updated codelists and analysis

opensafely · Feb 20, 2024 · 5639d56 · 5639d56
1 parent b300964
commit 5639d56
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Showing 64 changed files with 38,621 additions and 1,061 deletions.
diff --git a/analysis/codelists.py b/analysis/codelists.py
diff --git a/analysis/dataset_definition.py b/analysis/dataset_definition.py
diff --git a/analysis/dummydata/dummydata_infants.R b/analysis/dummydata/dummydata_infants.R
@@ -188,22 +188,22 @@ sim_list = lst(
     ~ as.integer(runif(n = ..n, index_day, index_day + 365))
   ),
 
-  ##exclusion criteria 
-
-  #severe combined immunodeficiency syndrome 
-  severe_immunodeficiency = bn_node(
-    ~ rbernoulli(n = ..n, p = 0.02)
-  ),
-
-  #ventilator dependence
-  ventilator_dependent = bn_node(
-    ~ rbernoulli(n = ..n, p = 0.01)
-  ),
-
-  #risk group 
-  risk_group_infants = bn_node(
-    ~ rbernoulli(n = ..n, p = 0.01)
-  )
+  # ##exclusion criteria 
+  # 
+  # #severe combined immunodeficiency syndrome 
+  # severe_immunodeficiency = bn_node(
+  #   ~ rbernoulli(n = ..n, p = 0.02)
+  # ),
+  # 
+  # #ventilator dependence
+  # ventilator_dependent = bn_node(
+  #   ~ rbernoulli(n = ..n, p = 0.01)
+  # ),
+  # 
+  # #risk group 
+  # risk_group_infants = bn_node(
+  #   ~ rbernoulli(n = ..n, p = 0.01)
+  # )
 
 )
 

diff --git a/analysis/dummydata/dummydata_older_adults.R b/analysis/dummydata/dummydata_older_adults.R
@@ -260,16 +260,16 @@ sim_list = lst(
     ~ as.integer(runif(n = ..n, index_day, index_day + 365))
   ),
 
-  ##exclusion criteria 
-
-  #care home resident
-  care_home_tpp = bn_node(
-    ~ rbernoulli(n = ..n, p = 0.01)
-  ),
-
-  care_home_code = bn_node(
-    ~ rbernoulli(n = ..n, p = 0.1)
-  )
+  # ##exclusion criteria 
+  # 
+  # #care home resident
+  # care_home_tpp = bn_node(
+  #   ~ rbernoulli(n = ..n, p = 0.01)
+  # ),
+  # 
+  # care_home_code = bn_node(
+  #   ~ rbernoulli(n = ..n, p = 0.1)
+  # )
 
 )
 

