer.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-peptic_ulcer.csv
needs:
- make_model_input-cohort_prevax-main-peptic_ulcer
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-peptic_ulcer.csv
make_model_input-cohort_prevax-main-upper_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-upper_gi_bleeding
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-upper_gi_bleeding.rds
cox_ipw-cohort_prevax-main-upper_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-upper_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-upper_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-main-upper_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-upper_gi_bleeding.csv
make_model_input-cohort_prevax-main-variceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-variceal_gi_bleeding
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-variceal_gi_bleeding.rds
cox_ipw-cohort_prevax-main-variceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-variceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-variceal_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-main-variceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-variceal_gi_bleeding.csv
make_model_input-cohort_unvax-main-acute_pancreatitis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-acute_pancreatitis
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-acute_pancreatitis.rds
cox_ipw-cohort_unvax-main-acute_pancreatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-acute_pancreatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-acute_pancreatitis.csv
needs:
- make_model_input-cohort_unvax-main-acute_pancreatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-acute_pancreatitis.csv
make_model_input-cohort_unvax-main-appendicitis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-appendicitis
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-appendicitis.rds
cox_ipw-cohort_unvax-main-appendicitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-appendicitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-appendicitis.csv
needs:
- make_model_input-cohort_unvax-main-appendicitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-appendicitis.csv
make_model_input-cohort_unvax-main-dyspepsia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-dyspepsia
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-dyspepsia.rds
cox_ipw-cohort_unvax-main-dyspepsia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-dyspepsia.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-dyspepsia.csv
needs:
- make_model_input-cohort_unvax-main-dyspepsia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-dyspepsia.csv
make_model_input-cohort_unvax-main-gallstones_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-gallstones_disease
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-gallstones_disease.rds
cox_ipw-cohort_unvax-main-gallstones_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-gallstones_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-gallstones_disease.csv
needs:
- make_model_input-cohort_unvax-main-gallstones_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-gallstones_disease.csv
make_model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-gastro_oesophageal_reflux_disease
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease.rds
cox_ipw-cohort_unvax-main-gastro_oesophageal_reflux_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-gastro_oesophageal_reflux_disease.csv
needs:
- make_model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-gastro_oesophageal_reflux_disease.csv
make_model_input-cohort_unvax-main-ibs:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-ibs
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-ibs.rds
cox_ipw-cohort_unvax-main-ibs:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-ibs.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-ibs.csv
needs:
- make_model_input-cohort_unvax-main-ibs
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-ibs.csv
make_model_input-cohort_unvax-main-lower_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-lower_gi_bleeding
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-lower_gi_bleeding.rds
cox_ipw-cohort_unvax-main-lower_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-lower_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-lower_gi_bleeding.csv
needs:
- make_model_input-cohort_unvax-main-lower_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-lower_gi_bleeding.csv
make_model_input-cohort_unvax-main-nonalcoholic_steatohepatitis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-nonalcoholic_steatohepatitis
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-nonalcoholic_steatohepatitis.rds
cox_ipw-cohort_unvax-main-nonalcoholic_steatohepatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-nonalcoholic_steatohepatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-nonalcoholic_steatohepatitis.csv
needs:
- make_model_input-cohort_unvax-main-nonalcoholic_steatohepatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-nonalcoholic_steatohepatitis.csv
make_model_input-cohort_unvax-main-nonvariceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-nonvariceal_gi_bleeding
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-nonvariceal_gi_bleeding.rds
cox_ipw-cohort_unvax-main-nonvariceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-nonvariceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-nonvariceal_gi_bleeding.csv
needs:
- make_model_input-cohort_unvax-main-nonvariceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-nonvariceal_gi_bleeding.csv
make_model_input-cohort_unvax-main-peptic_ulcer:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-peptic_ulcer
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-peptic_ulcer.rds
cox_ipw-cohort_unvax-main-peptic_ulcer:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-peptic_ulcer.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-peptic_ulcer.csv
needs:
- make_model_input-cohort_unvax-main-peptic_ulcer
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-peptic_ulcer.csv
make_model_input-cohort_unvax-main-upper_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-upper_gi_bleeding
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-upper_gi_bleeding.rds
cox_ipw-cohort_unvax-main-upper_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-upper_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-upper_gi_bleeding.csv
needs:
- make_model_input-cohort_unvax-main-upper_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-upper_gi_bleeding.csv
make_model_input-cohort_unvax-main-variceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-variceal_gi_bleeding
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-variceal_gi_bleeding.rds
cox_ipw-cohort_unvax-main-variceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-variceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-variceal_gi_bleeding.csv
needs:
- make_model_input-cohort_unvax-main-variceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-variceal_gi_bleeding.csv
