data-raw/R/bds_lexicon.R

In stefvanbuuren/minihealth: Mini Dossier for Individual Health Data

# Create the BDS lexicon

create_bds_lexicon <- function(){
  bds_lexicon <- data.frame(
    bdsnummer = c(19, 20, 62, 63, 66, 71, 82, 91, 110, 235, 245, 252,
                  238, 240, 510),
    description = c("Geslacht",
                    "Geboortedatum",
                    "Relatie tot jeugdige ouder/verzorger",
                    "Geboortedatum ouder/verzorger",
                    "Opleiding ouder/verzorger",
                    "Geboorteland ouder/verzorger",
                    "Zwangerschapsduur",
                    "Roken tijdens de zwangerschap",
                    "Geboortegewicht",
                    "Lengte",
                    "Gewicht",
                    "Hoofdomtrek",
                    "Lengte biologische moeder",
                    "Lengte biologische vader",
                    "Passief roken in huis"),
    description_EN = c("Sex of child",
                       "Date of birth",
                       "Caretaker relation",
                       "Caretaker date of birth",
                       "Caretaker education",
                       "Caretaker birth country",
                       "Gestational age",
                       "Smoking during pregnancy",
                       "Birth weight",
                       "Length/height",
                       "Body weight",
                       "Head circumference",
                       "Height biological mother",
                       "Height biological father",
                       "Passive smoking"),
    expected = c("one of: 0, 1, 2, 3",
                 "yyyymmdd",
                 "one of: 01, 02, 03, 04, 05, 06, 07, 08, 98",
                 "yyyymmdd",
                 "one of: 01, 02, 03, 04, 05, 06, 07, 08, 98, 00",
                 "4-digit code",
                 "in days",
                 "one of: 1, 2, 99",
                 "in grammes",
                 "in milimeters",
                 "in grammes",
                 "in milimeters",
                 "in milimeters",
                 "in milimeters",
                 "one of: 01, 02, 03, 04"),
    stringsAsFactors = FALSE
  )
}

bds_lexicon <- create_bds_lexicon()

library(dscore)
library(dplyr)
library(openxlsx)

# append Van Wiechen BDS definition
project <- path.expand("~/Package/dscore/dscore")
fn <- file.path(project, "data-raw/data/bds_edited.csv")
ib <- read.csv2(file = fn, stringsAsFactors = FALSE)
idx <- !is.na(ib$bds)
expected <- rep("one of: 1, 2", sum(idx))
expected[substr(ib$type[idx], 1, 1) == "m"] <- "one of: 1, 2, 3"
ddi <- data.frame(bdsnummer = ib$bds[idx],
                  description = ib$bds_label[idx],
                  description_EN = ib$labelEN[idx],
                  expected = expected,
                  stringsAsFactors = FALSE)
Encoding(ddi$description) <- "UTF-8"
Encoding(ddi$description_EN) <- "UTF-8"

bds_lexicon <- rbind(bds_lexicon, ddi)
usethis::use_data(bds_lexicon, overwrite = TRUE)