## ----eval=F------------------------------------------------------------------- # ## get MSF standard dictionary for measles # recode_dict <- msf_dict("measles", compact = FALSE) |> # select("variable" = data_element_shortname, # "values_short" = option_code, # "values_long" = option_name) # # ## browse dictionary # View(recode_dict) ## ----eval=F------------------------------------------------------------------- # ## Add the appropriate column names after the equals signs # # linelist_cleaned <- rename(linelist_cleaned, # acute_otitis_media = , # BOOLEAN (REQUIRED) # age_days = , # INTEGER_POSITIVE (REQUIRED) # age_months = , # INTEGER_POSITIVE (REQUIRED) # age_years = , # INTEGER_POSITIVE (REQUIRED) # candidiasis = , # BOOLEAN (REQUIRED) # case_number = , # TEXT (REQUIRED) # cough = , # BOOLEAN (REQUIRED) # croup = , # BOOLEAN (REQUIRED) # date_of_consultation_admission = , # DATE (REQUIRED) # residential_status = , # TEXT (optional) # residential_status_brief = , # TEXT (optional) # treatment_facility_name = , # TEXT (optional) # treatment_facility_site = , # TEXT (optional) # treatment_location = , # ORGANISATION_UNIT (optional) # trimester = # TEXT (optional) # ) # # ## ----eval=F------------------------------------------------------------------- # linelist_processing <- linelist_processing |> # mutate(sex_id = case_match( # sex_id, # c("M", "m") ~ "Male", # c("F", "FEMALE") ~ "Female" , # .default = sex_id )) |> # # mutate(outcome = case_match( # outcome, # c("Dead in facility - short") ~ "Dead in facility (<4h)", # c("Dead in facility - long") ~ "Dead in facility (>4h)", # c("Sent home", "Home") ~ "Discharged home", # c("Death in community", "Dead in community") ~ "Dead in community", # c("DOA") ~ "Dead on arrival", # c("Left") ~ "Left against medical advice", # c("Transferred - MSF") ~ "Transferred (to an MSF facility)", # c("Transferred - External") ~ "Transferred (to External Facility)", # .default = outcome)) #