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rxImport: Import Data to .xdf or data frame

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Description

Import data into an .xdf file or data.frame. rxImport is multi-threaded.

Usage

  rxImport(inData, outFile = NULL, varsToKeep = NULL, 
          varsToDrop = NULL, rowSelection = NULL, 
          transforms = NULL, transformObjects = NULL,
          transformFunc = NULL, transformVars = NULL,  
          transformPackages = NULL, transformEnvir = NULL,
          append = "none", overwrite = FALSE, numRows = -1,
          stringsAsFactors = NULL, colClasses = NULL, colInfo = NULL,
          rowsPerRead = NULL, type = "auto", maxRowsByCols = NULL, 
          reportProgress = rxGetOption("reportProgress"),
          verbose = 0,
          xdfCompressionLevel = rxGetOption("xdfCompressionLevel"),
          createCompositeSet = NULL,
          blocksPerCompositeFile = 3,
          ...)

Arguments

inData

a character string with the path for the data to import (delimited, fixed format, SPSS, SAS, ODBC, or XDF). Alternatively, a data source object representing the input data source can be specified. (See RxTextData, RxSasData, RxSpssData, and RxOdbcData.) If a character string is supplied and type is set to "auto", the type of file is inferred from its extension, with the default being a text file. A data.frame can also be used for inData.

outFile

a character string representing the output .xdf file, a RxHiveData data source, aRxParquetData data source or a RxXdfData object. If NULL, a data frame will be returned in memory.

varsToKeep

character vector of variable names to include when reading from the input data file. If NULL, argument is ignored. Cannot be used with varsToDrop. Not supported for ODBC or fixed format text files.

varsToDrop

character vector of variable names to exclude when reading from the input data file. If NULL, argument is ignored. Cannot be used with varsToKeep. Not supported for ODBC or fixed format text files.

rowSelection

name of a logical variable in the data set (in quotes) or a logical expression using variables in the data set to specify row selection. For example, rowSelection = "old" will use only observations in which the value of the variable old is TRUE. rowSelection = (age > 20) & (age < 65) & (log(income) > 10) will use only observations in which the value of the age variable is between 20 and 65 and the value of the log of the income variable is greater than 10. The row selection is performed after processing any data transformations (see the arguments transforms or transformFunc). As with all expressions, rowSelection can be defined outside of the function call using the expression function.

transforms

an expression of the form list(name = expression, ...) representing the first round of variable transformations. As with all expressions, transforms (or rowSelection) can be defined outside of the function call using the expression function.

transformObjects

a named list containing objects that can be referenced by transforms, transformsFunc, and rowSelection.

transformFunc

variable transformation function. See rxTransform for details.

transformVars

character vector of input data set variables needed for the transformation function. See rxTransform for details.

transformPackages

character vector defining additional R packages (outside of those specified in rxGetOption("transformPackages")) to be made available and preloaded for use in variable transformation functions, e.g., those explicitly defined in RevoScaleR functions via their transforms and transformFunc arguments or those defined implicitly via their formula or rowSelection arguments. The transformPackages argument may also be NULL, indicating that no packages outside rxGetOption("transformPackages") will be preloaded.

transformEnvir

user-defined environment to serve as a parent to all environments developed internally and used for variable data transformation. If transformEnvir = NULL, a new "hash" environment with parent baseenv() is used instead.

append

either "none" to create a new .xdf file or "rows" to append rows to an existing .xdf file. If outFile exists and append is "none", the overwrite argument must be set to TRUE. Ignored if a data frame is returned.

overwrite

logical value. If TRUE, the existing outData will be overwritten. Ignored if a dataframe is returned.

numRows

integer value specifying the maximum number of rows to import. If set to -1, all rows will be imported.

stringsAsFactors

logical indicating whether or not to automatically convert strings to factors on import. This can be overridden by specifying "character" in colClasses and colInfo. If TRUE, the factor levels will be coded in the order encountered. Since this factor level ordering is row dependent, the preferred method for handling factor columns is to use colInfo with specified "levels".

colClasses

character vector specifying the column types to use when converting the data. The element names for the vector are used to identify which column should be converted to which type.

