R Data Import/export
R Data Import/Export
Version 2.10.1 (2009-12-14)
R Development Core Team
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Copyright c 2000–2009 R Development Core Team
ISBN 3-900051-10-0
i
Table of Contents
Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.1
Imports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2
Export to text files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.3
XML. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2
Spreadsheet-like data . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.1
Variations on read.table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2
Fixed-width-format files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.3
Data Interchange Format (DIF) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.4
Using scan directly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.5
Re-shaping data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.6
Flat contingency tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3
Importing from other statistical systems . . . . 12
3.1
EpiInfo, Minitab, S-PLUS, SAS, SPSS, Stata, Systat . . . . . . . . . . 12
3.2
Octave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
4
Relational databases . . . . . . . . . . . . . . . . . . . . . . . . . . 14
4.1
Why use a database? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
4.2
Overview of RDBMSs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
4.2.1
SQL queries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
4.2.2
Data types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
4.3
R interface packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
4.3.1
Packages DBI and RMySQL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
4.3.2
Package RODBC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
5
Binary files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5.1
Binary data formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5.2
dBase files (DBF) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
6
Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
6.1
Types of connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
6.2
Output to connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
6.3
Input from connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
6.3.1
Pushback . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
6.4
Listing and manipulating connections . . . . . . . . . . . . . . . . . . . . . . . . . 25
6.5
Binary connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
6.5.1
Special values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
ii
7
Network interfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
7.1
Reading from sockets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
7.2
Using download.file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
7.3
DCOM interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
7.4
CORBA interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
8
Reading Excel spreadsheets . . . . . . . . . . . . . . . . . . 29
Appendix A
References . . . . . . . . . . . . . . . . . . . . . . . . 30
Function and variable index . . . . . . . . . . . . . . . . . . . . . . 31
Concept index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Acknowledgements
1
Acknowledgements
The relational databases part of this manual is based in part on an earlier manual by
Douglas Bates and Saikat DebRoy. The principal author of this manual was Brian Ripley.
Many volunteers have contributed to the packages used here. The principal authors of
the packages mentioned are
CORBA
Duncan Temple Lang
foreign
Thomas Lumley, Saikat DebRoy, Douglas Bates, Duncan
Murdoch and Roger Bivand
hdf5
Marcus Daniels
ncdf
David Pierce
ncvar
Juerg Schmidli
rJava
Simon Urbanek
RMySQL
David James and Saikat DebRoy
RNetCDF
Pavel Michna
RODBC
Michael Lapsley and Brian Ripley
RSPerl
Duncan Temple Lang
RSPython
Duncan Temple Lang
SJava
John Chambers and Duncan Temple Lang
XML
Duncan Temple Lang
Brian Ripley is the author of the support for connections.
Chapter 1: Introduction
2
1 Introduction
Reading data into a statistical system for analysis and exporting the results to some other
system for report writing can be frustrating tasks that can take far more time than the
statistical analysis itself, even though most readers will find the latter far more appealing.
This manual describes the import and export facilities available either in R itself or via
packages which are available from CRAN. Some of the packages described are still under
development but they already provide useful functionality.
Unless otherwise stated, everything described in this manual is available on all platforms
running R.
In general, statistical systems like R are not particularly well suited to manipulations of
large-scale data. Some other systems are better than R at this, and part of the thrust of this
manual is to suggest that rather than duplicating functionality in R we can make another
system do the work! (For example Therneau & Grambsch (2000) comment that they prefer
to do data manipulation in SAS and then use survival in S for the analysis.) Several recent
packages allow functionality developed in languages such as Java, perl and python to be
directly integrated with R code, making the use of facilities in these languages even more
appropriate. (See the SJava, RSPerl and RSPython packages from the Omegahat project,
http://www.omegahat.org, and the rJava package from CRAN.)
It is also worth remembering that R like S comes from the Unix tradition of small re-
usable tools, and it can be rewarding to use tools such as awk and perl to manipulate data
before import or after export. The case study in Becker, Chambers & Wilks (1988, Chapter
9) is an example of this, where Unix tools were used to check and manipulate the data
before input to S. R itself takes that approach, using perl to manipulate its databases of
help files rather than R itself, and the function read.fwf used a call to a perl script until
it was decided not to require perl at run-time. The traditional Unix tools are now much
more widely available, including on Windows.
