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Added cx variables + created summary_table fuction
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@marrpesce
marrpesce committed Nov 29, 2024
1 parent 2f036ba commit 21c17e7
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214 changes: 109 additions & 105 deletions analysis/cx_function.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -94,8 +94,52 @@ def first_prior_meds(codelist, index_date, where=True):
######################
# Composed variables #
######################
#Asthma
# Immunosuppression
def is_immunosuppressed(index_date):
# Immunosuppression diagnosis
immdx = has_prior_event(immdx_cov, index_date)
# Immunosuppression medication (within the last 3 years)
immrx_cov = has_prior_meds(
immrx,
index_date,
where=medications.date.is_on_or_after(index_date - days(int(3 * 365.25)))
)
# Immunosuppression admin date (within the last 3 years)
immadm_cov = has_prior_event(
immadm,
index_date,
where=clinical_events.date.is_on_or_after(index_date - days(int(3 * 365.25)))
)
# Chemotherapy medication date (within the last 3 years)
dxt_chemo_cov = has_prior_event(
dxt_chemo,
index_date,
where=clinical_events.date.is_on_or_after(index_date - days(int(3 * 365.25)))
)
# Immunosuppression group
return case(
when(immdx.is_not_null()).then(True),
when(immrx_cov.is_not_null()).then(True),
when(immadm_cov.is_not_null()).then(True),
when(dxt_chemo_cov.is_not_null()).then(True),
otherwise=False
)

#Patients with Chronic Kidney Disease
def has_ckd(index_date, where=True):
# Chronic kidney disease diagnostic codes
ckd = has_prior_event(ckd_cov, index_date)
# Chronic kidney disease codes - all stages
ckd15_date = last_prior_event(ckd15, index_date).date
# Chronic kidney disease codes-stages 3 - 5
ckd35_date = last_prior_event(ckd35, index_date).date
return case(
when(ckd).then(True),
when((ckd35_date >= ckd15_date)).then(True),
otherwise=False
)

#Asthma
# redfine Asthma as per green book
# Poorly controlled asthma is defined as:
# - ≥2 courses of oral corticosteroids in the preceding 24 months OR
Expand Down Expand Up @@ -131,6 +175,37 @@ def has_asthma(index_date, where=True):
otherwise=False
)

# Patients with Morbid Obesity
#Need to include that they need to be >18yo
def has_sev_obes(index_date):
# Last BMI stage event
bmi_stage_event = last_prior_event(
bmi_stage,
index_date
)
# Last severe obesity event (after the BMI stage event, with valid numeric value)
sev_obesity_event = last_prior_event(
sev_obesity,
index_date,
where=((clinical_events.date >= bmi_stage_event.date) &
(clinical_events.numeric_value != 0.0)
)
)
# Last BMI event not 0
bmi_event = last_prior_event(
bmi,
index_date,
where=(clinical_events.numeric_value != 0.0)
)
# Severe obesity
return case(
when(sev_obesity_event.date > bmi_event.date).then(True),
when(bmi_event.numeric_value >= 40.0).then(True),
otherwise=False
)



def preg_group(index_date):
# Pregnancy delivery code date
pregAdel_date = last_prior_event(
Expand Down Expand Up @@ -162,8 +237,7 @@ def preg_group(index_date):
)


#Diabetes
# Diabetes and diabetes resolution code date
#Patients with Diabetes
def has_diab(index_date, where=True):
diab_date = last_prior_event(diab, index_date).date
dmres_date = last_prior_event(dmres, index_date).date
Expand All @@ -178,20 +252,6 @@ def has_diab(index_date, where=True):
otherwise=False
)

#Kidney
def has_ckd(index_date, where=True):
# Chronic kidney disease diagnostic codes
ckd = has_prior_event(ckd_cov, index_date)
# Chronic kidney disease codes - all stages
ckd15_date = last_prior_event(ckd15, index_date).date
# Chronic kidney disease codes-stages 3 - 5
ckd35_date = last_prior_event(ckd35, index_date).date
return case(
when(ckd).then(True),
when((ckd35_date >= ckd15_date)).then(True),
otherwise=False
)