  • Allowable column types are:

    • "logical" (stored as uchar),
    • "integer" (stored as int32),
    • "float32" (the default for floating point data for .xdf files),
    • "numeric" (stored as float64 as in R),
    • "character" (stored as string),
    • "factor" (stored as uint32),
    • "ordered" (ordered factor stored as uint32. Ordered factors are treated the same as factors in RevoScaleR analysis functions.),
    • "int16" (alternative to integer for smaller storage space),
    • "uint16" (alternative to unsigned integer for smaller storage space),
    • "Date" (stored as Date, i.e. float64. Not supported for import types "textFast", "fixedFast", or "odbcFast".)
    • "POSIXct" (stored as POSIXct, i.e. float64. Not supported for import types "textFast", "fixedFast", or "odbcFast".)

  • Note for "factor" and "ordered" types, the levels will be coded in the order encountered. Since this factor level ordering is row dependent, the preferred method for handling factor columns is to use colInfo with specified "levels".

  • Note that equivalent types share the same bullet in the list above; for some types we allow both 'R-friendly' type names, as well as our own, more specific type names for .xdf data.

  • Note also that specifying the column as a "factor" type is currently equivalent to "string" - for the moment, if you wish to import a column as factor data you must use the colInfo argument, documented below.

colInfo

list of named variable information lists. Each variable information list contains one or more of the named elements given below. When importing fixed format data, either colInfo or an .sts schema file should be supplied. For fixed format text files, only the variables specified will be imported. For all text types, the information supplied for colInfooverrides that supplied for colClasses.

  • Currently available properties for a column information list are:
  • type - character string specifying the data type for the column. See colClasses argument description for the available types. If the type is not specified for fixed format data, it will be read as character data.
  • newName - character string specifying a new name for the variable.
  • description - character string specifying a description for the variable.
  • levels - character vector containing the levels when type = "factor". If the levels property is not provided, factor levels will be determined by the values in the source column. If levels are provided, any value that does not match a provided level will be converted to a missing value.
  • newLevels - new or replacement levels specified for a column of type "factor". It must be used in conjunction with the levels argument. After reading in the original data, the labels for each level will be replaced with the newLevels.
  • low - the minimum data value in the variable (used in computations using the F() function.)
  • high - the maximum data value in the variable (used in computations using the F() function.)
  • start - the left-most position, in bytes, for the column of a fixed format file respectively. When all elements of colInfo have start, the text file is designated as a fixed format file. When none of the elements have it, the text file is designated as a delimited file. Specification of start must always be accompanied by specification of width.
  • width - the number of characters in a fixed-width character column or the column of a fixed format file. If widthis specified for a character column, it will be imported as a fixed-width character variable. Any characters beyond the fixed width will be ignored. Specification of width is required for all columns of a fixed format file.
  • decimalPlaces - the number of decimal places.

rowsPerRead

number of rows to read at a time.

type

character string set specifying file type of inData. This is ignored if inData is a data source. Possible values are:

  • "auto": file type is automatically detected by looking at file extensions and argument values.
  • "textFast": delimited text import using faster, more limited import mode. By default variables containing the values TRUE and FALSE or T and F will be created as logical variables.
  • "text": delimited text import using enhanced, slower import mode (not supported with HDFS). This allows for importing Date and POSIXct data types, handling the delimiter character inside a quoted string, and specifying decimal character and thousands separator. (See RxTextData.)
  • "fixedFast": fixed format text import using faster, more limited import mode. You must specify a .sts format file or colInfo specifications with start and widthfor each variable.
  • "fixed": fixed format text import using enhanced, slower import mode (not supported with HDFS). This allows for importing Date and POSIXct data types and specifying decimal character and thousands separator. You must specify a .sts format file or colInfo specifications with start and widthfor each variable.
  • "sas": SAS data files. (See RxSasData.)
  • "spss": SPSS data files. (See RxSpssData.)
  • "odbcFast": ODBC import using faster, more limited import mode.
  • "odbc": ODBC import using slower, enhanced import on Windows. (See RxOdbcData.)

maxRowsByCols

the maximum size of a data frame that will be read in if outData is set to NULL, measured by the number of rows times the number of columns. If the number of rows times the number of columns being imported exceeds this, a warning will be reported and a smaller number of rows will be read in than requested. If maxRowsByCols is set to be too large, you may experience problems from loading a huge data frame into memory.

