3 Using Oracle R Enterprise

Long Names

Oracle R Enterprise handles R naming conventions for ore.frame columns, instead of a more restrictive Database names. ore.frame column names can be longer than 30 bytes, contain double quotes, and be non-unique.

Load an R Data Frame into the Database

Follow these steps to load data from R data frames on your system to the Oracle database:

1. Load contents of the file to an R data frame using read.table() or read.csv() functions documented in R online help.

2. Then use ore.create()to load a data frame to a table:

   ore.create(data_frame, table="TABLE_NAME")
   

Step 2 loads data_frame into the database table TABLE_NAME.

For an example, see Example: Load Data.

R> df <- data.frame(A=1:26, B=letters[1:26])
R> dim(df)
[1] 26  2
R> class(df)
[1] "data.frame"
R> head(df)
  A B
1 1 a
2 2 b
3 3 c
4 4 d
5 5 e
6 6 f
R> ore.create(df, table="DF_TABLE")
R> ore.ls()
[1] "DF_TABLE" 
R> class(DF_TABLE)
[1] "ore.frame"
attr(,"package")
[1] "OREbase"
R> dim(DF_TABLE)
[1] 26  2
R> head(DF_TABLE)
  A B
0 1 a
1 2 b
2 3 c
3 4 d
4 5 e
5 6 f
R> exists("DF_TABLE")[1] TRUE

Materialize R Data

The ore.push(data.frame) function stores an R object in the database as a temporary object, and returns a handle to that object. It converts data frame, matrix, and vector objects to a table, and list, model, and other objectss to a serialized object.

The object that you create exists during the R session; to store the data in a permanent way, see Persist and Manage R Objects in the Database

This example pushes the numerical vector created by the R command c(1,2,3,4,5) to v, an Oracle R Enterprise object:

R> v <- ore.push(c(1,2,3,4,5))
R> class(v)
[1] "ore.numeric"
attr(,"package")
[1] "OREbase"
R> head(v)
[1] 1 2 3 4 5

Verify that an ore.frame Exists

ore.exists() checks for the existence of an ore.frame object in the ORE schema environment. For ore.exists()to find an ore.frame object the object must have been synchronized with ore.sync() first.

The objects available in the ORE environment are not necessarily the same as the database objects. One should not use ore.exists() to check for table existence.

For an example, see Example: Load Data.

ore.exists(name, schema)has these arguments:

• name: A character string specifying the name of the ore.frame object

• schema: A character string specifying the name of database schema to check

ore.exists() returns TRUE if the object exists in the ORE schema and FALSE, if it does not exist.

Drop a Database Table

To drop a table in the database use

ore.drop(table="NAMEOFTABLE")

For example, these commands drop the table v and verifies that it does not exist:

R> ore.drop(table="v")
R> ore.exists("v")
[1] FALSE

If you drop a table that does not exist, there is no error message.

Pull a Database Table to an R Frame

To pull the contents of an Oracle Database table or view to an in-memory R data frame use ore.pull(OBJECT_NAME)for the name of an object returned by ore.ls().

Suppose that your Oracle Database contains the table NARROW. Then ore.pull() creates the data frame df_narrow from the table NARROW. When you verify that df_narrow is a data frame. The warning message appears because the table NARROW is not indexed:

R> df_narrow <- ore.pull(NARROW)
Warning message:
ORE object has no unique key - using random order 
R> class(df_narrow)
[1] "data.frame"

Order in Tables

Almost all data in R is a vector or is based on vectors (vectors themselves, lists, matrices, data frames, and so forth). The elements of a vector have an explicit order. Each element has an index. R code actively uses this order of elements.

However, database-backed relational data (tables and views) does not define any order of rows and thus cannot be directly mapped to R data structures. You can define an explicit order on database tables and views via an ORDER BY clause. The order is usually achieved by having a unique identifier (single- or multi- column key). Ordering in this way can be inefficient and slow for some operations that lead to unnecessary sorting.

row.names<- defines ordering but doesn't actually index a table. The assignment option provides a way to specify a unique column. Initially it supports at least one column but may support multi-column specifications as well. When row.names<- is applied to unordered frames, it returns an error.

