Data Management Using R – Interfacing with the Structured Query Language

1. Data Management Using R – Interfacing with the Structured Query Language STAT 7550 – Statistical Computing Utah State University November 21, 2008 Bill Welbourn

2. Objectives of the Project • Introduce the notion of the database. • Database applications. • General overview of the SQLite Relational Database Management System (RDBMS). • Explain how R1 (and other programming languages) interfaces with the SQLite RDBMS. Highlights of the R commands for the interface to the SQLite RDBMS, the RSQLite library. • A working example, demonstrating the procedure for storing and retrieving an R dataframe within a SQLite database. • Further motivation for the use of the R-SQLite interface, working with “massive” databases. 1R Development Core Team (2008), Version 2.8.0.

3. Database What is a Database? • Essentially a series of structured files on a computer that are organized in a highly efficient manner. • The organization is comprised in a hierarchical manner, from the “top, down,” as shown in Figure 1 below. Figure 1: The anatomy of a database

4. Components of a Table • As Figure 1 suggests, at the highest level, a database is comprised of a series of tables. • Each table is made up of a series of columns. Think of the columns as characteristics (variables) collected for a study. • Data is stored in rows of the table, where each row of the table is called a record. Records of a table are essentially synonymous with observations for a study. • The location where each row intersects a column is known as a field. • Each table contains specific, common data. A table of a database is analogous to a worksheet within an Excel workbook.

5. What is a Relational Database? • It is a database comprised of tables which relate to one another. The table relationships are based on “Key fields.” • To illustrate, consider two relational tables within a database. A column of each table is affixed with the same naming convention, say “ID.” Each field within these columns is designated a unique (key) label, so that a one-to-one (relationship) mapping between the tables is obtained. Figure 2: Example of two relational tables

6. Three Types of Relationships • One-to-One • A record in table one must have a record in table two, and vice-versa. Example: More variables (columns) were collected in a study than allowed to be stored in a single database table. Study participants (observations/records) are labeled with unique ID’s which allow for the table-to-table relationship to be established. • One-to-Many • A record in table one has many corresponding records in table two, while table two has many records which correspond to a single record in table one. Example: Study participant identifiers (unique ID’s) are stored in table one, while repeated measurements are stored in table two. • Many-to-Many • Like the one-to-many relationship, table one has many corresponding records in table two. However, unlike the one-to-many relationship, table two has many corresponding records in table one. Example: Customer product orders. Each order can contain multiple products, and one product can be in many orders.

7. Database Applications • World Wide Web. • Medical Data. • Data analysis situations which warrant the consideration in utilizing a database: • You possess a flat (text) file(s) with an inordinate number of observations. • You have collected an insurmountable quantity of characteristics for your observations (e.g., genetic data). • You are ready to execute a large simulation analysis. • You need to prepare a portable file, so that another statistician has easy access to your data. • Anytime there is data in your possession. It is fairly straightforward to maintain a SQL database in R.

8. The SQLite RDBMS • Created by D. Richard Hipp. Version 1.0 releasedAugust 17, 2000. Most recent version, 3.6.4, releasedOctober 15, 2008. • An ACID (Atomicity, Consistency, Isolation, Durability) compliant RDBMS. In computer science, ACID is a set of properties which guarantee that database transactions (logical operations) are processed reliably. • Contained in a relatively small (~500kB) C programming library. • It is not a database, rather a system which manages databases. Microsoft Access, in contrast, is simply a program used to create a database.

9. The SQLite RDBMS (cont.) • The columns of a table for a SQL database, typically are assigned a “type” (e.g., string, integer, float, double). This is analogous to defining variables in the C programming language. However, SQLite (automatically) assigns types to individual values. • Allows for multithread reading of a database. The writing of a database can only occur if no other access to the database is present. • Interfacing with programming languages (e.g., BASIC, C, C++, Perl, Ruby, and R). • Most widely deployed SQL RDBMS.

10. Interfacing the SQLite RDBMS • Consists of three components: The application (such as R) which requires access to the database; an interface; and the RDBMS. • An interface acts as an interpreter, translating commands from the application, so that the database is accessible to the user. In R, the interface lies within the DBI library. • The interface communicates with the database via the applicable database driver. The database driver knows how to “talk” to the database. In R, the SQLite database driver and the source (C library) for the SQLite engine are included within the RSQLite library.