make_model_input-cohort_vax-main-acute_pancreatitis:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-acute_pancreatitis
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-acute_pancreatitis.rds
cox_ipw-cohort_vax-main-acute_pancreatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-acute_pancreatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-acute_pancreatitis.csv
needs:
- make_model_input-cohort_vax-main-acute_pancreatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-acute_pancreatitis.csv
make_model_input-cohort_vax-main-appendicitis:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-appendicitis
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-appendicitis.rds
cox_ipw-cohort_vax-main-appendicitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-appendicitis.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-appendicitis.csv
needs:
- make_model_input-cohort_vax-main-appendicitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-appendicitis.csv
make_model_input-cohort_vax-main-dyspepsia:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-dyspepsia
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-dyspepsia.rds
cox_ipw-cohort_vax-main-dyspepsia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-dyspepsia.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-dyspepsia.csv
needs:
- make_model_input-cohort_vax-main-dyspepsia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-dyspepsia.csv
make_model_input-cohort_vax-main-gallstones_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-gallstones_disease
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-gallstones_disease.rds
cox_ipw-cohort_vax-main-gallstones_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-gallstones_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-gallstones_disease.csv
needs:
- make_model_input-cohort_vax-main-gallstones_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-gallstones_disease.csv
make_model_input-cohort_vax-main-gastro_oesophageal_reflux_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-gastro_oesophageal_reflux_disease
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-gastro_oesophageal_reflux_disease.rds
cox_ipw-cohort_vax-main-gastro_oesophageal_reflux_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-gastro_oesophageal_reflux_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-gastro_oesophageal_reflux_disease.csv
needs:
- make_model_input-cohort_vax-main-gastro_oesophageal_reflux_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-gastro_oesophageal_reflux_disease.csv
make_model_input-cohort_vax-main-ibs:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-ibs
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-ibs.rds
cox_ipw-cohort_vax-main-ibs:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-ibs.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-ibs.csv
needs:
- make_model_input-cohort_vax-main-ibs
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-ibs.csv
make_model_input-cohort_vax-main-lower_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-lower_gi_bleeding
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-lower_gi_bleeding.rds
cox_ipw-cohort_vax-main-lower_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-lower_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-lower_gi_bleeding.csv
needs:
- make_model_input-cohort_vax-main-lower_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-lower_gi_bleeding.csv
make_model_input-cohort_vax-main-nonalcoholic_steatohepatitis:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-nonalcoholic_steatohepatitis
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-nonalcoholic_steatohepatitis.rds
cox_ipw-cohort_vax-main-nonalcoholic_steatohepatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-nonalcoholic_steatohepatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-nonalcoholic_steatohepatitis.csv
needs:
- make_model_input-cohort_vax-main-nonalcoholic_steatohepatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-nonalcoholic_steatohepatitis.csv
make_model_input-cohort_vax-main-nonvariceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-nonvariceal_gi_bleeding
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-nonvariceal_gi_bleeding.rds
cox_ipw-cohort_vax-main-nonvariceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-nonvariceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-nonvariceal_gi_bleeding.csv
needs:
- make_model_input-cohort_vax-main-nonvariceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-nonvariceal_gi_bleeding.csv
make_model_input-cohort_vax-main-peptic_ulcer:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-peptic_ulcer
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-peptic_ulcer.rds
cox_ipw-cohort_vax-main-peptic_ulcer:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-peptic_ulcer.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-peptic_ulcer.csv
needs:
- make_model_input-cohort_vax-main-peptic_ulcer
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-peptic_ulcer.csv
make_model_input-cohort_vax-main-upper_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-upper_gi_bleeding
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-upper_gi_bleeding.rds
cox_ipw-cohort_vax-main-upper_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-upper_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-upper_gi_bleeding.csv
needs:
- make_model_input-cohort_vax-main-upper_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-upper_gi_bleeding.csv
make_model_input-cohort_vax-main-variceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-variceal_gi_bleeding
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-variceal_gi_bleeding.rds
cox_ipw-cohort_vax-main-variceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-variceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-variceal_gi_bleeding.csv
needs:
- make_model_input-cohort_vax-main-variceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-variceal_gi_bleeding.csv
make_model_input-cohort_prevax-sub_age_18_39-acute_pancreatitis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-acute_pancreatitis
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-acute_pancreatitis.rds
cox_ipw-cohort_prevax-sub_age_18_39-acute_pancreatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-acute_pancreatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-acute_pancreatitis.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-acute_pancreatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-acute_pancreatitis.csv
make_model_input-cohort_prevax-sub_age_18_39-appendicitis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-appendicitis
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-appendicitis.rds
cox_ipw-cohort_prevax-sub_age_18_39-appendicitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-appendicitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-appendicitis.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-appendicitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-appendicitis.csv
