Recoding for Medical Diagnosis
Opened this issue · 2 comments
cynthiahqy commented
Please paste collapse code & renaming code chunks
DanyangDai commented
med_his_1 <- med_his_0 %>%
mutate(CDC_records = if_else(samodify %in% c("CHRONIC CARDIAC DISEASE (NOT HYPERTENSION)", "ISCHAEMIC HEART DISEASE", "CARDIOMYOPATHY", "CONGENITAL HEART DISEASE","CHRONIC CARDIAC DISEASE (NOT HYPERTENSION)_NEOPLASM (UNSPECIFIED)"),"yes",NA),
CKD_records = if_else(samodify == "CHRONIC KIDNEY DISEASE","yes", NA),
CPD_records = if_else((samodify %in% c("CHRONIC PULMONARY DISEASE (NOT ASTHMA)", "CHRONIC PULMONARY DISEASE (NOT SPECIFIED)")),"yes", NA),
DB1_records = if_else((samodify == "DIABETES MELLITUS - TYPE 1"),"yes", NA),
DB2_records = if_else((samodify == "DIABETES MELLITUS - TYPE 2"),"yes", NA),
DB_records = if_else((samodify == "DIABETES MELLITUS - TYPE NOT SPECIFIED"),"yes", NA),
asthma_records = if_else((samodify == "ASTHMA"),"yes", NA),
hypertension_records = if_else((samodify == "HYPERTENSION"),"yes", NA),
obesity_records = if_else((samodify == "OBESITY"),"yes", NA),
malnutrition_records = if_else((samodify == "MALNUTRITION"),"yes", NA),
dementia_records = if_else((samodify == "DEMENTIA"),"yes", NA),
precovid_records = if_else((samodify %in% c( "PREVIOUS COVID-19 INFECTION", "PREVIOUS COVID-19 INFECTION - CONFIRMED BY TESTING", "PREVIOUS COVID-19 INFECTION - NOT CONFIRMED BY TESTING" )),"yes", NA),
liver_records = if_else((samodify %in% c("MODERATE OR SEVERE LIVER DISEASE", "MILD LIVER DISEASE", "LIVER DISEASE (SEVERITY NOT SPECIFIED)")),"yes", NA),
AKI_records = if_else((samodify == "ACUTE KIDNEY INJURY"),"yes", NA)) med_his_list <- list(CDC = c("CHRONIC CARDIAC DISEASE (NOT HYPERTENSION)", "ISCHAEMIC HEART DISEASE", "CARDIOMYOPATHY", "CONGENITAL HEART DISEASE","CHRONIC CARDIAC DISEASE (NOT HYPERTENSION)_NEOPLASM (UNSPECIFIED)"),
CKD = c("CHRONIC KIDNEY DISEASE"),
CPD = c("CHRONIC PULMONARY DISEASE (NOT ASTHMA)", "CHRONIC PULMONARY DISEASE (NOT SPECIFIED)"),
DB1 = c("DIABETES MELLITUS - TYPE 1"),
DB2 = c("DIABETES MELLITUS - TYPE 2"),
DB = c("DIABETES MELLITUS - TYPE NOT SPECIFIED"),
asthma = c("ASTHMA"),
hypertension = c("HYPERTENSION"),
obesity = c("OBESITY"),
malutrition = c("MALNUTRITION"),
dementia = c("DEMENTIA"),
precovid = c("PREVIOUS COVID-19 INFECTION", "PREVIOUS COVID-19 INFECTION - CONFIRMED BY TESTING", "PREVIOUS COVID-19 INFECTION - NOT CONFIRMED BY TESTING"),
liver = c("MODERATE OR SEVERE LIVER DISEASE", "MILD LIVER DISEASE", "LIVER DISEASE (SEVERITY NOT SPECIFIED)"),
aki_medhis = c("ACUTE KIDNEY INJURY"))cynthiahqy commented
Example using upcoming features in v0.0.0.9019
med_his_list <- list(CDC = c("CHRONIC CARDIAC DISEASE (NOT HYPERTENSION)", "ISCHAEMIC HEART DISEASE", "CARDIOMYOPATHY", "CONGENITAL HEART DISEASE","CHRONIC CARDIAC DISEASE (NOT HYPERTENSION)_NEOPLASM (UNSPECIFIED)"),
CKD = c("CHRONIC KIDNEY DISEASE"),
CPD = c("CHRONIC PULMONARY DISEASE (NOT ASTHMA)", "CHRONIC PULMONARY DISEASE (NOT SPECIFIED)"),
DB1 = c("DIABETES MELLITUS - TYPE 1"),
DB2 = c("DIABETES MELLITUS - TYPE 2"),
DB = c("DIABETES MELLITUS - TYPE NOT SPECIFIED"),
asthma = c("ASTHMA"),
hypertension = c("HYPERTENSION"),
obesity = c("OBESITY"),
malutrition = c("MALNUTRITION"),
dementia = c("DEMENTIA"),
precovid = c("PREVIOUS COVID-19 INFECTION", "PREVIOUS COVID-19 INFECTION - CONFIRMED BY TESTING", "PREVIOUS COVID-19 INFECTION - NOT CONFIRMED BY TESTING"),
liver = c("MODERATE OR SEVERE LIVER DISEASE", "MILD LIVER DISEASE", "LIVER DISEASE (SEVERITY NOT SPECIFIED)"),
aki_medhis = c("ACUTE KIDNEY INJURY"))
## verify
med_his_list |>
verify_named_no_dup_values()
## sample crossmap
med_hist_xmap <- as_pairs_from_named(med_his_list, names_to = "analysis_group", values_to = "symptom") |>
add_weights_unit(weights_into = "w") |>
as_xmap_df(from = symptom, to = analysis_group, weights = w)