Helper functions to assist with RedCAP data cleaning

RedCAP.R

factor_table <- function(x) tibble(key = str_split(x, "\\|")[[1]]) %>%
  separate(key, into = c("key", "value"), sep = ",", extra = "merge") %>%
  mutate(across(everything(), trimws))

factor_convert <- function(x, d, dict) {
  y <- factor_table(dict[dict$`Variable / Field Name` == cur_column(),]$`Choices, Calculations, OR Slider Labels`)
  factor(x, levels = y$key, labels = y$value)
}

checkbox_labels <- function(x, dict) {
  
  d <- factor_table(dict[dict$`Variable / Field Name` == x,]$`Choices, Calculations, OR Slider Labels`) %>%
    mutate(across("key", ~paste(x, ., sep = "___")))
  
  o <- as.list(d$value)
  names(o) <- d$key
  
  o
}

variable_labels <- function(d, dict) map_chr(names(d),
                                             ~ifelse(.x %in% dict$`Variable / Field Name`,
                                                     dict[dict$`Variable / Field Name` == .x,]$`Field Label`,
                                                     .x), dict = dict)

clean <- function(d, dict) {
  
  dict <- dict[dict$`Variable / Field Name` %in% names(d),] # remove items from dictionary that aren't in the dataset

  d <- mutate(d, 
              across(c(dict[map_lgl(dict$`Text Validation Type OR Show Slider Number` == "number", isTRUE),]$`Variable / Field Name`,
                       dict[map_lgl(dict$`Field Type` == "yesno", isTRUE),]$`Variable / Field Name`), as.numeric),
              across(dict[map_lgl(dict$`Field Type` == "yesno", isTRUE),]$`Variable / Field Name`, as.logical),
              across(starts_with(paste0(dict[map_lgl(dict$`Field Type` == "checkbox", isTRUE),]$`Variable / Field Name`, "___")), ~as.logical(as.numeric(.))),
              across(dict[map_lgl(dict$`Field Type` %in% c("dropdown", "radio"), isTRUE),]$`Variable / Field Name`, factor_convert, d = d, dict = dict),
              across(dict[map_lgl(dict$`Text Validation Type OR Show Slider Number` == "number", isTRUE),]$`Variable / Field Name`, as.numeric)) %>%
    set_variable_labels(.labels = variable_labels(., dict))
  
  # Apply checkbox labels
  
  for (i in dict[map_lgl(dict$`Field Type` == "checkbox", isTRUE),]$`Variable / Field Name`) {
    d <- set_variable_labels(d, .labels = checkbox_labels(i, dict))
  }
  
  d
}