You can use the integer indexing created by the ordering infrastructure to perform sampling and partitioning, as described in Sampling and Partitioning.

Suppose that the table NARROW is not indexed. The following example illustrates using row.names to create an indexed table:

R> row.names(head(NARROW))
Error: ORE object has no unique key
In addition: Warning message:
ORE object has no unique key - using random order 
R> 
R> row.names(NARROW) <- NARROW$ID
R> 
R> row.names(head(NARROW[,1:3]))
[1] "101501" "101502" "101503" "101504" "101505" "101506"
R> 
R> head(NARROW[,1:3])
           ID GENDER AGE
101501 101501   <NA>  41
101502 101502   <NA>  27
101503 101503   <NA>  20
101504 101504   <NA>  45
101505 101505   <NA>  34
101506 101506   <NA>  38

Sampling and Partitioning

The ordering (indexing) for tables described in Order in Tables can be used to perform sampling and partitioning.

This section provides examples of

• Indexing

• Sampling

• Random Partitioning

R> tmp <- ASTHMA
R> tmp[c(1L, 2L, 1L),]
Error: ORE object has no unique key
R> rownames(tmp) <- tmp
R> tmp[c(1L, 2L, 1L),]
         CITY ASTHMA COUNT
1|0|65      1      0    65
1|0|65.1    1      0    65
1|1|35      1      1    35
R> tmp[c(1L, 2L, 1L),]@dataQry

# Generate random data
set.seed(123)
N <- 1000000
mydata <- data.frame(x = rnorm(N, mean = 20, sd = 2),
                     group =
                     sample(letters, N, replace = TRUE,
                            prob = (26:1)/sum(26:1)))
mydata$y <-
    rbinom(N, 1,
           1/(1+exp(-(.5 - 0.25 * mydata$x + .1 * as.integer(mydata$group)))))
MYDATA <- ore.push(mydata)
rm(mydata)
 
# Create a function that creates random row indices from large tables
mysampler <- function(n, size, replace = FALSE)
{
    #' Random Whole Number Sampler
    #' @param n       number of observations in sample
    #' @param size    total number of observations
    #' @param replace indicator for sampling with replacement
    #' @return numeric vector containing the sample indices
    n    <- round(n)
    size <- round(size)
    if    (n < 0) stop("'n' must be a non-negative number")
    if (size < 1) stop("'size' must be a positive number")
    if (!replace && (n > size))
        stop("'n' cannot exceed 'size' when 'replace = FALSE'")
    if (n == 0)
        numeric()
    else if (replace)
        round(runif(n, min = 0.5, max = size + 0.5))
    else
    {
        maxsamp <- seq(size + 0.5, by = -1, length.out = n)
        samp <- round(runif(n, min = 0.5, max = maxsamp))
        while(length(bump1 <- which(duplicated(samp))))
            samp[bump1] <- samp[bump1] + 1
        samp
    }
}
 
# Data set and sample size
N <- nrow(MYDATA)
sampleSize <- 500
 
# 1. Simple random sampling
srs <- mysampler(sampleSize, N)
simpleRandomSample <- ore.pull(MYDATA[srs, , drop = FALSE])
 
# 2. Systematic sampling
systematic <- round(seq(1, N, length.out = sampleSize))
systematicSample <- ore.pull(MYDATA[systematic, , drop = FALSE])
 
# 3. Stratified sampling
stratifiedSample <-
    do.call(rbind,
            lapply(split(MYDATA, MYDATA$group),
                   function(y)
                   {
                       ny <- nrow(y)
                       y[mysampler(sampleSize * ny/N, ny), , drop = FALSE]
                   }))
 
# 4. Cluster sampling
clusterSample <- do.call(rbind, sample(split(MYDATA, MYDATA$group), 2))
 
# 5a. Accidental/Convenience sampling (via row order access)
convenientSample1 <- head(MYDATA, sampleSize)
 
# 5b. Accidental/Convenience sampling (via hashing)
maxHash <- 2^32 # maximum allowed in ore.hash
convenient2 <- (ore.hash(rownames(MYDATA), maxHash)/maxHash) <= (sampleSize/N)
convenientSample2 <- ore.pull(MYDATA[convenient2, , drop = FALSE])
Random

nrowX <- nrow(x)
x$partition <- sample(rep(1:k, each = nrowX/k, length.out = nrowX), replace = TRUE)

results <- ore.groupApply(x, x$partition, function(y) {...}, parallel = TRUE)

Persist and Manage R Objects in the Database

R objects exist for the duration of the current session, unless they are explicitly saved. For example, if you build a model in a particular R session, the model is not available when the session is closed, unless the model was explicitly saved.

