From 74f747e934565cea02c4ef2a9bc31f33943e3d29 Mon Sep 17 00:00:00 2001 From: Martina Pesce <82039235+marrpesce@users.noreply.github.com> Date: Thu, 19 Dec 2024 15:09:45 +0000 Subject: [PATCH] Removed primis_variables() and fixed related bugs --- analysis/dataset_definition_snapshot.py | 2 +- analysis/dataset_definition_varying.py | 7 +-- analysis/process.R | 24 ++++----- analysis/report_history.R | 69 +++++++++++++------------ analysis/variables_function.py | 20 ++++--- 5 files changed, 64 insertions(+), 58 deletions(-) diff --git a/analysis/dataset_definition_snapshot.py b/analysis/dataset_definition_snapshot.py index 2f695b0..f1ad147 100644 --- a/analysis/dataset_definition_snapshot.py +++ b/analysis/dataset_definition_snapshot.py @@ -65,4 +65,4 @@ demographic_variables(dataset = dataset, index_date = snapshot_date) primis_variables(dataset = dataset, index_date = snapshot_date) -other_cx_variables(dataset = dataset, index_date = snapshot_date) \ No newline at end of file +# other_cx_variables(dataset = dataset, index_date = snapshot_date) \ No newline at end of file diff --git a/analysis/dataset_definition_varying.py b/analysis/dataset_definition_varying.py index ac5149d..08e311f 100644 --- a/analysis/dataset_definition_varying.py +++ b/analysis/dataset_definition_varying.py @@ -68,10 +68,11 @@ demographic_variables(dataset = dataset, index_date = current_vax.date, var_name_suffix = suffix) # primis variables - primis_variables(dataset = dataset, index_date = current_vax.date, var_name_suffix = suffix) +# primis_variables(dataset = dataset, index_date = current_vax.date, var_name_suffix = suffix) + dataset.add_column(f"primis_atrisk_{i}", primis_atrisk(current_vax.date)) # at risk - # primis variables - other_cx_variables(dataset = dataset, index_date = current_vax.date, var_name_suffix = suffix) + # other clinical variables +# other_cx_variables(dataset = dataset, index_date = current_vax.date, var_name_suffix = suffix) previous_vax_date = current_vax.date diff --git a/analysis/process.R b/analysis/process.R index 3c72414..bbd134f 100644 --- a/analysis/process.R +++ b/analysis/process.R @@ -109,18 +109,18 @@ data_vax <- matches("imd_\\d+"), matches("imd_quintile_\\d+"), # ... more clinical (PRIMIS) characteristics here - matches("primis_atrisk_\\d+"), # Clinically vulnerable - matches("crd_\\d+"), #chronic respiratory disease - matches("chd_\\d+"), #chronic heart disease - matches("ckd_\\d+"), #chronic kidney disease - matches("cld_\\d+"), # chronic liver disease - matches("cns_\\d+"), # chronic neurological disease - matches("learndis_\\d+"), # learning Disability - matches("diabetes_\\d+"), #diabetes - matches("immunosuppressed_\\d+"), #immunosuppress grouped - matches("asplenia_\\d+"), # asplenia or dysfunction of the spleen - matches("severe_obesity_\\d+"), #immunosuppress grouped - matches("smi_\\d+"), #severe mental illness + matches("primis_atrisk_\\d+") #, # Clinically vulnerable +# matches("crd_\\d+"), #chronic respiratory disease +# matches("chd_\\d+"), #chronic heart disease +# matches("ckd_\\d+"), #chronic kidney disease +# matches("cld_\\d+"), # chronic liver disease +# matches("cns_\\d+"), # chronic neurological disease +# matches("learndis_\\d+"), # learning Disability +# matches("diabetes_\\d+"), #diabetes +# matches("immunosuppressed_\\d+"), #immunosuppress grouped +# matches("asplenia_\\d+"), # asplenia or dysfunction of the spleen +# matches("severe_obesity_\\d+"), #immunosuppress grouped +# matches("smi_\\d+"), #severe mental illness ) %>% pivot_longer( cols = -patient_id, diff --git a/analysis/report_history.R