Data Sources in RevoScaleR

Article
06/04/2017

Important

This content is being retired and may not be updated in the future. The support for Machine Learning Server will end on July 1, 2022. For more information, see What's happening to Machine Learning Server?

A data source in RevoScaleR is an R object representing a data set. It is the return object of rxImport for read operations and rxDataStep for write operations. Although the data itself may be on disk, a data source is an in-memory object that allows you to treat data from disparate sources in a consistent manner within RevoScaleR.

Behind the scenes, rxImport often creates data sources implicitly to facilitate data import. You can explicitly create data sources for more control over how data is imported, such as setting arguments to control how many rows are read into the object. This article explains how to create a variety of data sources and use them in an analytical context.

Data Source Constructors

To create data sources directly, use the constructors listed in the following table:

Source Data	Data Source Constructor
Text (fixed-format or delimited)	RxTextData
SAS	RxSasData
SPSS	RxSpssData
ODBC Database	RxOdbcData
Teradata Database	RxTeradata
SQL Server Database	RxSqlServerData
Spark data: Hive, Parquet and ORC	RxSparkData or RxHiveData, RxParquetData, RxOrcData
.xdf data files	RxXdfData

XDF files are the out files for rxImport read operations, but you also use them as a data source input when loading all or part of an .xdf into a data frame. Using an XDF data source is recommended for repeated analysis of a single data set. It is almost always faster to import data into an .xdf file and run analyses on the .xdf data source than to load data from an original data source.

When to create a data source

For simple data import, it's not necessary to explicitly create a data source. You can simply specify a file path for a file that rxImport can read, and RevoScaleR will read it using the default settings. However, if you need to provide additional options specific to that data source type, you should create a data source using a constructor from the previous list.

How to create a data source

You can create a data source the same way you create any object in R, by giving it a name and using a constructor. The first argument of any RevoScaleR data source is the source data:

# Load sample text file on Linux
> myTextDS <- RxTextData("/usr/lib64/microsoft-r/3.3/lib64/R/library/RevoScaleR/SampleData/claims.txt")

# Load sample text file on Windows. Remember to replace Window's \ with R's /
> myTextDS <- RxTextData("C:/Program Files/Microsoft/ML Server/R_SERVER/library/RevoScaleR/SampleData/claims.txt")

As a coding best practice, create a file object first, and pass that to the data source:

> mySrcObj <- file.path(rxGetOption("sampleDataDir"), "claims.txt")
  	> myTextDS <- RxTextData(mySrcObj)

After the data source object is created, you can return object properties, precomputed metadata, and rows.

# Return properties
> myTextDS
RxTextData Source
"C:/Program Files/Microsoft/ML Server/R_SERVER/library/RevoScaleR/SampleData/claims.txt"
centuryCutoff: 20
rowsToSniff: 10000
rowsToSkip: 0
defaultReadBufferSize: 10000
isFixedFormat: FALSE
useFastRead: TRUE
fileSystem: 
	fileSystemType: native

	# Return variable metadata
	> rxGetVarInfo(myTextDS)
		Var 1: RowNum, Type: integer
		Var 2: age, Type: character
		Var 3: car.age, Type: character
		Var 4: type, Type: character
		Var 5: cost, Type: numeric, Storage: float32
		Var 6: number, Type: numeric, Storage: float32

	# Return first 10 rows			
	> rxGetInfo(myTextDS, numRows=10)
		File name: C:/Program Files/Microsoft/ML Server/R_SERVER/library/RevoScaleR/SampleData/claims.txt 
		Data Source: Text 
		Data (10 rows starting with row 1):
		RowNum   age car.age type cost number
		1       1 17-20     0-3    A  289      8
		2       2 17-20     4-7    A  282      8
		3       3 17-20     8-9    A  133      4
		4       4 17-20     10+    A  160      1
		5       5 17-20     0-3    B  372     10
		6       6 17-20     4-7    B  249     28
		7       7 17-20     8-9    B  288      1
		8       8 17-20     10+    B   11      1
		9       9 17-20     0-3    C  189      9
		10     10 17-20     4-7    C  288     13

Use standard R methods

A number of standard R methods can be used with RevoScaleR data sources. You might be familiar with names for viewing variable names, or head for viewing the first few rows:

> names(myTextDS)
[1] "RowNum"	"age"	"car.age"	"type"	"cost"	"number"

> head(myTextDS)
RowNum	age	car.age	type	cost	number
1	1		17-20	0-3		A	289		 8
2	2		17-20	4-7		A	282		 8
3	3		17-20	8-9		A	133		 4
4	4		17-20	10+		A	160		 1
5	5		17-20	0-3		B	372		10
6	6		17-20	4-7		B	249		28

By loading data into a data frame using rxImport, you can use additional functions, such as the dim function to return dimensions, and colnames or dimnames as an alternative to RxGetVarInfo to obtain variable names.

#  Load data into a data frame
newDF <- rxImport(inData = myTextDS)
dim(newDF)
[1] 128   6

You can obtain the number of variables using the length function:

length(newDF)
	[1] 6

View the last rows of a data source using the tail function:

tail(claimsDS)
	RowNum age car.age type cost number
123    123 60+     8-9    C  227     20
124    124 60+     10+    C  119      6
125    125 60+     0-3    D  385     62
126    126 60+     4-7    D  324     22
127    127 60+     8-9    D  192      6
128    128 60+     10+    D  123      6

By adding outFile to rxImport, you create an XDF data source, which you can return using summary:

newDF <- rxImport(inData = myTextDS, outFile = "claims.xdf", overwrite = TRUE)
	Rows Read: 128, Total Rows Processed: 128, Total Chunk Time: 0.009 seconds
summary(newDF)
	. . .
	Data: object (RxXdfData Data Source)
	File name: claims.xdf
	. . .

