R/read_bsid.R

In D-score/gsedread: Tools for reading the GSED validation data

#' Read data from Bayley Scales of Infant Development III
#'
#' @param onedrive Character, the location of the local OneDrive sync
#' @param path Character, path name within the OneDrive
#' @param verbose Logical. Print diagnostic info? Defaults to `FALSE`.
#' @param progress Logical. Show progress in interactive session. Default to `FALSE`.
#' @param warnings Logical. Show warnings generated by `readr::read_csv()`.
#' Defaults to `FALSE`.
#' @return A tibble with the original data and two column names: `file`
#' (containing the original file name) and `adm` (fixed or adaptive).
#' @export
read_bsid <- function(onedrive = Sys.getenv("ONEDRIVE_GSED"),
                      path = "GSED Final Collated Phase 1 Data Files 18_05_22",
                      verbose = FALSE,
                      progress = FALSE,
                      warnings = FALSE) {
  if (nchar(onedrive) == 0L) {
    stop("Environmental variable ONEDRIVE_GSED not set.", call. = FALSE)
  }

  # hardcode files names
  files_fixed <- c(
    "tan/tza-bsid-iii-2021-11-07.csv",
    "pak/pak_bsid-iii_2022_05_17.csv",
    "ban/ban-bsid-iii-2022-05-17.csv")

  # read
  files <- file.path(onedrive, path, files_fixed)
  date_formats <- c("%d-%m-%Y", "%d/%m/%Y", "%Y-%m-%d")
  types <- c("tan", "pak", "ban")
  data <- read_files("bsid", types, files, 1:length(files),
                     date_formats, NULL,
                     verbose, progress, warnings)

  # post-process to consistent names
  data[[1]] <- data[[1]] %>%
    rename(Study_Country = .data$st_country___bsid,
           date_of_visit = .data$screen_id_bsid,
           Parent_study_ID = .data$screen_no__bsid)
  data[[2]] <- data[[2]] %>%
    rename(ra_code_bsid = .data$Researcher_Code,
           date_of_visit = .data$DATE_OF_VISIT,
           visit_age_bsid = .data$Age_at_assessment)
  data[[3]] <- data[[3]] %>%
    rename(Study_Country = .data$st_country___bsid,
           Parent_study_ID = .data$screen_no__bsid)
  nm3 <- names(data[[3]])
  nm3[8:339] <- tolower(nm3[8:339])
  nm3[8:16] <- paste0("bsid_cog0", 1:9)
  nm3[99:107] <- paste0("bsid_rc0", 1:9)
  nm3[148:156] <- paste0("bsid_ec0", 1:9)
  nm3[196:204] <- paste0("bsid_fm0", 1:9)
  nm3[262:270] <- paste0("bsid_gsm0", 1:9)
  names(data[[3]]) <- nm3

  # bind
  # remove orphan records without a GSED_ID
  data %>%
    bind_rows(.id = "file") %>%
    filter(!is.na(.data$GSED_ID)) %>%
    rename(
      age = .data$visit_age_bsid,
      date = .data$date_of_visit,
      worker_code = .data$ra_code_bsid,
      parent_id = .data$Parent_study_ID) %>%
    mutate(adm = "fixed") %>%
    select(.data$GSED_ID, .data$age,
           .data$file, .data$adm, .data$parent_id, .data$worker_code, .data$date,
           .data$age_adj_premature,
           contains("bsid"), -contains("raw"), -contains("comment")) %>%
    arrange(.data$GSED_ID, .data$age)
}