Oracle R Enterprise supports persistence for R objects onto the database.

Persistence provides these advantages:

• You can access the same R and Oracle R Enterprise object (for example, a model) among different R sessions.

• You can build a model in R and use it for prediction and scoring in embedded Oracle R Enterprise.

Oracle R Enterprise creates datastores to contain persisted objects.

Persisted objects reside in a datastore. The following Oracle R Enterprise functionality allows you manage persistence:

• ore.save()

• ore.load()

• ore.delete()

• ore.datastore()

• ore.datastoreSummary()

ore.save({...}, list = character(0), name, envir = parent.frame(), overwrite = FALSE, append = FALSE, description = character(0)))

ore.save(list=ls(), name="ds_1", description = "example datastore")

ore.save(x, y, z, name="ds_2", overwrite=TRUE)

ore.save(x, y, z, name="ds_3", append=TRUE)

ore.load(name, list = character(0), envir = parent.frame())

ore.load("ds_1")

ore.load("ds_1", list=c("x", "Y", "z"))

ore.delete(name)

ore.delete("ds_1")

ore.datastore(name, pattern)

ore.datastore()

ore.datastoreSummary(name)

ore.datastoreSummary(name = "ds_1")

Build and Use a Regression Model

This example illustrates building a regression model using a CRAN package. You can prepare the data used for training in the database (filtering out observations that are not of interest, selecting attributes, imputing missing values, and so forth). Suppose that the preprocessed data is in the table ONTIME_S_PREPROCESSED_SUBSET. Then pull the prepared training set (which is usually small enough to fit in desktop R memory) into the R client to execute the model build.

You can use the resulting model to score (predict) large numbers of rows, in parallel, in Oracle Database. The data are stored in ONTIME_S_FINAL_DATA_TO_BE_SCORED.

Note that scoring is a trivially parallelizable operation because one row can be scored independent of and in parallel with another row. The model built on the desktop is shipped to the database to perform scoring on vast numbers of rows in the database.

The computations are divided into these steps:

1. Build a model in the desktop:

   dat <- ore.pull(ONTIME_S_PREPROCESSED_SUBSET)
   mod <- glm(ARRDELAY ~ DISTANCE + DEPDELAY, dat)
   mod
   summary(mod)
   

2. Score in-parallel in the database using embedded R:

   prd <- predict(mod, newdata=ONTIME_S_FINAL_DATA_TO_BE_SCORED)
   class(prd)
   # Add predictions as a new column
   res <- cbind(newdat, PRED = prd)
   head(res)
   

R provides many other ways to build regression models, such as lm().

For other ways to build regression models, see Oracle R Enterprise Versions of R Models and In-Database Predictive Models in Oracle R Enterprise.

Perform R Computation in Oracle Database

This example illustrates off loading R computation to execute in the embedded R engine. To off load an R computation, simply include the R code within a closure (that is, function() {}) and invoke ore.doEval(). ore.doEval() schedules execution of the R code with the database-embedded R engine and returns the results back to the desktop for continued analysis:

library(biglm)
mod <- ore.doEval(
   function() {
      library(biglm)
      dat <- ore.pull(ore.get("ONTIME_S"))
      mod <- biglm(ARRDELAY ~ DISTANCE + DEPDELAY, dat)
      mod
     }, ore.connect = TRUE);
print(mod)
mod=ore.pull(mod)
print(mod)