make_model_input-cohort_prevax-sub_age_18_39-dyspepsia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-dyspepsia
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-dyspepsia.rds
cox_ipw-cohort_prevax-sub_age_18_39-dyspepsia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-dyspepsia.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-dyspepsia.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-dyspepsia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-dyspepsia.csv
make_model_input-cohort_prevax-sub_age_18_39-gallstones_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-gallstones_disease
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-gallstones_disease.rds
cox_ipw-cohort_prevax-sub_age_18_39-gallstones_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-gallstones_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-gallstones_disease.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-gallstones_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-gallstones_disease.csv
make_model_input-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease.rds
cox_ipw-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-gastro_oesophageal_reflux_disease.csv
make_model_input-cohort_prevax-sub_age_18_39-ibs:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-ibs
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-ibs.rds
cox_ipw-cohort_prevax-sub_age_18_39-ibs:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-ibs.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-ibs.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-ibs
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-ibs.csv
make_model_input-cohort_prevax-sub_age_18_39-lower_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-lower_gi_bleeding
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-lower_gi_bleeding.rds
cox_ipw-cohort_prevax-sub_age_18_39-lower_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-lower_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-lower_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-lower_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-lower_gi_bleeding.csv
make_model_input-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis.rds
cox_ipw-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-nonalcoholic_steatohepatitis.csv
make_model_input-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding.rds
cox_ipw-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-nonvariceal_gi_bleeding.csv
make_model_input-cohort_prevax-sub_age_18_39-peptic_ulcer:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-peptic_ulcer
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-peptic_ulcer.rds
cox_ipw-cohort_prevax-sub_age_18_39-peptic_ulcer:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-peptic_ulcer.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-peptic_ulcer.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-peptic_ulcer
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-peptic_ulcer.csv
make_model_input-cohort_prevax-sub_age_18_39-upper_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-upper_gi_bleeding
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-upper_gi_bleeding.rds
cox_ipw-cohort_prevax-sub_age_18_39-upper_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-upper_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-upper_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-upper_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-upper_gi_bleeding.csv
make_model_input-cohort_prevax-sub_age_18_39-variceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-variceal_gi_bleeding
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-variceal_gi_bleeding.rds
cox_ipw-cohort_prevax-sub_age_18_39-variceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-variceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-variceal_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-variceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-variceal_gi_bleeding.csv
make_model_input-cohort_unvax-sub_age_18_39-acute_pancreatitis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-acute_pancreatitis
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-acute_pancreatitis.rds
cox_ipw-cohort_unvax-sub_age_18_39-acute_pancreatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-acute_pancreatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-acute_pancreatitis.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-acute_pancreatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-acute_pancreatitis.csv
make_model_input-cohort_unvax-sub_age_18_39-appendicitis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-appendicitis
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-appendicitis.rds
cox_ipw-cohort_unvax-sub_age_18_39-appendicitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-appendicitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-appendicitis.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-appendicitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-appendicitis.csv
make_model_input-cohort_unvax-sub_age_18_39-dyspepsia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-dyspepsia
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-dyspepsia.rds
cox_ipw-cohort_unvax-sub_age_18_39-dyspepsia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-dyspepsia.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-dyspepsia.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-dyspepsia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-dyspepsia.csv
make_model_input-cohort_unvax-sub_age_18_39-gallstones_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-gallstones_disease
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-gallstones_disease.rds
cox_ipw-cohort_unvax-sub_age_18_39-gallstones_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-gallstones_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-gallstones_disease.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-gallstones_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-gallstones_disease.csv
make_model_input-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease.rds
cox_ipw-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-gastro_oesophageal_reflux_disease.csv
make_model_input-cohort_unvax-sub_age_18_39-ibs:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-ibs
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-ibs.rds
cox_ipw-cohort_unvax-sub_age_18_39-ibs:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-ibs.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-ibs.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-ibs
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-ibs.csv
make_model_input-cohort_unvax-sub_age_18_39-lower_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-lower_gi_bleeding
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-lower_gi_bleeding.rds
cox_ipw-cohort_unvax-sub_age_18_39-lower_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-lower_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-lower_gi_bleeding.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-lower_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-lower_gi_bleeding.csv