reportProgress

integer value with options:

  • 0: no progress is reported.
  • 1: the number of processed rows is printed and updated.
  • 2: rows processed and timings are reported.
  • 3: rows processed and all timings are reported.

verbose

integer value. If 0, no additional output is printed. If 1, information on the import type is printed if type is set to auto.

xdfCompressionLevel

integer in the range of -1 to 9. The higher the value, the greater the amount of compression - resulting in smaller files but a longer time to create them. If xdfCompressionLevel is set to 0, there will be no compression and files will be compatible with the 6.0 release of Revolution R Enterprise. If set to -1, a default level of compression will be used.

createCompositeSet

logical value or NULL. If TRUE, a composite set of files will be created instead of a single .xdf file. A directory will be created whose name is the same as the .xdf file that would otherwise be created, but with no extension. Subdirectories data and metadata will be created. In the data subdirectory, the data will be split across a set of .xdfd files (see blocksPerCompositeFile below for determining how many blocks of data will be in each file). In the metadata subdirectory there is a single .xdfm file, which contains the meta data for all of the .xdfd files in the data subdirectory. When the compute context is RxHadoopMR a composite set of files is always created.

blocksPerCompositeFile

integer value. If createCompositeSet=TRUE, and if the compute context is not RxHadoopMR, this will be the number of blocks put into each .xdfd file in the composite set. When importing is being done on Hadoop using MapReduce, the number of rows per .xdfd file is determined by the rows assigned to each MapReduce task, and the number of blocks per .xdfd file is therefore determined by rowsPerRead. If the outFile is an RxXdfData object, set the value for blocksPerCompositeFile there instead.

...

additional arguments to be passed directly to the underlying data source objects to be imported. These argument values will override the existing values in an existing data source, if it is passed in as the inData. See RxTextData, RxSasData, RxSpssData, and RxOdbcData.

Details

If a data source is passed in as inData, argument values specified in the call to rxImport will override any existing specifications in the data source. Setting type to "text", "fixed", or "odbc" is equivalent to setting useFastRead to FALSE in an RxTextData or RxOdbcData input data source. Similarly, setting type to "textFast", "fixedFast", or "odbcFast" is equivalent to setting useFastRead to TRUE.

The input and output data sources are automatically opened and closed within the rxImport function.

For reasons of performance, the textFast 'type' does not properly handle text files that contain the delimiter character inside a quoted string (for example, the entry "Wade, John" inside a comma delimited file. Use the text 'type' if your data set contains character data with this characteristic.

For information on using a .sts schema file for fixed format text import, see the RxTextData help file.

Encoding Details

Some files or data sources contain character data encoded in a particular format (for example, Excel files will always use UTF-16). Others may contain encoding information inside the file itself. When not determined by the file type, or specified within the file, character data in the input file or data source must be encoded as ASCII or UTF-8 in order to be imported correctly. If the data contains UTF-8 multibyte (i.e., non-ASCII) characters, make sure the type parameter is set to "text" or "fixed" for text import and "odbc" for ODBC import as the 'fast' versions of these values may not handle extended UTF-8 characters correctly.

Value

If an outFile is not specified, an output data frame is returned. If an outFile is specified, an RxXdfData data source is returned that can be used in subsequent RevoScaleR analysis.

Author(s)

Microsoft Corporation Microsoft Technical Support

See Also

RxDataSource-class, rxDataStep, RxTextData, RxSasData, RxSpssData, RxOdbcData, RxXdfData, rxSplit, rxTransform.

Examples



 ##############################################################################
 # Import a comma-delimited text file into an .xdf file
 ##############################################################################
 # Create names for input and output data files
 sampleDataDir <- rxGetOption("sampleDataDir")
 inputFile <- file.path(sampleDataDir, "claims.txt")
 outputFile <- file.path(tempdir(), "claims.xdf")

 # Import the data
 rxImport( inData = inputFile, outFile = outputFile)

 # Look at summary information 
 rxGetInfo( data = outputFile, getVarInfo = TRUE)

 # Clean-up: remove data file
 file.remove( outputFile )

 ##############################################################################
 # Import a small SAS file into a data frame in memory
 ##############################################################################
 # Specify a SAS file name
 claimsSasFileName <- file.path(rxGetOption("sampleDataDir"), "claims.sas7bdat")