Build a Series of Regression Models Using Data Parallelism

This example illustrates database-driven data parallelism at work in building a series of regression models using a CRAN package. One model is built per unique value of a factor. The database orchestrates the parallel and concurrent building of the models, one per factor and brings the list of all models built to the user desktop for further analysis:

modList <- ore.groupApply(
  # Organize input to the R script – This is always an Oracle R Enterprise   
  # data frame
   X=ONTIME_S,
  # Specify the grouping column. Here we request one model per unique value of
  # ONTIME_S$DEST
   INDEX=ONTIME_S$DEST,
  # Model building code goes inside the closure. Input and grouping 
  # conditions can be referenced as parameters to the function
    function(x) {
     library(biglm)
     biglm(ARRDELAY ~ DISTANCE + DEPDELAY, x)
     });

   modList_local <- ore.pull(modList)
# Print the model for just one destination - BOSTON
summary(modList_local$BOS)

Load a Data Frame to a Table

Start R, load the ORE packages via library(ORE), and then connect to the database.

Follow these steps to load an R data frame to a database table:

1. This example uses the R data set iris.

   The iris data set is located in the datasets package that is part of the R distribution:

   R> find("iris")
   [1] "package:datasets"
   

   Use the R command class to verify that iris is an R data frame:

   R> class(iris)
   [1] "data.frame"
   

   iris consist of measurements of parts of iris flowers. Use the R command head to see a small sample of the data in iris.

   R> head(iris)
         Sepal.Length Sepal.Width Petal.Length Petal.Width Species
   1          5.1         3.5          1.4         0.2  setosa
   2          4.9         3.0          1.4         0.2  setosa
   3          4.7         3.2          1.3         0.2  setosa
   4          4.6         3.1          1.5         0.2  setosa
   5          5.0         3.6          1.4         0.2  setosa
   6          5.4         3.9          1.7         0.4  setosa
   

2. Now load the data frame iris into the database that you are connected to.

   Suppose that the database table version of iris is named IRIS_TABLE. Drop IRIS_TABLE to make sure that no table of this name exists in the connected schema:

   ore.drop(table = "IRIS_TABLE")
   

   If IRIS_TABLE doesn't exist, you do not get a message.

3. Now create a database table with the data contained in iris:

   ore.create(iris, table = "IRIS_TABLE")
   

   Use ore.ls() to verify that the table was created:

   R> ore.ls()
   [1] "IRIS_TABLE" "NARROW"     "ONTIME_S" 
   

4. IRIS_TABLE is a database-resident table with just metadata on the R side:

   R> class(IRIS_TABLE)
   [1] "ore.frame"
   attr(,"package")
   [1] "OREbase"
   

5. Use head to see the column names and the first few values in IRIS_TABLE:

   R> head(IRIS_TABLE)
     SEPAL_LENGTH SEPAL_WIDTH PETAL_LENGTH PETAL_WIDTH SPECIES
   0          5.1         3.5          1.4         0.2  setosa
   1          4.9         3.0          1.4         0.2  setosa
   2          4.7         3.2          1.3         0.2  setosa
   3          4.6         3.1          1.5         0.2  setosa
   4          5.0         3.6          1.4         0.2  setosa
   5          5.4         3.9          1.7         0.4  setosa
   

6. Use class to see the data type of the column SPECIES.

   R > class(IRIS_TABLE$SPECIES)
   [1] "raw"
   

You can use R functions to analyze the data in the table. Here are some simple examples taken from the example basic.R:

• Use unique to get a list of the unique entries in a column. This example finds the unique SPECIES:

  R> unique(IRIS_TABLE$SPECIES)
  [1] setosa     versicolor virginica 
  Levels: setosa versicolor virginica
  

• Find the minimum, maximum, and mean of PETAL_LENGTH:

  R> min(IRIS_TABLE$PETAL_LENGTH)
  [1] 1
  R> max(IRIS_TABLE$PETAL_LENGTH)
  [1] 6.9
  R> mean(IRIS_TABLE$PETAL_LENGTH)
  [1] 3.758
  

If you need information about an R function, use the command help(function-name).

