R/readHSB_SR.R

In EdSurvey: Analysis of NCES Education Survey and Assessment Data

#' @title Connect to HS&B Study Senior Data
#'
#' @description Opens a connection to a High School & Beyond 1980--1986 Senior cohort data file and
#'              returns an \code{edsurvey.data.frame} with
#'              information about the file and data.
#'
#' @param HSR8086_PRI_FilePath a character value to the main study-derived
#'                             analytical data file (HSR8086_REV.PRI).
#'                             Located within the \code{REVISED_ASCII} Folder.
#' @param HSR8086_SASSyntax_Path a character value to the SAS syntax file for
#'                               parsing the \code{HSR8086_REV.PRI} data file.
#'                               Located within the \code{SAS_EXTRACT_LOGIC} Folder.
#' @param forceReread a logical value to force rereading of all processed data.
#'                    The default value of \code{FALSE} will speed up the read
#'                    function by using existing read-in data already processed.
#' @param verbose a logical value that will determine if you want verbose output
#'                while the \code{readHSB_Senior} function is running to
#'                indicate processing progress. The default value is \code{TRUE}.
#'
#' @details
#' Reads in the specified \code{HSR8086_SASSyntax_Path} file to parse
#' the \code{HSR8086_PRI_FilePath} file.
#' A cached data file and metadata file will be saved in the same
#' directory and filename as the \code{HSR8086_PRI_FilePath} file,
#' having new file extensions of .txt and .meta, respectively.
#'
#' Please note the original source \code{repcode} variable has been split
#' into two variables named \code{repcode_str} for the stratum value
#' and \code{repcode_psu} for the primary sampling unit (PSU) value in the resulting
#' cache data.
#'
#' @return
#'  an \code{edsurvey.data.frame} for the HS&B Senior 1980--1986 longitudinal dataset
#'
#' @seealso \code{\link{readECLS_K2011}}, \code{\link{readNAEP}}, and \code{\link{getData}}
#' @author Tom Fink
#' @example /man/examples/readHSB_SR.R
#'
readHSB_Senior <- function(HSR8086_PRI_FilePath,
                           HSR8086_SASSyntax_Path,
                           forceReread = FALSE,
                           verbose = TRUE) {
  # temporarily adjust any necessary option settings; revert back when done
  userOp <- options(OutDec = ".")
  on.exit(options(userOp), add = TRUE)

  HSR8086_PRI_FilePath <- suppressWarnings(normalizePath(unique(HSR8086_PRI_FilePath), winslash = "/"))
  HSR8086_SASSyntax_Path <- suppressWarnings(normalizePath(unique(HSR8086_SASSyntax_Path), winslash = "/"))

  if (!file.exists(HSR8086_PRI_FilePath)) {
    stop(paste0("Cannot find specified data file ", sQuote("HSR8086_PRI_FilePath"), " in path ", sQuote(file.path(HSR8086_PRI_FilePath)), "."))
  }
  if (!file.exists(HSR8086_SASSyntax_Path)) {
    stop(paste0("Cannot find specified data file ", sQuote("HSR8086_SASSyntax_Path"), " in path ", sQuote(file.path(HSR8086_SASSyntax_Path)), "."))
  }

  # prep the data cache items
  cacheFilename <- gsub("\\.pri$", ".txt", HSR8086_PRI_FilePath, ignore.case = TRUE)
  metaFilename <- gsub("\\.pri$", ".meta", HSR8086_PRI_FilePath, ignore.case = TRUE)

  runProcessing <- TRUE # set default value
  # check and validate any cached files to see if they should be used
  if (file.exists(cacheFilename)) {
    if (file.exists(metaFilename)) {
      cacheRDS <- readRDS(metaFilename) # get the cache info from the .meta file

      if (!cacheMetaReqUpdate(cacheRDS$cacheFileVer, "HS&B")) {
        runProcessing <- FALSE
        fileFormat <- cacheRDS$fileFormat
      }
    }
  }

  # define omittedLevels for the clean step below
  omittedLevels <- c(
    "{DON'T KNOW}", "{DONT'T KNOW}",
    "{LEGITIMATE SKIP}", "{MISSING, LEGIT SKIP}",
    "{MISSING}", "{MULTIPLE PUNCH}", "{OUT OF RANGE}",
    "{REFUAL}", "{REFUSAL}", "{UNC VERBATIM}",
    "{UNC. VERBATIM}", "{UNCODABLE VERBATIM}",
    "(Missing)", NA
  )

  # force reprocess if called for
  if (forceReread == TRUE) {
    runProcessing <- TRUE
  }

  if (runProcessing == TRUE) {
    if (verbose) {
      cat(paste0("Processing SAS syntax file.\n"))
    }

    fileFormat <- parseSAS_FileFormat_HSB(HSR8086_SASSyntax_Path) # get the file format from the master.txt file

    # the bypart field is defined in the layout file, but doesn't actually exist in the datafile!
    # this causes all sorts of FWF issues when reading in the original .PRI file as well as subsequent output
    fileFormat <- subset(fileFormat, fileFormat$variableName != "bypart")

