inst/app/www/prepare_data_odk.R

In ocelhay/AMULaos: App on Antimicrobial Use (AMU) in Laos.

# patient <- read_excel("./inst/app/www/data/LAMPA_PATIENT.xlsx", skip = 1)
patient <- read_excel("./www/data/LAMPA_PATIENT.xlsx", skip = 1)

patient <- janitor::clean_names(patient) %>%
  rename(specialty = activity)

# add patient identifier and complete data
patient <- patient %>%
  arrange(label, form_cycle) %>%
  mutate(patient_id = 1:nrow(patient) - (form_cycle - 1))

patient <- patient %>%
  group_by(patient_id) %>%
  fill(form_cycle:specialty) %>%
  ungroup()

# transform columns
patient <- patient %>%
  mutate(surdate = dmy(surdate),
         antistdate = dmy(antistdate),
         antienddate = dmy(antienddate),
         age_year = case_when(
           !is.na(ageyr) ~ ageyr,
           !is.na(agemo) ~ agemo / 12,
           !is.na(ageday) ~ ageday / 365.25)) %>%
  mutate(age_category = case_when(
      age_year < 1 ~ "< 1 y.o.",
      age_year < 5 ~ "1 to 5 y.o.",
      age_year < 15 ~ "5 to 15 y.o.",
      age_year < 120 ~ "> 15 y.o.",
      TRUE ~ "Unknown")) %>%
  mutate(age_category = factor(age_category, levels = c("< 1 y.o.", "1 to 5 y.o.", "5 to 15 y.o.",
                                                        "> 15 y.o.", "Unknown")))

patient$weight[patient$weight == 999] <- NA


if(! all(patient$typeind %in% c("Treat infection", "Completely unknown", "More than one day surgical prophylaxis", 
                                "Medical prophylaxis", "completely unknown", "Single dose surgical prophylaxis", 
                                "One day (multiple dose) surgical prophylaxix"))) error("Unexpected Type Indication")

patient$typeind_cat <- "Unknown"
patient$typeind_cat[patient$typeind == "Treat infection"] <- "Treatment"
patient$typeind_cat[patient$typeind %in% 
                      c("More than one day surgical prophylaxis", "Medical prophylaxis", 
                        "Single dose surgical prophylaxis", "One day (multiple dose) surgical prophylaxix")] <- "Prophylaxis"

# ward <- read_excel("./inst/app/www/data/LAMPA_WARD.xlsx", skip = 1)
ward <- read_excel("./www/data/LAMPA_WARD.xlsx", skip = 1)

ward <- janitor::clean_names(ward)

ward$surdate <- dmy(ward$surdate)

ward$specialty <- "Unknown"
ward[ward$ipdopd == "Inpatient", "specialty"] <- ward[ward$ipdopd == "Inpatient", "deptype"]
ward[ward$ipdopd == "Outpatient", "specialty"] <- ward[ward$ipdopd == "Outpatient", "opdtype"]

# Recode ward specialty so that it matches with patient specialty
ward$specialty <- recode(ward$specialty, 
                         "Intensive Care Unit" = "Intensive Care", 
                         "Obstetrics and Gynaecology" = "General practice",
                         "Paediatrics" = "General practice")

test_data_odk(patient, ward)