1.1 Imports
The easiest form of data to import into R is a simple text file, and this will often be
acceptable for problems of small or medium scale. The primary function to import from
a text file is scan, and this underlies most of the more convenient functions discussed in
Chapter 2 [Spreadsheet-like data], page 6.
However, all statistical consultants are familiar with being presented by a client with
a floppy disc or CD-R of data in some proprietary binary format, for example ‘an Excel
spreadsheet’ or ‘an SPSS file’. Often the simplest thing to do is to use the originating
application to export the data as a text file (and statistical consultants will have copies of
the most common applications on their computers for that purpose). However, this is not
always possible, and Chapter 3 [Importing from other statistical systems], page 12 discusses
what facilities are available to access such files directly from R. For Excel spreadsheets, the
available methods are summarized in Chapter 8 [Reading Excel spreadsheets], page 29.
In a few cases, data have been stored in a binary form for compactness and speed of
access. One application of this that we have seen several times is imaging data, which
is normally stored as a stream of bytes as represented in memory, possibly preceded by a
Chapter 1: Introduction
3
header. Such data formats are discussed in Chapter 5 [Binary files], page 21 and Section 6.5
[Binary connections], page 25.
For much larger databases it is common to handle the data using a database management
system (DBMS). There is once again the option of using the DBMS to extract a plain file,
but for many such DBMSs the extraction operation can be done directly from an R package:
See Chapter 4 [Relational databases], page 14. Importing data via network connections is
discussed in Chapter 7 [Network interfaces], page 27.
1.2 Export to text files
Exporting results from R is usually a less contentious task, but there are still a number of
pitfalls. There will be a target application in mind, and normally a text file will be the
most convenient interchange vehicle. (If a binary file is required, see Chapter 5 [Binary
files], page 21.)
Function cat underlies the functions for exporting data. It takes a file argument, and
the append argument allows a text file to be written via successive calls to cat. Better,
especially if this is to be done many times, is to open a file connection for writing or
appending, and cat to that connection, then close it.
The most common task is to write a matrix or data frame to file as a rectangular grid
of numbers, possibly with row and column labels.
This can be done by the functions
write.table and write. Function write just writes out a matrix or vector in a specified
number of columns (and transposes a matrix). Function write.table is more convenient,
and writes out a data frame (or an object that can be coerced to a data frame) with row
and column labels.
There are a number of issues that need to be considered in writing out a data frame to
a text file.
1. Precision
Most of the conversions of real/complex numbers done by these functions is to full
precision, but those by write are governed by the current setting of options(digits).
For more control, use format on a data frame, possibly column-by-column.
2. Header line
R prefers the header line to have no entry for the row names, so the file looks like
dist
climb
time
Greenmantle
2.5
650
16.083
...
Some other systems require a (possibly empty) entry for the row names, which is what
write.table will provide if argument col.names = NA is specified. Excel is one such
system.
3. Separator
A common field separator to use in the file is a comma, as that is unlikely to appear in
any of the fields, in English-speaking countries. Such files are known as CSV (comma
separated values) files, and wrapper function write.csv provides appropriate defaults.
In some locales the comma is used as the decimal point (set this in write.table by dec
= ",") and there CSV files use the semicolon as the field separator: use write.csv2
for appropriate defaults.
Chapter 1: Introduction
4
Using a semicolon or tab (sep = "\t") are probably the safest options.
4. Missing values
By default missing values are output as NA, but this may be changed by argument na.
Note that NaNs are treated as NA by write.table, but not by cat nor write.
5. Quoting strings
By default strings are quoted (including the row and column names). Argument quote
controls quoting of character and factor variables.
Some care is needed if the strings contain embedded quotes. Three useful forms are
> df <- data.frame(a = I("a \" quote"))
> write.table(df)
"a"
"1" "a \" quote"
> write.table(df, qmethod = "double")
"a"
"1" "a "" quote"
> write.table(df, quote = FALSE, sep = ",")
a
1,a " quote
The second is the form of escape commonly used by spreadsheets.
Function write.matrix in package MASS provides a specialized interface for writing
matrices, with the option of writing them in blocks and thereby reducing memory usage.
It is possible to use sink to divert the standard R output to a file, and thereby capture
the output of (possibly implicit) print statements. This is not usually the most efficient
route, and the options(width) setting may need to be increased.