    # the REPCODE field contains both the stratum and PSU in one field, redefine the fileformat to split it into two vars for analysis
    rowIdx <- which(fileFormat$variableName == "repcode", arr.ind = TRUE)

    tempFF <- fileFormat[1:(rowIdx - 1), ]
    repcodeFF <- fileFormat[rowIdx, ]
    tempFF2 <- fileFormat[(rowIdx + 1):nrow(fileFormat), ]
    repcodeFF2 <- repcodeFF # duplicate copy of the repCodeFF

    repcodeFF$variableName <- "repcode_str"
    repcodeFF$End <- repcodeFF$End - 1
    repcodeFF$Width <- repcodeFF$Width - 1
    repcodeFF$Labels <- "REPLICATED SAMPLE CODE - stratum"

    repcodeFF2$variableName <- "repcode_psu"
    repcodeFF2$Start <- repcodeFF2$Start + 2
    repcodeFF2$Width <- repcodeFF2$Width - 2
    repcodeFF2$Labels <- "REPLICATED SAMPLE CODE - psu"

    # rebuild the parts after the repcode variable was dissected into it's parts
    fileFormat <- rbind.data.frame(tempFF, repcodeFF, repcodeFF2, tempFF2, stringsAsFactors = FALSE)
    rownames(fileFormat) <- 1:nrow(fileFormat)

    # recalibrate the start/end positions so they are correct
    fileFormat$Start <- c(1, 1 + cumsum(fileFormat$Width))[seq_along(fileFormat$Width)]
    fileFormat$End <- cumsum(fileFormat$Width)

    lafObj <- laf_open_fwf(HSR8086_PRI_FilePath, fileFormat$dataType, fileFormat$Width, fileFormat$variableName)

    fileFormat <- identifyHSB_SRWeights(fileFormat)
    fileFormat <- valueLabelCleanupFF(fileFormat, omittedLevels, c("{$ ZERO}", "{NON-PARTICIPANT}"))
    fileFormat <- writeCacheWithRepWgt_HSB(lafObj, fileFormat, "repcode_str", "repcode_psu", cacheFilename, verbose)

    # write cache file and .meta
    cacheFile <- list(
      ver = ifelse(any(search() %in% "EdSurvey"), packageVersion("EdSurvey"), "Invalid"),
      cacheFileVer = 1,
      ts = Sys.time(),
      fileFormat = fileFormat
    )

    saveRDS(cacheFile, metaFilename)
  } # end if(runProcessing==TRUE)

  lafObj <- laf_open_fwf(cacheFilename, column_types = fileFormat$dataType, column_widths = fileFormat$Width, column_names = fileFormat$variableName)

  weights <- buildHSB_SRWeightList(fileFormat)
  if (!is.null(weights)) {
    attributes(weights)$default <- "" # set default weight
  }

  pvs <- list() # no plausible values or achievement levels

  edsurvey.data.frame(
    userConditions = list(),
    defaultConditions = NULL,
    dataList = buildHSB_SRDataList(lafObj, fileFormat),
    weights = weights,
    pvvars = pvs,
    subject = "",
    year = "1980-1986",
    assessmentCode = "Longitudinal",
    dataType = "Longitudinal Data",
    gradeLevel = "Senior",
    achievementLevels = NULL, # no achievement levels
    omittedLevels = omittedLevels,
    survey = "HS&B",
    country = "USA",
    psuVar = "repcode_psu",
    stratumVar = "repcode_str",
    jkSumMultiplier = 1 / 184, # 184 replicate weights
    validateFactorLabels = TRUE, # the validateFactorLabels will check in `getData` if all values have a defined label, any missing labels will be automatically added.
    reqDecimalConversion = FALSE
  ) # decimal conversion is not needed
}


# identified the HS&B Senior weights based on the file format data.frame and marks them as weights TRUE/FALSE in the fileFormat
identifyHSB_SRWeights <- function(fileFormat) {
  varNames <- fileFormat$variableName

  # identify weight variables
  wgtVars <- grep("wt(2|3|4){0,1}$", varNames, ignore.case = TRUE, value = TRUE)

  # TRUE/FALSE on if the variable is a weight at all
  fileFormat$weights <- fileFormat$variableName %in% wgtVars

  return(fileFormat)
}


writeCacheWithRepWgt_HSB <- function(dataLaF, fileFormat, stratumVar, psuVar, cachePath, verbose) {
  if (verbose) {
    cat(paste0("Generating JK2 replicate weights.\n"))
  }

  wgtVars <- fileFormat$variableName[fileFormat$weights == TRUE]

  wgtDFAll <- NULL # overall for all weights
  wgtDFtemp <- NULL # temporary for weight loop

  newFF <- fileFormat[FALSE, ]

