As part of our consulting practice Win-Vector LLC has been helping a few clients stand-up advanced analytics and machine learning stacks using R and substantial data stores (such as relational database variants such as PostgreSQL or big data systems such as Spark).

Often we come to a point where we or a partner realize: "the design would be a whole lot easier if we could phrase it in terms of higher order data operators."

The R package DBI gives us direct access to SQL and the package dplyr gives us access to a transform grammar that can either be executed or translated into SQL.

But, as we point out in the replyr README: moving from in-memory R to large data systems is always a bit of a shock as you lose a lot of your higher order data operators or transformations. Missing operators include:

• union (binding by rows many data frames into a single data frame).
• split (splitting a single data frame into many data frames).
• pivot (moving row values into columns).
• un-pivot (moving column values to rows).

I can repeat this. If you are an R user used to using one of dplyr::bind_rows() , base::split(), tidyr::spread(), or tidyr::gather(): you will find these functions do not work on remote data sources, but have replacement implementations in the replyr package.

For example:

library("RPostgreSQL")

## Loading required package: DBI

suppressPackageStartupMessages(library("dplyr"))
isSpark <- FALSE

# Can work with PostgreSQL
my_db <- DBI::dbConnect(dbDriver("PostgreSQL"),
                        host = 'localhost',
                        port = 5432,
                        user = 'postgres',
                        password = 'pg')
 
# # Can work with Sparklyr
# my_db <-  sparklyr::spark_connect(version='2.2.0', 
#                                   master = "local")
# isSpark <- TRUE

d <- dplyr::copy_to(my_db, data.frame(x =  c(1,5), 
                                      group = c('g1', 'g2'),
                                      stringsAsFactors = FALSE), 
                    'd')
print(d)

## # Source:   table<d> [?? x 2]
## # Database: postgres 9.6.1 [postgres@localhost:5432/postgres]
##       x group
##   <dbl> <chr>
## 1     1    g1
## 2     5    g2

# show dplyr::bind_rows() fails.
dplyr::bind_rows(list(d, d))

## Error in bind_rows_(x, .id): Argument 1 must be a data frame or a named atomic vector, not a tbl_dbi/tbl_sql/tbl_lazy/tbl

The replyr package supplies R accessible implementations of these missing operators for large data systems such as PostgreSQL and Spark.

For example:

# using the development version of replyr https://github.com/WinVector/replyr
library("replyr") 

## Loading required package: seplyr

## Loading required package: wrapr

## Loading required package: cdata

packageVersion("replyr")

## [1] '0.8.2'

# binding rows
dB <- replyr_bind_rows(list(d, d))
print(dB)

## # Source:   table<replyr_bind_rows_jke6fkxtgqc0flj6edix_0000000002> [?? x
## #   2]
## # Database: postgres 9.6.1 [postgres@localhost:5432/postgres]
##       x group
##   <dbl> <chr>
## 1     1    g1
## 2     5    g2
## 3     1    g1
## 4     5    g2

# splitting frames
replyr_split(dB, 'group')

## $g2
## # Source:   table<replyr_gapply_bogqnrfrzfi7m9amnhcz_0000000001> [?? x 2]
## # Database: postgres 9.6.1 [postgres@localhost:5432/postgres]
##       x group
##   <dbl> <chr>
## 1     5    g2
## 2     5    g2
## 
## $g1
## # Source:   table<replyr_gapply_bogqnrfrzfi7m9amnhcz_0000000003> [?? x 2]
## # Database: postgres 9.6.1 [postgres@localhost:5432/postgres]
##       x group
##   <dbl> <chr>
## 1     1    g1
## 2     1    g1

# pivoting
pivotControl <-  buildPivotControlTable(d, 
                                        columnToTakeKeysFrom = 'group', 
                                        columnToTakeValuesFrom = 'x',
                                        sep = '_')
dW <- moveValuesToColumnsQ(keyColumns = NULL,
                           controlTable = pivotControl,
                           tallTableName = 'd',
                           my_db = my_db, strict = FALSE) %>%
  compute(name = 'dW')
print(dW)

## # Source:   table<dW> [?? x 2]
## # Database: postgres 9.6.1 [postgres@localhost:5432/postgres]
##   group_g1 group_g2
##      <dbl>    <dbl>
## 1        1        5

# un-pivoting
unpivotControl <- buildUnPivotControlTable(nameForNewKeyColumn = 'group',
                                           nameForNewValueColumn = 'x',
                                           columnsToTakeFrom = colnames(dW))
moveValuesToRowsQ(controlTable = unpivotControl,
                  wideTableName = 'dW',
                  my_db = my_db)

## # Source:   table<mvtrq_j0vu8nto5jw38f3xmcec_0000000001> [?? x 2]
## # Database: postgres 9.6.1 [postgres@localhost:5432/postgres]
##      group     x
##      <chr> <dbl>
## 1 group_g1     1
## 2 group_g2     5

The point is: using the replyr package you can design in terms of higher-order data transforms, even when working with big data in R. Designs in terms of these operators tend to be succinct, powerful, performant, and maintainable.

To master the terms moveValuesToRows and moveValuesToColumns I suggest trying the following two articles:

• Theory of coordinatized data.
• Fluid data transforms.

if(isSpark) {
  status <- sparklyr::spark_disconnect(my_db)
} else {
  status <- DBI::dbDisconnect(my_db)
}
my_db <- NULL

Categories: Coding Pragmatic Data Science Tutorials

Tagged as: big dat data science Programming R R and big data Statistics

jmount

Data Scientist and trainer at Win Vector LLC. One of the authors of Practical Data Science with R.