Function write.foreign in package foreign uses write.table to produce a text file and
also writes a code file that will read this text file into another statistical package. There is
currently support for export to SPSS and Stata.
1.3 XML
When reading data from text files, it is the responsibility of the user to know and to specify
the conventions used to create that file, e.g. the comment character, whether a header line is
present, the value separator, the representation for missing values (and so on) described in
Section 1.2 [Export to text files], page 3. A markup language which can be used to describe
not only content but also the structure of the content can make a file self-describing, so
that one need not provide these details to the software reading the data.
The eXtensible Markup Language – more commonly known simply as XML – can be
used to provide such structure, not only for standard datasets but also more complex
data structures. XML is becoming extremely popular and is emerging as a standard for
general data markup and exchange. It is being used by different communities to describe
geographical data such as maps, graphical displays, mathematics and so on.
The XML package provides general facilities for reading and writing XML documents
within both R and S-PLUS in the hope that we can easily make use of this technology as it
evolves. Several people are exploring how we can use XML for, amongst other things, repre-
senting datasets to be shared across different applications; storing R and S-PLUS objects so
Chapter 1: Introduction
5
they can be shared by both systems; representing plots via SVG (Scalable Vector Graphics,
a dialect of XML); representing function documentation; generating “live” analyses/reports
that contain text, data and code.
A description of the facilities of the XML package is outside the scope of this document:
see the package’s Web page at http://www.omegahat.org/RSXML for details and examples.
Package StatDataML on CRAN is one example building on XML.
Chapter 2: Spreadsheet-like data
6
2 Spreadsheet-like data
In Section 1.2 [Export to text files], page 3 we saw a number of variations on the format of
a spreadsheet-like text file, in which the data are presented in a rectangular grid, possibly
with row and column labels. In this section we consider importing such files into R.
2.1 Variations on read.table
The function read.table is the most convenient way to read in a rectangular grid of data.
Because of the many possibilities, there are several other functions that call read.table
but change a group of default arguments.
Beware that read.table is an inefficient way to read in very large numerical matrices:
see scan below.
Some of the issues to consider are:
1. Encoding
If the file contains non-ASCII character fields, ensure that it is read in the correct
encoding. This is mainly an issue for reading Latin-1 files in a UTF-8 locale, which
can be done by something like
read.table(file("file.dat", encoding="latin1"))
Note that this will work in any locale which can represent Latin-1 names.
2. Header line
We recommend that you specify the header argument explicitly, Conventionally the
header line has entries only for the columns and not for the row labels, so is one field
shorter than the remaining lines. (If R sees this, it sets header = TRUE.) If presented
with a file that has a (possibly empty) header field for the row labels, read it in by
something like
read.table("file.dat", header = TRUE, row.names = 1)
Column names can be given explicitly via the col.names; explicit names override the
header line (if present).
3. Separator
Normally looking at the file will determine the field separator to be used, but with
white-space separated files there may be a choice between the default sep = "" which
uses any white space (spaces, tabs or newlines) as a separator, sep = " " and sep =
"\t". Note that the choice of separator affects the input of quoted strings.
If you have a tab-delimited file containing empty fields be sure to use sep = "\t".
4. Quoting
By default character strings can be quoted by either ‘"’ or ‘’’, and in each case all the
characters up to a matching quote are taken as part of the character string. The set of
valid quoting characters (which might be none) is controlled by the quote argument.
For sep = "\n" the default is changed to quote = "".
If no separator character is specified, quotes can be escaped within quoted strings by
immediately preceding them by ‘\’, C-style.
If a separator character is specified, quotes can be escaped within quoted strings by
doubling them as is conventional in spreadsheets. For example
Chapter 2: Spreadsheet-like data
7
’One string isn’’t two’,"one more"
can be read by
read.table("testfile", sep = ",")
This does not work with the default separator.
5. Missing values
By default the file is assumed to contain the character string NA to represent missing
values, but this can be changed by the argument na.strings, which is a vector of one
or more character representations of missing values.
Empty fields in numeric columns are also regarded as missing values.
In numeric columns, the values NaN, Inf and -Inf are accepted.
6. Unfilled lines
It is quite common for a file exported from a spreadsheet to have all trailing empty
fields (and their separators) omitted. To read such files set fill = TRUE.
7. White space in character fields
If a separator is specified, leading and trailing white space in character fields is regarded
as part of the field. To strip the space, use argument strip.white = TRUE.