  # build the JK2 replicate weights================
  for (w in wgtVars) {
    weight <- dataLaF[ , w]
    jkrep <- dataLaF[ , psuVar]
    jkzone <- dataLaF[ , stratumVar]
    ujkz <- sort(unique(jkzone[ , 1]))
    jkvars <- c()

    for (i in ujkz) {
      # first group
      coli <- paste0(w, "_JK2_", -1 + i * 2) # create replicate variable name
      jkvars <- c(jkvars, coli)
      jkw <- weight
      jkw[jkzone == i & jkrep == 1] <- 0
      jkw[jkzone == i & jkrep != 1] <- 2 * jkw[jkzone == i & jkrep != 1]
      jkw[is.na(jkw[ , 1]), 1] <- 0 # turn any NAs to a zero value

      if (!is.null(wgtDFtemp)) {
        wgtDFtemp <- cbind(wgtDFtemp, jkw[ , 1])
      } else {
        wgtDFtemp <- jkw[ , 1]
      }


      tempFF <- fileFormat[fileFormat$variableName == w, ]
      tempFF$variableName <- coli
      tempFF$Labels <- paste0(tempFF$Labels, " Replicate ", -1 + i * 2)
      tempFF$labelValues <- ""
      tempFF$weights <- FALSE

      # ensure we have adequate size for the fileFormat otherwise it will throw off our spacing
      testFmt <- format(jkw[ , 1], scientific = FALSE, width = tempFF$Width, nsmall = tempFF$Decimal, justify = "right", drop0trailing = FALSE)
      tempFF$Width <- max(nchar(testFmt))

      newFF <- rbind(newFF, tempFF)

      # second group
      coli <- paste0(w, "_JK2_", i * 2)
      jkvars <- c(jkvars, coli)
      jkw <- weight
      jkw[jkzone == i & jkrep == 1] <- 2 * jkw[jkzone == i & jkrep == 1]
      jkw[jkzone == i & jkrep != 1] <- 0
      jkw[is.na(jkw[ , 1]), 1] <- 0 # turn any NAs to a zero value

      wgtDFtemp <- cbind(wgtDFtemp, jkw[ , 1])

      tempFF <- fileFormat[fileFormat$variableName == w, ]
      tempFF$variableName <- coli
      tempFF$Labels <- paste0(tempFF$Labels, " Replicate ", i * 2)
      tempFF$labelValues <- ""
      tempFF$weights <- FALSE

      # ensure we have adequate size for the fileFormat otherwise it will throw off our spacing
      testFmt <- format(jkw[ , 1], scientific = FALSE, width = tempFF$Width, nsmall = tempFF$Decimal, justify = "right", drop0trailing = FALSE)
      tempFF$Width <- max(nchar(testFmt))

      newFF <- rbind(newFF, tempFF)
    }

    if (!is.null(wgtDFAll)) {
      wgtDFAll <- cbind(wgtDFAll, wgtDFtemp)
    } else {
      wgtDFAll <- wgtDFtemp
    }

    wgtDFtemp <- NULL
  }


  newFF <- rbind(fileFormat, newFF)

  # recalibrate the start/end positions so they are correct
  newFF$Start <- c(1, 1 + cumsum(newFF$Width))[seq_along(newFF$Width)]
  newFF$End <- cumsum(newFF$Width)

  if (verbose) {
    cat(paste0("Writing cache data file.\n"))
  }
  # write out the cachefile
  cacheFull <- cbind(dataLaF[], wgtDFAll)

  newFF <- writeDF_FWF(df = cacheFull, fileFormat = newFF, savePath = cachePath, verbose = verbose)

  return(newFF)
}

# prepares the weight list for the edsurvey.data.frame based on the identified TRUE weights in the fileFormat
buildHSB_SRWeightList <- function(fileFormat) {
  wgtVars <- fileFormat[fileFormat$weights == TRUE, "variableName"]

  # no wgts found
  if (length(wgtVars) == 0) {
    return(NULL)
  }

  weights <- list()

  for (i in seq_along(wgtVars)) {
    tempVar <- wgtVars[i] # full variable name of the weight var
    baseWgtVar <- paste0(tempVar, "_jk2_")
    wgtPattern <- paste0("^", baseWgtVar, "\\d+$")

    ujkz <- unique(tolower(grep(wgtPattern, fileFormat$variableName, value = TRUE, ignore.case = TRUE)))
    ujkz <- sub(baseWgtVar, "", ujkz, ignore.case = TRUE) # strip away and leave just the numeric variable name ending as a string

    if (length(ujkz) > 0) {
      tmpWgt <- list()

      tmpWgt[[1]] <- list(jkbase = baseWgtVar, jksuffixes = as.character(ujkz))

      names(tmpWgt)[[1]] <- tempVar
      weights <- c(weights, tmpWgt)
    }
  }

  return(weights)
}

buildHSB_SRDataList <- function(lafObj, fileFormat) {
  dataList <- list()

  # build the list hierarchical based on the order in which the data levels would be merged in getData
  dataList[["Data"]] <- dataListItem(
    lafObject = lafObj,
    fileFormat = fileFormat,
    levelLabel = "Data",
    forceMerge = TRUE,
    parentMergeLevels = NULL,
    parentMergeVars = NULL,
    mergeVars = NULL,
    ignoreVars = NULL,
    isDimLevel = TRUE
  )

  return(dataList)
}