For .xdf file data sources, dimnames returns only column names. Row names are not provided because .xdf files do not contain row names:

colnames(newDF)
	[1] "RowNum"  "age"     "car.age" "type"    "cost"    "number"

dimnames(newDF)
	[[1]]
	NULL
	[[2]]
	[1] "RowNum"  "age"     "car.age" "type"    "cost"    "number"

Data source by compute context

In the local compute context, all of RevoScaleR’s supported data sources are available to you. In a distributed context, the data source object aligns to the compute context. Thus, RxInSqlServer only supports RxSqlServerData objects. Likewise for RxInTeradata, which supports only the RxTeradata data sources. For more information, see Compute context.

Data Source	RxLocalSeq	RxSpark	RxHadoopMR	RxInSqlServer	RxInTeradata
Delimited Text (RxTextData)	x	x	x
Fixed-Format Text (RxTextData)	x
.xdf data files (RxXdfData)	x	x	x
SAS data files (RxSasData)	x
SPSS data files (RxSpssData)	x
ODBC data (RxOdbcData)	x
SQL Server database (RxSqlServerData)	x			x
Teradata database (RxTeradata)	x				x
Spark data RxSparkData	x	x

Examples

The following examples show how to instantiate and use various data sources.

RxSasData

Sample data includes claims.sas7bdat, which you can load without having SAS installed.

inFileSAS <- file.path(rxGetOption("sampleDataDir"), "claims.sas7bdat") 
sourceDataSAS <- RxSasData(inFileSAS, stringsAsFactors=TRUE)

Retrieve variables in the data by calling R's names function:

names(sourceDataSAS)
	[1] "RowNum"  "age"     "car_age" "type"    "cost"    "number"

Compute a regression, passing the data source as the data argument to rxLinMod:

rxLinMod(cost ~ age + car_age, data = sourceDataSAS)

	Rows Read: 128, Total Rows Processed: 128, Total Chunk Time: 0.003 seconds 
	Computation time: 0.014 seconds.
	Call:
	rxLinMod(formula = cost ~ age + car_age, data = sourceDataSAS)

	Linear Regression Results for: cost ~ age + car_age
	Data: sourceDataSAS (RxSasData Data Source)
	File name:
		C:/Program Files/Microsoft/ML Server/R_SERVER/library/RevoScaleR/SampleData/claims.sas7bdat
	Dependent variable(s): cost
	Total independent variables: 13 (Including number dropped: 2)
	Number of valid observations: 123
	Number of missing observations: 5 
	
	Coefficients:
					cost
	(Intercept) 117.38544
	age=17-20    88.15174
	age=21-24    34.15903
	age=25-29    54.68750
	age=30-34     2.93750
	age=35-39   -20.77430
	age=40-49     1.68750
	age=50-59    63.12500
	age=60+       Dropped
	car_age=0-3 159.30531

RxSpssData

Similarly, you could use the SPSS version of the claims data as follows:

inFileSpss <- file.path(rxGetOption("sampleDataDir"), "claims.sav") 
sourceDataSpss <- RxSpssData(inFileSpss, stringsAsFactors=TRUE)
rxLinMod(cost ~ age + car_age, data=sourceDataSpss)

RxXdfData

This example shows how to create a data source from the built-in claims.xdf data set:

claimsPath <-  file.path(rxGetOption("sampleDataDir"), "claims.xdf")
claimsDs <- RxXdfData(claimsPath)

Use the open method rxOpen to open the data source:

rxOpen(claimsDs)

Use the method rxReadNext to read the next block of data from the data source:

claims <- rxReadNext(claimsDs)

Use the rxClose method to close the data source:

rxClose(claimsDs)

XDF data sources with biglm

Since data sources for xdf files read data in chunks, it is a good match for the CRAN package biglm. The biglm package does a linear regression on an initial chunk of data, then updates the results with subsequent chunks. Below is a function that loops through an xdf file object and creates and updates the biglm results.

#  Using an Xdf Data Source with biglm
	
if ("biglm" %in% .packages()){
require(biglm)
biglmxdf <- function(dataSource, formula)
{	
	moreData <- TRUE
	df <- rxReadNext(dataSource)
	biglmRes <- biglm(formula, df)	
	while (moreData)
	{
		df <- rxReadNext(dataSource)	
		if (length(df) != 0)
		{
			biglmRes <- update(biglmRes, df)						
		}
		else
		{
			moreData <- FALSE
		}
	}							
	return(biglmRes)			
}

To use the function, we first open the data file. For example, we can again use the large airline data set AirOnTime87to12.xdf:

bigDataDir <- "C:/MRS/Data"
bigAirData <- file.path(bigDataDir, "AirOnTime87to12/AirOnTime87to12.xdf")
dataSource <- RxXdfData(bigAirData, 
	varsToKeep = c("DayOfWeek", "DepDelay","ArrDelay"), blocksPerRead = 15)
rxOpen(dataSource)

Then we will time the computation, doing the regression for all the rows— 148,619,655 if you are using the full data set. Note that it takes several minutes to load the data, even on a very fast machine.

system.time(bigLmRes <- biglmxdf(dataSource, ArrDelay~DayOfWeek))
rxClose(dataSource)

We can see the coefficients by looking at a summary of the object returned:

summary(bigLmRes)

} # End of use of biglm

It is, of course, much faster to compute a linear model using the rxLinMod function, but the biglm package provides alternative methods of computation.

Next Steps

Continue on to the following data import articles to learn more about XDF and other data formats:

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