# Severe mental illness
def has_sev_mental(index_date, where=True):
sev_mental_date = last_prior_event(sev_mental, index_date).date
Expand All @@ -203,79 +263,8 @@ def has_sev_mental(index_date, where=True):
otherwise=False
)

# Immunosuppression
def is_immunosuppressed(index_date):
# Immunosuppression diagnosis
immdx = has_prior_event(immdx_cov, index_date)
# Immunosuppression medication (within the last 3 years)
immrx_cov = has_prior_meds(
immrx,
index_date,
where=medications.date.is_on_or_after(index_date - days(int(3 * 365.25)))
)
# Immunosuppression admin date (within the last 3 years)
immadm_cov = has_prior_event(
immadm,
index_date,
where=clinical_events.date.is_on_or_after(index_date - days(int(3 * 365.25)))
)
# Chemotherapy medication date (within the last 3 years)
dxt_chemo_cov = has_prior_event(
dxt_chemo,
index_date,
where=clinical_events.date.is_on_or_after(index_date - days(int(3 * 365.25)))
)
# Immunosuppression group
return case(
when(immdx.is_not_null()).then(True),
when(immrx_cov.is_not_null()).then(True),
when(immadm_cov.is_not_null()).then(True),
when(dxt_chemo_cov.is_not_null()).then(True),
otherwise=False
)

#Sever obesity


#def has_sev_obes (index_date):
# # Most recent BMI measurement and value
# bmi_record = (
# clinical_events.where(
# clinical_events.snomedct_code.is_in(["60621009", "846931000000101"])
# # Ignore out-of-range values
# & (clinical_events.numeric_value > 4)
# & (clinical_events.numeric_value < 200)
# & (clinical_events.date >= index_date)
# Ignore measurements taken when patient was younger than 16
# & (clinical_events.date >= patients.date_of_birth + years(16))
# )
# .sort_by(clinical_events.date)
# .last_for_patient()
# )
# bmi_num = bmi_record.numeric_value
# bmi_date = bmi_record.date
# # Most recent BMI-related events
# bmi_stage_event = last_prior_event(
# bmi_stage,
# index_date)
# bmi_event = last_prior_event(
# bmi,
# index_date,
# where=(clinical_events.numeric_value != 0.0)
# )
# sev_obesity_event = last_prior_event(
# sev_obesity,
# where=(
# (clinical_events.date >= bmi_stage_event.date) &
# (clinical_events.numeric_value != 0.0)
# )
# )
# # Severe obesity
# return case(
# when(sev_obesity_event.date > bmi_event.date).then(True),
# when(bmi_num >= 40.0).then(True),
# otherwise=False
# )


## functions to define variables across multiple study definitions

Expand All @@ -289,27 +278,42 @@ def demographic_variables(dataset, index_date, var_name_suffix=""):


# PRIMIS variables
# Green book:
# Clinical risk groups >16 (16/9/2024):
# chronic respiratory disease (include asthma),
# chronic heart disease and vascular disease,
# chronic kidney disease
# chronic liver disease
# chronic neurological disease (include severe learning disability)
# diabetes mellitus and other endocrine disorders
# immunosupression
# asplenia or dysfunction of the spleen
# morbid obesity
# severe mental illness
# x young adults Younger adults in long-stay nursing and residential care settings
# x pregnancy

def primis_variables(dataset, index_date, var_name_suffix=""):
## 1 code
dataset.add_column(f"chd{var_name_suffix}", has_prior_event(chd_cov, index_date)) #cronic heart disease
dataset.add_column(f"cld{var_name_suffix}", has_prior_event(cld, index_date)) # cronic liver disease
dataset.add_column(f"cns{var_name_suffix}", has_prior_event(cns_cov, index_date)) #chronic neurological disease
dataset.add_column(f"asplen{var_name_suffix}", has_prior_event(spln_cov, index_date)) # Asplenia or Dysfunction of the Spleen codes
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"learndis{var_name_suffix}", has_prior_event(learndis, index_date)) # Wider Learning Disability