8. Blank lines
By default, read.table ignores empty lines.
This can be changed by setting
blank.lines.skip = FALSE, which will only be useful in conjunction with fill =
TRUE, perhaps to use blank rows to indicate missing cases in a regular layout.
9. Classes for the variables
Unless you take any special action, read.table tries to select a suitable class for each
variable in the data frame. It tries in turn logical, integer, numeric and complex,
moving on if any entry is not missing and cannot be converted.1 If all of these fail, the
variable is converted to a factor.
Arguments colClasses and as.is provide greater control. as.is suppresses conver-
sion of character vectors to factors (only). Using colClasses allows the desired class
to be set for each column in the input.
Note that colClasses and as.is are specified per column, not per variable, and so
include the column of row names (if any).
10. Comments
By default, read.table uses ‘#’ as a comment character, and if this is encountered
(except in quoted strings) the rest of the line is ignored. Lines containing only white
space and a comment are treated as blank lines.
If it is known that there will be no comments in the data file, it is safer (and may be
faster) to use comment.char = "".
11. Escapes
Many OSes have conventions for using backslash as an escape character in text files,
but Windows does not (and uses backslash in path names). It is optional in R whether
such conventions are applied to data files.
1 This is normally fast as looking at the first entry rules out most of the possibilities.
Chapter 2: Spreadsheet-like data
8
Both read.table and scan have a logical argument allowEscapes. As from R 2.2.0
this is false by default, and backslashes are then only interpreted as (under circum-
stances described above) escaping quotes. If this set to be true, C-style escapes are
interpreted, namely the control characters \a, \b, \f, \n, \r, \t, \v and octal and
hexadecimal representations like \040 and \0x2A.
Any other escaped character is
treated as itself, including backslash.
Convenience functions read.csv and read.delim provide arguments to read.table
appropriate for CSV and tab-delimited files exported from spreadsheets in English-speaking
locales. The variations read.csv2 and read.delim2 are appropriate for use in countries
where the comma is used for the decimal point.
If the options to read.table are specified incorrectly, the error message will usually be
of the form
Error in scan(file = file, what = what, sep = sep, :
line 1 did not have 5 elements
or
Error in read.table("files.dat", header = TRUE) :
more columns than column names
This may give enough information to find the problem, but the auxiliary function
count.fields can be useful to investigate further.
Efficiency can be important when reading large data grids.
It will help to specify
comment.char = "", colClasses as one of the atomic vector types (logical, integer, nu-
meric, complex, character or perhaps raw) for each column, and to give nrows, the number
of rows to be read (and a mild over-estimate is better than not specifying this at all). See
the examples below.
2.2 Fixed-width-format files
Sometimes data files have no field delimiters but have fields in pre-specified columns. This
was very common in the days of punched cards, and is still sometimes used to save file
space.
Function read.fwf provides a simple way to read such files, specifying a vector of field
widths. The function reads the file into memory as whole lines, splits the resulting character
strings, writes out a temporary tab-separated file and then calls read.table.
This is
adequate for small files, but for anything more complicated we recommend using the facilities
of a language like perl to pre-process the file.
Function read.fortran is a similar function for fixed-format files, using Fortran-style
column specifications.
2.3 Data Interchange Format (DIF)
An old format sometimes used for spreadsheet-like data is DIF, or Data Interchange format.
Function read.DIF provides a simple way to read such files. It takes arguments similar
to read.table for assigning types to each of the columns.
In Windows, spreadsheets often store spreadsheet data on the clipboard in this format;
read.DIF("clipboard") can read it from there directly. It is slightly more robust than
read.table("clipboard") in handling spreadsheets with empty cells.
Chapter 2: Spreadsheet-like data
9
2.4 Using scan directly
Both read.table and read.fwf use scan to read the file, and then process the results of
scan. They are very convenient, but sometimes it is better to use scan directly.
Function scan has many arguments, most of which we have already covered under
read.table. The most crucial argument is what, which specifies a list of modes of variables
to be read from the file. If the list is named, the names are used for the components of the
returned list. Modes can be numeric, character or complex, and are usually specified by an
example, e.g. 0, "" or 0i. For example
cat("2 3 5 7", "11 13 17 19", file="ex.dat", sep="\n")
scan(file="ex.dat", what=list(x=0, y="", z=0), flush=TRUE)
returns a list with three components and discards the fourth column in the file.