Handle NULL Values Using airquality

Oracle Database has logical values: TRUE, FALSE, NULL. There is a 3x3 table that defines truth values for propositions with AND and OR. NULL is treated as an unknown value. For some operations the result is either deterministic (for example TRUE OR NULL) or unknown (TRUE AND NULL). If logical values are used in a WHERE clause, only rows with the condition TRUE are selected; FALSE and NULL are ignored. R, on the other hand, keeps TRUE and NA. Rows with NA are selected with value NA.

The option ore.na.extract controls whether NAs are selected or not. The default is to treat NA as SQL treats FALSE.

The demo nulls.R is the only sample that does not use iris as data. nulls.R compares the handling of NULLs in SQL with the handling of NAs in R.

In R, NA is a logical constant of length 1 which contains a missing value indicator. In the database, null refers to the absence of a value in a column of a row. Nulls indicate missing, unknown, or inapplicable data.

Follow these steps to understand the demo nulls.R:

1. This demo uses the data frame airquality. Verify that the data set is a data frame and look at the few rows of the data frame:

   R> class(airquality)
   [1] "data.frame"
   R> head(airquality)
     Ozone Solar.R Wind Temp Month Day
   1    41     190  7.4   67     5   1
   2    36     118  8.0   72     5   2
   3    12     149 12.6   74     5   3
   4    18     313 11.5   62     5   4
   5    NA      NA 14.3   56     5   5
   6    28      NA 14.9   66     5   6
   

2. Load airquality into the database as "AIRQUALITY":

   ore.drop(table = "AIRQUALITY")
   ore.create(airquality, table = "AIRQUALITY")
   

   Use ore.ls() to verify that the table was created. If you wish, use class(AIRQUALITY) to verify that AIRQUALITY is a database-resident table with just metadata on the R side.

3. Examine how R handles NAs. Return all observations where ozone < 30 is TRUE:

   R> nrow(airquality[airquality$Ozone < 30,])[1] 92
   

   Compare this with the results when NAs are explicitly excluded:

   R> nrow(airquality[airquality$Ozone < 30 & !is.na(airquality$Ozone),])
   [1] 55
   

4. The default behavior for SQL tables is to exclude NULLS in output:

   nrow(AIRQUALITY[AIRQUALITY$OZONE < 30,])
   [1] 55
   

   To handle NULLs the same way that R handles NA, request the behavior explicitly:

   options(ore.na.extract = TRUE)
   nrow(AIRQUALITY[AIRQUALITY$OZONE < 30,])
   [1] 92
   

Oracle R Enterprise Demos

These scripts have been added as demos to the ORE package.

To list all of the demos included with Oracle R Enterprise, type

R> demo(package = "ORE")

To run one of these scripts, specify the name of the demo in a demo function call. For example, to run aggregate.R, type

R> demo("aggregate", package = "ORE")

These demos are shipped with Oracle R Enterprise:

aggregate      Aggregation
analysis       Basic analysis & data processing operations
basic          Basic connectivity to database
binning        Binning logic
columnfns      Column functions
cor            Correlation matrix
crosstab       Frequency cross tabulations
datastore      DataStore operations
datetime       Date/Time operations
derived        Handling of derived columns
distributions  Distribution, density, and quantile functions
do_eval        Embedded R processing
freqanalysis   Frequency cross tabulations
graphics       Demonstrates visual analysis
group_apply    Embedded R processing by group
hypothesis     Hyphothesis testing functions
matrix         Matrix related operations
nulls          Handling of NULL in SQL vs. NA in R
odm_ai         Oracle Data Mining: attribute importance
odm_dt         Oracle Data Mining: decision trees
odm_glm        Oracle Data Mining: generalized linear models
odm_kmeans     Oracle Data Mining: enhanced k-means clustering
odm_nb         Oracle Data Mining: naive Bayes classification
odm_svm        Oracle Data Mining: support vector machines
push_pull      RDBMS <-> R data transfer
rank           Attributed-based ranking of observations
reg            Ordinary least squares linear regression
row_apply      Embedded R processing by row chunks
sampling       Random row sampling and partitioning of an ore.frame
sql_like       Mapping of R to SQL commands
stepwise       Stepwise OLS linear regression
summary        Summary functionality
table_apply    Embedded R processing of entire table