11. The R-SQLite Interface Figure 3: The process flow between the application and the database Application (e.g., R) Interface (e.g.,DBI library in R) Driver (e.g., SQLite in R) Database

12. Accessing a SQLite DB • A five step cycle: • Connect to the database. In R, to establish the connection to a database, issue the commands: dbDriver(); and dbConnect(). • Issue a query or command to the database. To issue a query in R, the command, dbSendQuery(), is (typically) used. Queries consist of SQL commands. setwd("c:/SQL"); library(DBI); library(RSQLite) dbfile<-"DATA.dbsql"; drv<-dbDriver("SQLite") con<-dbConnect(drv,dbname = dbfile) rs <- dbSendQuery(con, "select v1,v2,v3 from Table1 where v1==1") rs<-dbSendQuery(con,"select * from Table1")

13. Accessing a SQLite DB (cont.) • If a query was issued, we need to retrieve the applicable recordset. To do this in R, we use the command, fetch(). The recordset will exist as a dataframe in R. • Clear the query result, manipulate the recordset, and update the database. To clear a query in R, use the command, dbClearResult(). To update a database, issue the R command, dbWriteTable(). • Close the connection to the database. To do this in R, use the command, dbDisconnect(). d1<-fetch(rs, n = -1) dbClearResult(rs) dbWriteTable(con, “Table”, data frame, append, row.names, overwrite) dbDisconnect(con)

14. Example 1 • You have recorded n (unique) observations (records) for a study, and collected m-1 characteristics (excluding the unique observation identifier) for each observation. Having the option to store your data as a flat file or as a (single table) SQL database, which should you choose? • To address this issue, you decide to conduct a (small) simulation analysis, investigating data retrieval times for the two types of data repositories. Figure 4, shown on the subsequent slide, displays the results from a simulation, where m=50 and each (of the 49) characteristic is of type “double.” A total of 100 distinct values of n, n1,…,n100, were chosen, in accordance to the rule

15. Example 1 (cont.) Figure 4: Flat file – DB comparison

16. Example 2 • You have recorded data for n (unique) participants of a study, and collected m-1 characteristics (excluding the unique observation identifier) for each participant. Further, for the ith participant, you have recorded a total of i record(s). Having the option to store your data as a flat file or as a (single table) SQL database, which should you choose? Given the unique identifier for a participant, suppose it is desirable to have quick access to the records for each participant. • Figures 5 and 6, shown on the subsequent slides, display the results of data retrieval times, where n=200 and n=500, respectively, m=50, where each variable type is “double”. The displayed value for the vertical axis, is the required time to read in the i records for the ith participant.

17. Example 2 (cont.) Figure 5: Flat file – DB comparison, marginal read I

18. Example 2 (cont.) Figure 6: Flat file – DB comparison, marginal read II

19. Example 3 • You have recorded data for n (unique) participants of a study, and collected allele types at more than two million (2x106) single nucleotide polymophism (SNP) sites in the human nuclear genome. How could we utilize a relational database to represent the repository for these data? • It turns out that a SQLite database table is limited to 999 columns. So, we simply create a sufficient number of tables (each with say m columns), and populate the tabular columns with the SNP data, making sure to create a “Key” column for each table. • Figures 7 and 8, display the required time (by database table) to retrieve the first two columns – the “Key” along with a column of data – for SQL databases of size n=2,500 and n=25,000, respectively. For each database, a total of 2,106 tables were created, where m=951 columns for each database table. That is, these two databases, comprise slightly greater than five billion and 50 billion fields, respectively.

20. Example 3 (cont.) Figure 7: Retrieval Time for a Massive SQL Database I

21. Example 3 (cont.) Figure 8: Retrieval Time for a Massive SQL Database II

22. Example 3 (cont.) Figure 9: Retrieval Time for a Massive SQL Database III

23. Conclusion • Database advantages • Ability to store an extraordinary quantity of data. On a Windows NT platform, a SQL table can be as large as 2TB; on 64-bit operating systems, there is virtually no limit to the size of a SQL table. • A single file could be utilized as a central data warehouse. • Ability to create tabular relationships. • Database indexing makes for very fast data retrieval. • Portability. • Interfacing with programming languages. • Multithreading. • Database disadvantages • Can be a bit of a challenge to recall, “What data, lives in which table?” • There is no “safety net” when it comes to overwriting data in a database. • Essentially having to learn a new programming (querying) language. • Database administration is industry requires continuous careful maintenance.

24. References • Hogan, R (2002). A practical guide to database design. Prentice Hall, • Englewood Cliffs, NJ. • This is a good resource to obtain a working knowledge of what a database is all about. It covers the issues (e.g., who will use the database, and what should the database contain), say an employer, would consider prior to implementing a database in practice. It does not, however, discuss how to create and maintain the database, from a programming point of view (I.e., the SQL commands). • Maslakowski M, Butcher T (2000). SAMS teach yourself MySQL in 21 days. • Macmillan USA, Indianapolis, IN • Although the Windows version of R does not have the RMySQL binary package, this book is an excellent resource to “getting your feet wet” with the SQL programming language. The book lacks the theme of what the Hogan (2002) book comprises. Namely, the source does not talk about strategies in database design. • R Special Interest Group on Databases (R-SIG-DB). A common database • interface (DBI). Software version 0.2-4 retrieved from http://cran.r-project.org/, • September 27, 2008. • The DBI package is necessary (but not sufficient) to interface any database with R (see slide 11). The DBI.pdf (available at the web link provided above) is a good document to review, prior to creating your first database in R. It provides an overview of the DBI package, and like most programming in R, to learn (effective) database management in R will require practice through working with data frames.