There is a function readLines which will be more convenient if all you want is to read
whole lines into R for further processing.
One common use of scan is to read in a large matrix. Suppose file ‘matrix.dat’ just
contains the numbers for a 200 x 2000 matrix. Then we can use
A <- matrix(scan("matrix.dat", n = 200*2000), 200, 2000, byrow = TRUE)
On one test this took 1 second (under Linux, 3 seconds under Windows on the same machine)
whereas
A <- as.matrix(read.table("matrix.dat"))
took 10 seconds (and more memory), and
A <- as.matrix(read.table("matrix.dat", header = FALSE, nrows = 200,
comment.char = "", colClasses = "numeric"))
took 7 seconds. The difference is almost entirely due to the overhead of reading 2000 separate
short columns: were they of length 2000, scan took 9 seconds whereas read.table took 18
if used efficiently (in particular, specifying colClasses) and 125 if used naively.
Note that timings can depend on the type read and the data. Consider reading a million
distinct integers:
writeLines(as.character((1+1e6):2e6), "ints.dat")
xi <- scan("ints.dat", what=integer(0), n=1e6)
# 0.77s
xn <- scan("ints.dat", what=numeric(0), n=1e6)
# 0.93s
xc <- scan("ints.dat", what=character(0), n=1e6) # 0.85s
xf <- as.factor(xc)
# 2.2s
DF <- read.table("ints.dat")
# 4.5s
and a million examples of a small set of codes:
code <- c("LMH", "SJC", "CHCH", "SPC", "SOM")
writeLines(sample(code, 1e6, replace=TRUE), "code.dat")
y <- scan("code.dat", what=character(0), n=1e6)
# 0.44s
yf <- as.factor(y)
# 0.21s
DF <- read.table("code.dat")
# 4.9s
DF <- read.table("code.dat", nrows=1e6)
# 3.6s
Note that these timings depend heavily on the operating system (the basic reads in
Windows take at least as twice as long as these Linux times) and on the precise state of the
garbage collector.
Chapter 2: Spreadsheet-like data
10
2.5 Re-shaping data
Sometimes spreadsheet data is in a compact format that gives the covariates for each subject
followed by all the observations on that subject. R’s modelling functions need observations
in a single column. Consider the following sample of data from repeated MRI brain mea-
surements
Status
Age
V1
V2
V3
V4
P 23646 45190
50333
55166 56271
CC 26174 35535
38227
37911 41184
CC 27723 25691
25712
26144 26398
CC 27193 30949
29693
29754 30772
CC 24370 50542
51966
54341 54273
CC 28359 58591
58803
59435 61292
CC 25136 45801
45389
47197 47126
There are two covariates and up to four measurements on each subject. The data were
exported from Excel as a file ‘mr.csv’.
We can use stack to help manipulate these data to give a single response.
zz <- read.csv("mr.csv", strip.white = TRUE)
zzz <- cbind(zz[gl(nrow(zz), 1, 4*nrow(zz)), 1:2], stack(zz[, 3:6]))
with result
Status
Age values ind
X1
P 23646
45190
V1
X2
CC 26174
35535
V1
X3
CC 27723
25691
V1
X4
CC 27193
30949
V1
X5
CC 24370
50542
V1
X6
CC 28359
58591
V1
X7
CC 25136
45801
V1
X11
P 23646
50333
V2
...
Function unstack goes in the opposite direction, and may be useful for exporting data.
Another way to do this is to use the function reshape, by
> reshape(zz, idvar="id",timevar="var",
varying=list(c("V1","V2","V3","V4")),direction="long")
Status
Age var
V1 id
1.1
P 23646
1 45190
1
2.1
CC 26174
1 35535
2
3.1
CC 27723
1 25691
3
4.1
CC 27193
1 30949
4
5.1
CC 24370
1 50542
5
6.1
CC 28359
1 58591
6
7.1
CC 25136
1 45801
7
1.2
P 23646
2 50333
1
2.2
CC 26174
2 38227
2
...
Chapter 2: Spreadsheet-like data
11
The reshape has a more complicated syntax than stack but can be used for data where
the ‘long’ form has more than the one column in this example. With direction="wide",
reshape can also perform the opposite transformation.