 # Import the data into a data frame in memory
 claimsIn <- rxImport(inData = claimsSasFileName)
 head(claimsIn)

 ##############################################################################
 # Import a fixed format text file into an .xdf file
 ##############################################################################
 # Specify input and output file names

 claimsFF <- file.path(rxGetOption("sampleDataDir"), "claims.dat")
 claimsXdf <- file.path(tempdir(), "importedClaims.xdf")

 # Specify column information about the input file
 claimsFFColInfo <-
   list(rownames = list(start = 1, width = 3),
        age = list(type = "factor", start = 4, width = 5),
        car.age = list(type = "factor", start = 9, width = 3),
        type = list(type = "factor", start = 12, width = 1),
        cost = list(type = "numeric", start = 13, width = 6),
        number = list(type = "integer", start = 19, width = 3))

 # Import the data into the xdf file
 rxImport(inData = claimsFF, outFile = claimsXdf, 
   colInfo = claimsFFColInfo, 
   rowsPerRead = 65, # rowsPerRead will determine block size
   overwrite = TRUE)

 # Look at information about the new file
 rxGetInfo( data = claimsXdf, getVarInfo = TRUE)

 # Clean-up: delete the new file
 file.remove( claimsXdf)

 ##############################################################################
 # Import a fixed format text file using an RxTextData data source
 ##############################################################################

 claimsFF <- file.path(rxGetOption("sampleDataDir"), "claims.dat")
 claimsXdf <- file.path(tempdir(), "importedClaims.xdf")

 # Create an RxTextData data source

 claimsDS <- RxTextData( file = claimsFF,
   colInfo =  list(
      rownames = list(start = 1, width = 3),
        age = list(type = "factor", start = 4, width = 5),
        car.age = list(type = "factor", start = 9, width = 3),
        type = list(type = "factor", start = 12, width = 1),
        cost = list(type = "numeric", start = 13, width = 6),
        number = list(type = "integer", start = 19, width = 3)),
        rowsPerRead = 50 # rowsPerRead will determine block size
        )

 # Import the data specified in the data source into an xdf file

 rxImport(inData = claimsDS, outFile = claimsXdf,
   rowsPerRead = 65, # this will override 'rowsPerRead' in the data source
   overwrite = TRUE)

 # Clean-up: delete the new file
 file.remove( claimsXdf)


 ##############################################################################
 # Import a an SPSS file into an Xdf file
 ##############################################################################

 # Specify SPSS file name
 spssFileName <- file.path(rxGetOption("unitTestDataDir"), "claimsInt.sav")

 # Create an XDF data file path
 xdfFileName <- file.path(tempdir(), "ClaimsInt.xdf")

 # Import data; notice that factor variables are created for any
 # SPSS variables with value labels
 rxImport(inData = spssFileName, outFile = xdfFileName, overwrite = TRUE, reportProgress = 0)
 varInfo <- rxGetVarInfo( data = xdfFileName )
 varInfo

 # Reimport SPSS data, storing some variables as integer instead of
 # numeric

 spssColClasses <- c(RowNum = "integer", cost = "integer", 
   number = "integer")
 rxImport(inData = spssFileName, outFile = xdfFileName, colClasses = spssColClasses,
    overwrite = TRUE, reportProgress = 0)
 varInfo <- rxGetVarInfo( data = xdfFileName )
 varInfo  

 # Reimport SPSS data, changing re-specifing the strings used
 # for factor levels

 spssColInfo <- list(
   RowNum = list(type="integer", newName = "RowNumber"),
   cost = list(type="integer", newName = "TotalCost", description = "Cost of Auto"),
   number = list(type="integer", newName = "Number", description = "Number of Claims"),
   type = list(
   levels = as.character(1:4),
   newLevels = c("Small", "Medium", "Large", "Huge"))) 
 rxImport(inData = spssFileName, outFile = xdfFileName, 
     colInfo = spssColInfo, overwrite = TRUE, reportProgress = 0)
 varInfo <- rxGetVarInfo( data = xdfFileName )
 varInfo  

 # Clean-up: delete the new file
 file.remove( xdfFileName )