make_model_input-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis.rds
cox_ipw-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-nonalcoholic_steatohepatitis.csv
make_model_input-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding.rds
cox_ipw-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-nonvariceal_gi_bleeding.csv
make_model_input-cohort_unvax-sub_age_18_39-peptic_ulcer:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-peptic_ulcer
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-peptic_ulcer.rds
cox_ipw-cohort_unvax-sub_age_18_39-peptic_ulcer:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-peptic_ulcer.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-peptic_ulcer.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-peptic_ulcer
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-peptic_ulcer.csv
make_model_input-cohort_unvax-sub_age_18_39-upper_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-upper_gi_bleeding
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-upper_gi_bleeding.rds
cox_ipw-cohort_unvax-sub_age_18_39-upper_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-upper_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-upper_gi_bleeding.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-upper_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-upper_gi_bleeding.csv
make_model_input-cohort_unvax-sub_age_18_39-variceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-variceal_gi_bleeding
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-variceal_gi_bleeding.rds
cox_ipw-cohort_unvax-sub_age_18_39-variceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-variceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-variceal_gi_bleeding.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-variceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-variceal_gi_bleeding.csv
make_model_input-cohort_vax-sub_age_18_39-acute_pancreatitis:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-acute_pancreatitis
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-acute_pancreatitis.rds
cox_ipw-cohort_vax-sub_age_18_39-acute_pancreatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-acute_pancreatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-acute_pancreatitis.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-acute_pancreatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-acute_pancreatitis.csv
make_model_input-cohort_vax-sub_age_18_39-appendicitis:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-appendicitis
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-appendicitis.rds
cox_ipw-cohort_vax-sub_age_18_39-appendicitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-appendicitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-appendicitis.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-appendicitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-appendicitis.csv
make_model_input-cohort_vax-sub_age_18_39-dyspepsia:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-dyspepsia
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-dyspepsia.rds
cox_ipw-cohort_vax-sub_age_18_39-dyspepsia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-dyspepsia.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-dyspepsia.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-dyspepsia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-dyspepsia.csv
make_model_input-cohort_vax-sub_age_18_39-gallstones_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-gallstones_disease
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-gallstones_disease.rds
cox_ipw-cohort_vax-sub_age_18_39-gallstones_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-gallstones_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-gallstones_disease.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-gallstones_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-gallstones_disease.csv
make_model_input-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease.rds
cox_ipw-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-gastro_oesophageal_reflux_disease.csv
make_model_input-cohort_vax-sub_age_18_39-ibs:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-ibs
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-ibs.rds
cox_ipw-cohort_vax-sub_age_18_39-ibs:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-ibs.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-ibs.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-ibs
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-ibs.csv
make_model_input-cohort_vax-sub_age_18_39-lower_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-lower_gi_bleeding
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-lower_gi_bleeding.rds
cox_ipw-cohort_vax-sub_age_18_39-lower_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-lower_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-lower_gi_bleeding.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-lower_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-lower_gi_bleeding.csv
make_model_input-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis.rds
cox_ipw-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-nonalcoholic_steatohepatitis.csv
make_model_input-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding.rds
cox_ipw-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-nonvariceal_gi_bleeding.csv
make_model_input-cohort_vax-sub_age_18_39-peptic_ulcer:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-peptic_ulcer
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-peptic_ulcer.rds
cox_ipw-cohort_vax-sub_age_18_39-peptic_ulcer:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-peptic_ulcer.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-peptic_ulcer.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-peptic_ulcer
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-peptic_ulcer.csv
make_model_input-cohort_vax-sub_age_18_39-upper_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-upper_gi_bleeding
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-upper_gi_bleeding.rds
cox_ipw-cohort_vax-sub_age_18_39-upper_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-upper_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-upper_gi_bleeding.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-upper_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-upper_gi_bleeding.csv
make_model_input-cohort_vax-sub_age_18_39-variceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-variceal_gi_bleeding
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-variceal_gi_bleeding.rds
cox_ipw-cohort_vax-sub_age_18_39-variceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-variceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-variceal_gi_bleeding.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-variceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-variceal_gi_bleeding.csv
make_model_input-cohort_prevax-sub_age_40_59-acute_pancreatitis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-acute_pancreatitis