2.6 Flat contingency tables
Displaying higher-dimensional contingency tables in array form typically is rather incon-
venient. In categorical data analysis, such information is often represented in the form of
bordered two-dimensional arrays with leading rows and columns specifying the combina-
tion of factor levels corresponding to the cell counts. These rows and columns are typically
“ragged” in the sense that labels are only displayed when they change, with the obvious
convention that rows are read from top to bottom and columns are read from left to right.
In R, such “flat” contingency tables can be created using ftable, which creates objects of
class "ftable" with an appropriate print method.
As a simple example, consider the R standard data set UCBAdmissions which is a 3-
dimensional contingency table resulting from classifying applicants to graduate school at
UC Berkeley for the six largest departments in 1973 classified by admission and sex.
> data(UCBAdmissions)
> ftable(UCBAdmissions)
Dept
A
B
C
D
E
F
Admit
Gender
Admitted Male
512 353 120 138
53
22
Female
89
17 202 131
94
24
Rejected Male
313 207 205 279 138 351
Female
19
8 391 244 299 317
The printed representation is clearly more useful than displaying the data as a 3-dimensional
array.
There is also a function read.ftable for reading in flat-like contingency tables from files.
This has additional arguments for dealing with variants on how exactly the information on
row and column variables names and levels is represented. The help page for read.ftable
has some useful examples. The flat tables can be converted to standard contingency tables
in array form using as.table.
Note that flat tables are characterized by their “ragged” display of row (and maybe also
column) labels. If the full grid of levels of the row variables is given, one should instead use
read.table to read in the data, and create the contingency table from this using xtabs.
Chapter 3: Importing from other statistical systems
12
3 Importing from other statistical systems
In this chapter we consider the problem of reading a binary data file written by another
statistical system. This is often best avoided, but may be unavoidable if the originating
system is not available.
3.1 EpiInfo, Minitab, S-PLUS, SAS, SPSS, Stata, Systat
The recommended package foreign provides import facilities for files produced by these
statistical systems, and for export to Stata. In some cases these function may require
substantially less memory than read.table would. write.foreign (See Section 1.2 [Export
to text files], page 3) provides an export mechanism with support currently for SPSS and
Stata.
EpiInfo versions 5 and 6 stored data in a self-describing fixed-width text format.
read.epiinfo will read these ‘.REC’ files into an R data frame. EpiData also produces
data in this format.
Function read.mtp imports a ‘Minitab Portable Worksheet’. This returns the compo-
nents of the worksheet as an R list.
Function read.xport reads a file in SAS Transport (XPORT) format and return a list
of data frames. If SAS is available on your system, function read.ssd can be used to
create and run a SAS script that saves a SAS permanent dataset (‘.ssd’ or ‘.sas7bdat’)
in Transport format. It then calls read.xport to read the resulting file. (Package Hmisc
has a similar function sas.get, also running SAS.) For those without access to SAS but
running on Windows, the SAS System Viewer (a zero-cost download) can be used to open
SAS datasets and export them to e.g. ‘.csv’ format.
Function read.S which can read binary objects produced by S-PLUS 3.x, 4.x or 2000
on (32-bit) Unix or Windows (and can read them on a different OS). This is able to read
many but not all S objects: in particular it can read vectors, matrices and data frames and
lists containing those.
Function data.restore reads S-PLUS data dumps (created by data.dump) with
the same restrictions (except that dumps from the Alpha platform can also be read).
It should be possible to read data dumps from S-PLUS 5.x and later written with
data.dump(oldStyle=T).
If you have access to S-PLUS, it is usually more reliable to dump the object(s) in S-PLUS
and source the dump file in R. For S-PLUS 5.x and 6.x you may need to use dump(...,
oldStyle=T), and to read in very large objects it may be preferable to use the dump file
as a batch script rather than use the source function.
Function read.spss can read files created by the ‘save’ and ‘export’ commands in SPSS.
It returns a list with one component for each variable in the saved data set. SPSS variables
with value labels are optionally converted to R factors.
SPSS Data Entry is an application for creating data entry forms. By default it creates
data files with extra formatting information that read.spss cannot handle, but it is possible
to export the data in an ordinary SPSS format.
Stata ‘.dta’ files are a binary file format. Files from versions 5, 6, 7/SE and 8 of Stata
can be read and written by functions read.dta and write.dta. Stata variables with value
labels are optionally converted to (and from) R factor.