b/analysis/report_history.R index cc85868..7240aee 100644 --- a/analysis/report_history.R +++ b/analysis/report_history.R @@ -172,7 +172,8 @@ summary_stratified <- vax_dosenumber, vax_type8, vax_campaign, sex, ageband, ethnicity5, region, imd_quintile, # PRIMIS - crd, chd, ckd, cld, cns, learndis, diabetes, immunosuppressed, asplenia, severe_obesity, smi, primis_atrisk + # crd, chd, ckd, cld, cns, learndis, diabetes, immunosuppressed, asplenia, severe_obesity, smi, + primis_atrisk ) %>% summarise( n = ceiling_any(n(), 100) @@ -265,17 +266,17 @@ plot_vax_dates(vax_campaign, all) plot_vax_dates(vax_dosenumber, all) #PRIMIS -plot_vax_dates(crd, all) # chronic respiratory disease -plot_vax_dates(chd, all) # chronic heart disease -plot_vax_dates(ckd, all) # chronic kidney disease -plot_vax_dates(cld, all) # chronic liver disease -plot_vax_dates(cns, all) #chronic neurological -plot_vax_dates(learndis, all) # learning disability -plot_vax_dates(diabetes, all) # diabetes -plot_vax_dates(immunosuppressed, all) # immunosuppressed -plot_vax_dates(asplenia, all) # asplenia or dysfunction of the spleen -plot_vax_dates(severe_obesity, all) # obesity -plot_vax_dates(smi, all) # severe mental illness +#plot_vax_dates(crd, all) # chronic respiratory disease +#plot_vax_dates(chd, all) # chronic heart disease +#plot_vax_dates(ckd, all) # chronic kidney disease +#plot_vax_dates(cld, all) # chronic liver disease +# plot_vax_dates(cns, all) #chronic neurological +# plot_vax_dates(learndis, all) # learning disability +# plot_vax_dates(diabetes, all) # diabetes +# plot_vax_dates(immunosuppressed, all) # immunosuppressed +# plot_vax_dates(asplenia, all) # asplenia or dysfunction of the spleen +# plot_vax_dates(severe_obesity, all) # obesity +# plot_vax_dates(smi, all) # severe mental illness plot_vax_dates(primis_atrisk, all) # clinically vulnerable @@ -286,17 +287,17 @@ plot_vax_dates(region, vax_dosenumber) plot_vax_dates(imd_quintile, vax_dosenumber) plot_vax_dates(vax_campaign, vax_dosenumber) #PRIMIS -plot_vax_dates(crd, vax_dosenumber) # chronic respiratory disease -plot_vax_dates(chd, vax_dosenumber) # chronic heart disease -plot_vax_dates(ckd, vax_dosenumber) # chronic kidney disease -plot_vax_dates(cld, vax_dosenumber) # chronic liver disease -plot_vax_dates(cns, vax_dosenumber) # chronic neurological disease -plot_vax_dates(learndis, vax_dosenumber) # learning Disability -plot_vax_dates(diabetes, vax_dosenumber) # diabetes -plot_vax_dates(immunosuppressed, vax_dosenumber) # immunosuppressed -plot_vax_dates(asplenia, vax_dosenumber) # asplenia or dysfunction of the spleen -plot_vax_dates(severe_obesity, vax_dosenumber) # obesity -plot_vax_dates(smi, vax_dosenumber) # severe mental illness +#plot_vax_dates(crd, vax_dosenumber) # chronic respiratory disease +#plot_vax_dates(chd, vax_dosenumber) # chronic heart disease +# plot_vax_dates(ckd, vax_dosenumber) # chronic kidney disease +# plot_vax_dates(cld, vax_dosenumber) # chronic liver disease +# plot_vax_dates(cns, vax_dosenumber) # chronic neurological disease +# plot_vax_dates(learndis, vax_dosenumber) # learning Disability +# plot_vax_dates(diabetes, vax_dosenumber) # diabetes +# plot_vax_dates(immunosuppressed, vax_dosenumber) # immunosuppressed +# plot_vax_dates(asplenia, vax_dosenumber) # asplenia or dysfunction of the spleen +# plot_vax_dates(severe_obesity, vax_dosenumber) # obesity +# plot_vax_dates(smi, vax_dosenumber) # severe mental illness plot_vax_dates(primis_atrisk, vax_dosenumber) # Clinically vulnerable ## output plots of time since previous vaccination by type, dose number, and other