diff --git a/analysis/dummydata/dummyextract_infants_2016_2017.arrow b/analysis/dummydata/dummyextract_infants_2016_2017.arrow
diff --git a/analysis/dummydata/dummyextract_older_adults_2016_2017.arrow b/analysis/dummydata/dummyextract_older_adults_2016_2017.arrow
diff --git a/codelists/bristol-copd-medications-bnf.csv b/codelists/bristol-copd-medications-bnf.csv
diff --git a/codelists/codelists.json b/codelists/codelists.json
diff --git a/codelists/codelists.txt b/codelists/codelists.txt
@@ -1,30 +1,77 @@
 opensafely/ethnicity-snomed-0removed/2e641f61
+
+
+user/emprestige/rsv-identification-primary-care/5faa0ba9/
+user/emprestige/rsv-identification-secondary-care/560dcda6/
+user/emprestige/rsv-identification-primary-care-maximal-sensitivity/469a9874/
+user/emprestige/rsv-identification-prescriptions-maximal-sensitivity-dmd/65062298
+user/emprestige/rsv-exclusion-primary-care-maximal-sensitivity/0e4f7e8f/
+user/emprestige/rsv-exclusion-secondary-care-maximal-sensitivity/625ccb9f/
+
+user/emprestige/covid-19-identification-primary-care/2f7731a6/
+opensafely/covid-identification/2020-06-03
+user/emprestige/covid-19-identification-primary-care-maximal-sensitivity/703930b6/
+user/emprestige/covid-19-identification-prescriptions-dmd/32e73c2e
+user/emprestige/covid-19-exclusion-primary-care-maximal-sensitivity/03e32400/
+user/emprestige/covid-19-exclusion-secondary-care-maximal-sensitivity/1fa5572b/
+
+user/emprestige/influenza-identification-primary-care/2b370a92/
+user/emprestige/influenza-identification-secondary-care/3cfe5a71/
+user/emprestige/influenza-identification-primary-care-maximal-sensitivity/178d1749/
+user/emprestige/acute-respiratory-illness-primary-care/72ebf0ac/
+opensafely/symptoms-fever/758b5341/
+opensafely/symptoms-cough/72d8934b/
+user/emprestige/influenza-identification-prescriptions-maximal-sensitivity-dmd/4bf6af63
+user/emprestige/influenza-exclusion-primary-care-maximal-sensitivity/6ad3b0ca/
+user/emprestige/acute-respiratory-illness-secondary-care/1a3fd73f/
+user/emprestige/influenza-exclusion-secondary-care-maximal-sensitivity/38b4ca60/
+
+user/emprestige/respiratory-virus-unspecified-identification-primary-care/2b95afdb/
+user/emprestige/respiratory-virus-unspecified-exclusion-primary-care/26302fef/
+user/emprestige/respiratory-virus-unspecified-identification-secondary-care/12863ca6/
+user/emprestige/respiratory-virus-unspecified-exclusion-secondary-care/0fd37cb0/
+
+
 opensafely/smoking-clear/2020-04-29
 opensafely/smoking-unclear/2020-04-29
-nhsd-primary-care-domain-refsets/ast_cod/20210127
-opensafely/asthma-inhaler-steroid-medication/2020-04-15
-nhsd-primary-care-domain-refsets/astres_cod/20200812
 user/angel-wong/hazardous-drinking/3c786eff
 nhsd-primary-care-domain-refsets/illsub_cod/20210127
 nhsd-primary-care-domain-refsets/illsubint_cod/20210127
 nhsd-primary-care-domain-refsets/illsubassdec_cod/20200812
-nhsd-primary-care-domain-refsets/copd_cod/20210127
-bristol/copd-medications-bnf/4b00637c
-nhsd-primary-care-domain-refsets/copdres_cod/20200812
-nhsd-primary-care-domain-refsets/hyp_cod/20200812
-nhsd-primary-care-domain-refsets/dmtype1_cod/20210127
-nhsd-primary-care-domain-refsets/dmnontype1_cod/20210127
-nhsd-primary-care-domain-refsets/hf_cod/20210127
-nhsd-primary-care-domain-refsets/mi_cod/20210127
-bristol/ild-snomed/2f3e3051
-opensafely/covid-identification-in-primary-care-probable-covid-positive-test/508192f8
-opensafely/documented-influenza-illness/2020-05-18
-opensafely/covid-identification/2020-06-03
-nhsd-primary-care-domain-refsets/carehome_cod/20211221
+
 opensafely/chronic-cardiac-disease/2020-04-08
 nhsd-primary-care-domain-refsets/pulmohyp_cod/20210127
+nhsd-primary-care-domain-refsets/carehome_cod/20211221
 nhsd-primary-care-domain-refsets/tempcarhome_cod/20200812
-user/emprestige/rsv-identification-prescriptions-maximal-sensitivity-dmd/65062298
-user/emprestige/influenza-identification-prescriptions-maximal-sensitivity-dmd/4bf6af63
-user/emprestige/covid-19-identification-prescriptions-dmd/32e73c2e
-user/emprestige/copd-medications-new-dmd/1f3d48e5/
+
+primis-covid19-vacc-uptake/ast/v2.5
+primis-covid19-vacc-uptake/astrxm1/v2.5
+primis-covid19-vacc-uptake/astrxm2/v2.5
+nhsd-primary-care-domain-refsets/copd_cod/20210127
+user/emprestige/copd-medications-new-dmd/1f3d48e5
+nhsd-primary-care-domain-refsets/copdres_cod/20200812
+bristol/ild-snomed/2f3e3051
+opensafely/cystic-fibrosis/2020-07-20
+primis-covid19-vacc-uptake/diab/v2.5
+primis-covid19-vacc-uptake/dmres/v2.5
+primis-covid19-vacc-uptake/addis_cod/v2.5
+primis-covid19-vacc-uptake/bmi/v2.5
+primis-covid19-vacc-uptake/bmi_stage/v2.5
+primis-covid19-vacc-uptake/sev_obesity/v2.5
+primis-covid19-vacc-uptake/chd_cov/v2.5
+primis-covid19-vacc-uptake/ckd_cov/v2.5
+primis-covid19-vacc-uptake/ckd15/v2.5
+primis-covid19-vacc-uptake/ckd35/v2.5
+primis-covid19-vacc-uptake/cld/v2.5
+primis-covid19-vacc-uptake/resp_cov/v2.5
+primis-covid19-vacc-uptake/cns_cov/v2.5
+opensafely/cancer-excluding-lung-and-haematological-snomed/2020-04-15
+opensafely/haematological-cancer-snomed/2020-04-15
+opensafely/lung-cancer-snomed/2020-04-15
+primis-covid19-vacc-uptake/dxt_chemo_cod/v2.5
+primis-covid19-vacc-uptake/immdx_cov/v2.5
+primis-covid19-vacc-uptake/immrx/v2.5
+primis-covid19-vacc-uptake/immunosuppression-admin-codes/v2.5
+opensafely/sickle-cell-disease-snomed/2020-04-14/
+nhsd-primary-care-domain-refsets/hf_cod/20210127
+nhsd-primary-care-domain-refsets/mi_cod/20210127
diff --git a/codelists/nhsd-primary-care-domain-refsets-astres_cod.csv b/codelists/nhsd-primary-care-domain-refsets-astres_cod.csv
diff --git a/codelists/nhsd-primary-care-domain-refsets-dmnontype1_cod.csv b/codelists/nhsd-primary-care-domain-refsets-dmnontype1_cod.csv
diff --git a/codelists/nhsd-primary-care-domain-refsets-dmtype1_cod.csv b/codelists/nhsd-primary-care-domain-refsets-dmtype1_cod.csv