Chapter 3: Importing from other statistical systems
13
read.systat reads those Systat SAVE files that are rectangular data files (mtype = 1)
written on little-endian machines (such as from Windows). These have extension ‘.sys’ or
(more recently) ‘.syd’.
3.2 Octave
Octave is a numerical linear algebra system (http://www.octave.org), and function
read.octave in package foreign can read in files in Octave text data format created
using the Octave command save -ascii, with support for most of the common types of
variables, including the standard atomic (real and complex scalars, matrices, and N -d
arrays, strings, ranges, and boolean scalars and matrices) and recursive (structs, cells, and
lists) ones.
Chapter 4: Relational databases
14
4 Relational databases
4.1 Why use a database?
There are limitations on the types of data that R handles well. Since all data being manip-
ulated by R are resident in memory, and several copies of the data can be created during
execution of a function, R is not well suited to extremely large data sets. Data objects that
are more than a (few) hundred megabytes in size can cause R to run out of memory.
R does not easily support concurrent access to data. That is, if more than one user is
accessing, and perhaps updating, the same data, the changes made by one user will not be
visible to the others.
R does support persistence of data, in that you can save a data object or an entire
worksheet from one session and restore it at the subsequent session, but the format of the
stored data is specific to R and not easily manipulated by other systems.
Database management systems (DBMSs) and, in particular, relational DBMSs
(RDBMSs) are designed to do all of these things well. Their strengths are
1. To provide fast access to selected parts of large databases.
2. Powerful ways to summarize and cross-tabulate columns in databases.
3. Store data in more organized ways than the rectangular grid model of spreadsheets and
R data frames.
4. Concurrent access from multiple clients running on multiple hosts while enforcing se-
curity constraints on access to the data.
5. Ability to act as a server to a wide range of clients.
The sort of statistical applications for which DBMS might be used are to extract a 10%
sample of the data, to cross-tabulate data to produce a multi-dimensional contingency table,
and to extract data group by group from a database for separate analysis.
Increasingly OSes are themselves making use of DBMSs for these reasons, so it is nowa-
days likely that one will be already installed on your (non-Windows) OS. Akonadi is used
by KDE4 to store personal information and uses MySQL. Several Mac OS X applications,
including Mail and Address Book, use SQLite.
4.2 Overview of RDBMSs
Traditionally there had been large (and expensive) commercial RDBMSs (Informix; Oracle;
Sybase; IBM’s DB2; Microsoft SQL Server on Windows) and academic and small-system
databases (such as MySQL, PostgreSQL, Microsoft Access, . . . ), the former marked out
by much greater emphasis on data security features. The line is blurring, with the Open
Source MySQL and PostgreSQL having more and more high-end features, and free ‘express’
versions being made available for the commercial DBMSs.
There are other commonly used data sources, including spreadsheets, non-relational
databases and even text files (possibly compressed).
Open Database Connectivity
(ODBC) is a standard to use all of these data sources. It originated on Windows (see
http://www.microsoft.com/data/odbc/) but is also implemented on Linux/Unix.
Chapter 4: Relational databases
15
All of the packages described later in this chapter provide clients to client/server data-
bases. The database can reside on the same machine or (more often) remotely. There is an
ISO standard (in fact several: SQL92 is ISO/IEC 9075, also known as ANSI X3.135-1992,
and SQL99 is coming into use) for an interface language called SQL (Structured Query Lan-
guage, sometimes pronounced ‘sequel’: see Bowman et al. 1996 and Kline and Kline 2001)
which these DBMSs support to varying degrees.
4.2.1 SQL queries
The more comprehensive R interfaces generate SQL behind the scenes for common opera-
tions, but direct use of SQL is needed for complex operations in all. Conventionally SQL is
written in upper case, but many users will find it more convenient to use lower case in the
R interface functions.
A relational DBMS stores data as a database of tables (or relations) which are rather
similar to R data frames, in that they are made up of columns or fields of one type (numeric,
character, date, currency, . . . ) and rows or records containing the observations for one entity.
SQL ‘queries’ are quite general operations on a relational database. The classical query
is a SELECT statement of the type
SELECT State, Murder FROM USArrests WHERE Rape > 30 ORDER BY Murder
SELECT t.sch, c.meanses, t.sex, t.achieve
FROM student as t, school as c WHERE t.sch = c.id
SELECT sex, COUNT(*) FROM student GROUP BY sex
SELECT sch, AVG(sestat) FROM student GROUP BY sch LIMIT 10
The first of these selects two columns from the R data frame USArrests that has been
copied across to a database table, subsets on a third column and asks the results be sorted.
