R_tasks/prepare_CS.R

In gorkang/jsPsychHelpeR: Standardize and automatize data preparation and analysis of jsPsych experiments created with jsPsychMaker

##' Prepare CS
##'
##' Template for the functions to prepare specific tasks. Most of this file should not be changed
##' Things to change: 
##'   - Name of function: prepare_CS -> prepare_[value of short_name_scale_str] 
##'   - dimensions parameter in standardized_names()
##'   - 2 [ADAPT] chunks
##'
##' @title prepare_CS
##'
##' @param short_name_scale_str 
##' @param DF_clean
##'
##' @return
##' @author gorkang
##' @export
prepare_CS <- function(DF_clean, short_name_scale_str, output_formats) {

  # DEBUG
  # targets::tar_load_globals()
  # jsPsychHelpeR::debug_function(prepare_CS)


  # [ADAPT]: Items to ignore and reverse ---------------------------------------
  # ****************************************************************************
  
  items_to_ignore = c("000") # Ignore these items: If nothing to ignore, keep items_to_ignore = c("00")
  
  # IMPORTANT: in CS, the items are reversed ONLY for the TOTAL score calculation. SEE COLUMNS CS_[ItemNumber]_total_DIR
  items_to_reverse = c("03", "07", "11", "15")
  
  items_dimensions = list(
    Kindness = c("02", "06", "10", "14"),
    Indiference = c("03", "07", "11", "15"),
    CommonHumanity = c("04", "08", "12", "16"),
    Mindfulness = c("01", "05", "09", "13")
  )
  
  
  # [END ADAPT]: ***************************************************************
  # ****************************************************************************
  
  
  # Standardized names ------------------------------------------------------
  names_list = standardized_names(short_name_scale = short_name_scale_str, 
                                  dimensions = names(items_dimensions),
                                  help_names = FALSE) # [KEEP as FALSE]
  
  # Create long -------------------------------------------------------------
  DF_long_RAW = create_raw_long(DF_clean, 
                                short_name_scale = short_name_scale_str, 
                                numeric_responses = TRUE, # [TRUE or FALSE]
                                is_experiment = FALSE, 
                                help_prepare = FALSE) # Show n of items, responses,... [CHANGE to FALSE] 
  
  
  # Create long DIR ------------------------------------------------------------
  
  DF_long_DIR = 
    DF_long_RAW |> 
   dplyr::select(id, trialid, RAW) |>
    
    
  # [ADAPT]: RAW to DIR for individual items -----------------------------------
  # ****************************************************************************
  
    # Transformations
    dplyr::mutate(
      DIR =
       dplyr::case_when(
          is.na(RAW) ~ NA_real_,
          trialid %in% paste0(short_name_scale_str, "_", items_to_ignore) ~ NA_real_, # OR NA_character_
          TRUE ~ RAW
        )
    ) |> 
    
    # Invert items
    # Only invert items for calculation of global score ---
    dplyr::mutate(
      total_DIR =
       dplyr::case_when(
          DIR == 9999 ~ DIR, # To keep the missing values unchanged
          trialid %in% paste0(short_name_scale_str, "_", items_to_reverse) ~ (6 - DIR),
          TRUE ~ DIR
        )
    )
    
  # [END ADAPT]: ***************************************************************
  # ****************************************************************************
    

  # Create DF_wide_RAW_DIR -----------------------------------------------------
  DF_wide_RAW =
    DF_long_DIR |> 
    tidyr::pivot_wider(
      names_from = trialid, 
      values_from = c(RAW, DIR, total_DIR),
      names_glue = "{trialid}_{.value}") |> 
    
    # NAs for RAW and DIR items
    dplyr::mutate(!!names_list$name_RAW_NA := rowSums(is.na(across((-matches(paste0(short_name_scale_str, "_", items_to_ignore, "_RAW")) & matches("_RAW$"))))),
                  !!names_list$name_DIR_NA := rowSums(is.na(across((-matches(paste0(short_name_scale_str, "_", items_to_ignore, "_DIR")) & matches("_DIR$"))))))
    
  
  # Reliability -------------------------------------------------------------
  
  # REL1 = auto_reliability(DF_wide_RAW, short_name_scale = short_name_scale_str, items = items_dimensions[[1]])
  # items_RELd1 = REL1$item_selection_string
    
  
  # [ADAPT]: Scales and dimensions calculations --------------------------------
  # ****************************************************************************
    # [USE STANDARD NAMES FOR Scales and dimensions: name_DIRt, name_DIRd1, etc.] Check with: standardized_names(help_names = TRUE)

  DF_wide_RAW_DIR =
    DF_wide_RAW |> 
    dplyr::mutate(

      # Make sure to use the correct formula: rowMeans() / rowSums()
      
      # Score Dimensions (see standardized_names(help_names = TRUE) for instructions)
      !!names_list$name_DIRd[1] := rowMeans(across(all_of(paste0(short_name_scale_str, "_", items_dimensions[[1]], "_DIR"))), na.rm = TRUE), 
      !!names_list$name_DIRd[2] := rowMeans(across(all_of(paste0(short_name_scale_str, "_", items_dimensions[[2]], "_DIR"))), na.rm = TRUE),
      !!names_list$name_DIRd[3] := rowMeans(across(all_of(paste0(short_name_scale_str, "_", items_dimensions[[3]], "_DIR"))), na.rm = TRUE),
      !!names_list$name_DIRd[4] := rowMeans(across(all_of(paste0(short_name_scale_str, "_", items_dimensions[[4]], "_DIR"))), na.rm = TRUE),
      
      # Reliability Dimensions (see standardized_names(help_names = TRUE) for instructions)
      # !!names_list$name_RELd[1] := rowMeans(across(all_of(paste0(short_name_scale_str, "_", items_RELd1, "_DIR"))), na.rm = TRUE), 

      # Score Scale
      !!names_list$name_DIRt := rowSums(across(all_of(matches("_total_DIR$"))), na.rm = TRUE)
      
    )
    
  # [END ADAPT]: ***************************************************************
  # ****************************************************************************


  # CHECK NAs -------------------------------------------------------------------
  check_NAs(DF_wide_RAW_DIR)
  
  # Save files --------------------------------------------------------------
  save_files(DF_wide_RAW_DIR, short_name_scale = short_name_scale_str, is_scale = TRUE, output_formats = output_formats)
  
  # Output of function ---------------------------------------------------------
  return(DF_wide_RAW_DIR) 
 
}