characteristics ---- @@ -379,15 +380,15 @@ plot_vax_intervals(vax_dosenumber, all) #PRIMIS -plot_vax_intervals(crd, vax_dosenumber) # chronic respiratory disease -plot_vax_intervals(chd, vax_dosenumber) # chronic heart disease -plot_vax_intervals(ckd, vax_dosenumber) # chronic kidney disease -plot_vax_intervals(cld, vax_dosenumber) # chronic liver disease -plot_vax_intervals(cns, vax_dosenumber) # chronic neurological -plot_vax_intervals(learndis, vax_dosenumber) # learning disability -plot_vax_intervals(diabetes, vax_dosenumber) # diabetes -plot_vax_intervals(immunosuppressed, vax_dosenumber) # immunosuppressed -plot_vax_intervals(asplenia, vax_dosenumber) # asplenia or dysfunction of the spleen -plot_vax_intervals(severe_obesity, vax_dosenumber) # obesity -plot_vax_intervals(smi, vax_dosenumber) # severe mental illness +# plot_vax_intervals(crd, vax_dosenumber) # chronic respiratory disease +# plot_vax_intervals(chd, vax_dosenumber) # chronic heart disease +# plot_vax_intervals(ckd, vax_dosenumber) # chronic kidney disease +# plot_vax_intervals(cld, vax_dosenumber) # chronic liver disease +# plot_vax_intervals(cns, vax_dosenumber) # chronic neurological +# plot_vax_intervals(learndis, vax_dosenumber) # learning disability +# plot_vax_intervals(diabetes, vax_dosenumber) # diabetes +# plot_vax_intervals(immunosuppressed, vax_dosenumber) # immunosuppressed +# plot_vax_intervals(asplenia, vax_dosenumber) # asplenia or dysfunction of the spleen +# plot_vax_intervals(severe_obesity, vax_dosenumber) # obesity +# plot_vax_intervals(smi, vax_dosenumber) # severe mental illness plot_vax_intervals(primis_atrisk, vax_dosenumber) # Clinically vulnerable \ No newline at end of file diff --git a/analysis/variables_function.py b/analysis/variables_function.py index 3449b14..851c080 100644 --- a/analysis/variables_function.py +++ b/analysis/variables_function.py @@ -148,7 +148,11 @@ def has_severe_obesity(index_date): event_bmi = last_prior_event( bmi, index_date, - where=(clinical_events.numeric_value.is_not_null()) + where=( + clinical_events.numeric_value.is_not_null() & + (clinical_events.numeric_value > 4) & + (clinical_events.numeric_value < 200) + ) ) # Severe obesity severe_obesity = case( @@ -308,14 +312,14 @@ def primis_variables(dataset, index_date, var_name_suffix=""): ################################################################## -def other_cx_variables(dataset, index_date, var_name_suffix=""): +# def other_cx_variables(dataset, index_date, var_name_suffix=""): ## others of interest - dataset.add_column(f"sol_org_trans{var_name_suffix}", has_prior_event(solid_organ_transplant, index_date)) # Organs transplant - dataset.add_column(f"hiv{var_name_suffix}", has_prior_event(hiv_aids, index_date)) #HIV/AIDS - dataset.add_column(f"cancer{var_name_suffix}", - has_prior_event(cancer_nonhaem_snomed, index_date, where=clinical_events.date.is_after(index_date - days(int(3 * 365.25))))| - has_prior_event(cancer_haem_snomed, index_date, where=clinical_events.date.is_after(index_date - days(int(3 * 365.25)))) - ) #cancer +# dataset.add_column(f"sol_org_trans{var_name_suffix}", has_prior_event(solid_organ_transplant, index_date)) # Organs transplant +# dataset.add_column(f"hiv{var_name_suffix}", has_prior_event(hiv_aids, index_date)) #HIV/AIDS +# dataset.add_column(f"cancer{var_name_suffix}", +# has_prior_event(cancer_nonhaem_snomed, index_date, where=clinical_events.date.is_after(index_date - days(int(3 * 365.25))))| +# has_prior_event(cancer_haem_snomed, index_date, where=clinical_events.date.is_after(index_date - days(int(3 * 365.25)))) +# ) #cancer