## mx codes
dataset.add_column(f"crd{var_name_suffix}", has_prior_event(resp_cov, index_date)) #chronic respiratory disease
dataset.add_column(f"ast{var_name_suffix}", has_asthma(index_date)) #asthma
dataset.add_column(f"crd{var_name_suffix}", has_prior_event(resp_cov, index_date)| has_asthma(index_date)) #cronic respiratory disease
dataset.add_column(f"chd{var_name_suffix}", has_prior_event(chd_cov, index_date)) #chronic heart disease
dataset.add_column(f"ckd{var_name_suffix}", has_ckd(index_date)) #chronic kidney disease
dataset.add_column(f"cld{var_name_suffix}", has_prior_event(cld, index_date)) # chronic liver disease
dataset.add_column(f"cns{var_name_suffix}", has_prior_event(cns_cov, index_date)) # chronic neurological disease
dataset.add_column(f"learndis{var_name_suffix}", has_prior_event(learndis, index_date)) # learning Disability
dataset.add_column(f"diab{var_name_suffix}", has_diab(index_date)) #diabetes
dataset.add_column(f"sev_ment{var_name_suffix}", has_sev_mental(index_date)) #severe mental illness
dataset.add_column(f"immuno{var_name_suffix}", is_immunosuppressed(index_date)) #immunosuppress grouped
dataset.add_column(f"asplen{var_name_suffix}", has_prior_event(spln_cov, index_date)) # asplenia or dysfunction of the Spleen
dataset.add_column(f"obes{var_name_suffix}", has_sev_obes(index_date)) #immunosuppress grouped
dataset.add_column(f"sev_ment{var_name_suffix}", has_sev_mental(index_date)) #severe mental illness
# No:
# younger adults in long-stay nursing and residential care settings
# pregnancy

## 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"obes{var_name_suffix}", has_sev_obes(index_date)) #immunosuppress grouped


) #cancer
42 changes: 19 additions & 23 deletions analysis/dummydata_varying.R
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Original file line number Diff line number Diff line change
Expand Up @@ -201,36 +201,32 @@ sim_list_varying_i <- function(i) {
needs = vax_variable
),
#PRIMIS
"crd_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable), #chronic respiratory disease
"ast_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable), #asthma
"chd_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
needs = vax_variable), #chronic heart disease
"ckd_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable), #chronic kidney disease
"cld_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
"ast_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
needs = vax_variable), # chronic liver disease
"cns_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
"asplen_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
"sol_org_trans_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
"hiv_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
needs = vax_variable), # chronic neurological disease
"learndis_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
"crd_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
"ckd_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
needs = vax_variable), # learning Disability
"diab_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
"sev_ment_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
needs = vax_variable), #diabetes
"immuno_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
"cancer_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable),
needs = vax_variable), #immunosuppress grouped
"asplen_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable), # asplenia or Dysfunction of the Spleen
"obes_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable)
needs = vax_variable), #immunosuppress grouped
"sev_ment_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable), #severe mental illness
"cv_{i}" := bn_node( ~rbernoulli(n=..n, p = 0.02),
needs = vax_variable) # clinically vulnerable
)
}

Expand Down
29 changes: 14 additions & 15 deletions analysis/process.R
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Original file line number Diff line number Diff line change
Expand Up @@ -97,21 +97,20 @@ data_vax <-
matches("imd_\\d+"),
matches("imd_quintile_\\d+"),
# ... more clinical (PRIMIS) characteristics here
matches("chd_\\d+"),
matches("cld_\\d+"),
matches("ast_\\d+"),
matches("cns_\\d+"),
matches("asplen_\\d+"),
matches("sol_org_trans_\\d+"),
matches("hiv_\\d+"),
matches("learndis_\\d+"),
matches("crd_\\d+"),
matches("ckd_\\d+"),
matches("diab_\\d+"),
matches("sev_ment_\\d+"),
matches("immuno_\\d+"),
matches("cancer_\\d+"),
# matches("obes_\\d+"),
matches("cv_\\d+"), # Clinically vulnerable
matches("crd_\\d+"), #chronic respiratory disease
matches("ast_\\d+"), #asthma
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("diab_\\d+"), #diabetes
matches("immuno_\\d+"), #immunosuppress grouped
matches("asplen_\\d+"), # asplenia or dysfunction of the spleen
matches("obes_\\d+"), #immunosuppress grouped
matches("sev_ment_\\d+"), #severe mental illness
matches("cv_\\d+") # clinically vulnerable
) %>%
pivot_longer(
cols = -patient_id,
Expand Down
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