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-acute_pancreatitis.rds
cox_ipw-cohort_prevax-sub_age_40_59-acute_pancreatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-acute_pancreatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-acute_pancreatitis.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-acute_pancreatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-acute_pancreatitis.csv
make_model_input-cohort_prevax-sub_age_40_59-appendicitis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-appendicitis
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-appendicitis.rds
cox_ipw-cohort_prevax-sub_age_40_59-appendicitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-appendicitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-appendicitis.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-appendicitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-appendicitis.csv
make_model_input-cohort_prevax-sub_age_40_59-dyspepsia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-dyspepsia
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-dyspepsia.rds
cox_ipw-cohort_prevax-sub_age_40_59-dyspepsia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-dyspepsia.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-dyspepsia.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-dyspepsia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-dyspepsia.csv
make_model_input-cohort_prevax-sub_age_40_59-gallstones_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-gallstones_disease
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-gallstones_disease.rds
cox_ipw-cohort_prevax-sub_age_40_59-gallstones_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-gallstones_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-gallstones_disease.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-gallstones_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-gallstones_disease.csv
make_model_input-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease.rds
cox_ipw-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-gastro_oesophageal_reflux_disease.csv
make_model_input-cohort_prevax-sub_age_40_59-ibs:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-ibs
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-ibs.rds
cox_ipw-cohort_prevax-sub_age_40_59-ibs:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-ibs.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-ibs.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-ibs
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-ibs.csv
make_model_input-cohort_prevax-sub_age_40_59-lower_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-lower_gi_bleeding
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-lower_gi_bleeding.rds
cox_ipw-cohort_prevax-sub_age_40_59-lower_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-lower_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-lower_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-lower_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-lower_gi_bleeding.csv
make_model_input-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis.rds
cox_ipw-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-nonalcoholic_steatohepatitis.csv
make_model_input-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding.rds
cox_ipw-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-nonvariceal_gi_bleeding.csv
make_model_input-cohort_prevax-sub_age_40_59-peptic_ulcer:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-peptic_ulcer
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-peptic_ulcer.rds
cox_ipw-cohort_prevax-sub_age_40_59-peptic_ulcer:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-peptic_ulcer.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-peptic_ulcer.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-peptic_ulcer
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-peptic_ulcer.csv
make_model_input-cohort_prevax-sub_age_40_59-upper_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-upper_gi_bleeding
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-upper_gi_bleeding.rds
cox_ipw-cohort_prevax-sub_age_40_59-upper_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-upper_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-upper_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-upper_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-upper_gi_bleeding.csv
make_model_input-cohort_prevax-sub_age_40_59-variceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-variceal_gi_bleeding
needs:
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-variceal_gi_bleeding.rds
cox_ipw-cohort_prevax-sub_age_40_59-variceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-variceal_gi_bleeding.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-variceal_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-variceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-variceal_gi_bleeding.csv
make_model_input-cohort_unvax-sub_age_40_59-acute_pancreatitis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-acute_pancreatitis
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_40_59-acute_pancreatitis.rds
cox_ipw-cohort_unvax-sub_age_40_59-acute_pancreatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-acute_pancreatitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-acute_pancreatitis.csv
needs:
- make_model_input-cohort_unvax-sub_age_40_59-acute_pancreatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_40_59-acute_pancreatitis.csv
make_model_input-cohort_unvax-sub_age_40_59-appendicitis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-appendicitis
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_40_59-appendicitis.rds
cox_ipw-cohort_unvax-sub_age_40_59-appendicitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-appendicitis.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-appendicitis.csv
needs:
- make_model_input-cohort_unvax-sub_age_40_59-appendicitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_40_59-appendicitis.csv
make_model_input-cohort_unvax-sub_age_40_59-dyspepsia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-dyspepsia
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_40_59-dyspepsia.rds
cox_ipw-cohort_unvax-sub_age_40_59-dyspepsia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-dyspepsia.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-dyspepsia.csv
needs:
- make_model_input-cohort_unvax-sub_age_40_59-dyspepsia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_40_59-dyspepsia.csv
make_model_input-cohort_unvax-sub_age_40_59-gallstones_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-gallstones_disease
needs:
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_40_59-gallstones_disease.rds
cox_ipw-cohort_unvax-sub_age_40_59-gallstones_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-gallstones_disease.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-gallstones_disease.csv
needs:
- make_model_input-cohort_unvax-sub_age_40_59-gallstones_disease
outputs:
moderately_sensitive:
model_output: output/model_outpu