The second performs a database join on two tables student and school and returns four
columns.
The third and fourth queries do some cross-tabulation and return counts or
averages. (The five aggregation functions are COUNT(*) and SUM, MAX, MIN and AVG,
each applied to a single column.)
SELECT queries use FROM to select the table, WHERE to specify a condition for
inclusion (or more than one condition separated by AND or OR), and ORDER BY to sort
the result. Unlike data frames, rows in RDBMS tables are best thought of as unordered,
and without an ORDER BY statement the ordering is indeterminate. You can sort (in
lexicographical order) on more than one column by separating them by commas. Placing
DESC after an ORDER BY puts the sort in descending order.
SELECT DISTINCT queries will only return one copy of each distinct row in the selected
table.
The GROUP BY clause selects subgroups of the rows according to the criterion. If more
than one column is specified (separated by commas) then multi-way cross-classifications
can be summarized by one of the five aggregation functions. A HAVING clause allows the
select to include or exclude groups depending on the aggregated value.
If the SELECT statement contains an ORDER BY statement that produces a unique
ordering, a LIMIT clause can be added to select (by number) a contiguous block of output
Chapter 4: Relational databases
16
rows. This can be useful to retrieve rows a block at a time. (It may not be reliable unless
the ordering is unique, as the LIMIT clause can be used to optimize the query.)
There are queries to create a table (CREATE TABLE, but usually one copies a data
frame to the database in these interfaces), INSERT or DELETE or UPDATE data. A table
is destroyed by a DROP TABLE ‘query’.
Kline and Kline (2001) discuss the details of the implementation of SQL in SQL Server
2000, Oracle, MySQL and PostgreSQL.
4.2.2 Data types
Data can be stored in a database in various data types. The range of data types is DBMS-
specific, but the SQL standard defines many types, including the following that are widely
implemented (often not by the SQL name).
float(p )
Real number, with optional precision. Often called real or double or double
precision.
integer
32-bit integer. Often called int.
smallint
16-bit integer
character(n )
fixed-length character string. Often called char.
character varying(n )
variable-length character string. Often called varchar. Almost always has a
limit of 255 chars.
boolean
true or false. Sometimes called bool or bit.
date
calendar date
time
time of day
timestamp
date and time
There are variants on time and timestamp, with timezone. Other types widely imple-
mented are text and blob, for large blocks of text and binary data, respectively.
The more comprehensive of the R interface packages hide the type conversion issues from
the user.
4.3 R interface packages
There are several packages available on CRAN to help R communicate with DBMSs. They
provide different levels of abstraction. Some provide means to copy whole data frames to
and from databases. All have functions to select data within the database via SQL queries,
and to retrieve the result as a whole as a data frame or in pieces (usually as groups of rows).
All except RODBC are tied to one DBMS, but work is in progress towards a uni-
fied ‘front-end’ package DBI (http://developer.r-project.org/db) in conjunction with
a ‘back-end’, the most developed of which is RMySQL. Also on CRAN are the back-
ends ROracle, RPostgreSQL and RSQLite (which works with the bundled DBMS SQLite,
http://www.sqlite.org).
Chapter 4: Relational databases
17
Two earlier packages RmSQL and RPgSQL are now unsupported and in the archive area
on CRAN: the BioConductor project has updated RdbiPgSQL (formerly on CRAN). PL/R
(http://www.joeconway.com/plr/) is a project to embed R into PostgreSQL.
4.3.1 Packages DBI and RMySQL
Package RMySQL on CRAN provides an interface to the MySQL database system (see
http://www.mysql.com and Dubois, 2000.). The description here applies to version 0.5-0:
earlier versions had a substantially different interface. The current version requires the DBI
package, and this description will apply with minor changes to all the other back-ends to
DBI.
MySQL exists on Unix/Linux and Windows: as from version 3.23.x (Jan 2001) it is
released under GPL. MySQL is a ‘light and lean’ database. (It preserves the case of names
where the operating file system is case-sensitive, so not on Windows.) Package RMySQL
has been used on both Linux and Windows.
The call dbDriver("MySQL") returns a database connection manager object, and then a
call to dbConnect opens a database connection which can subsequently be closed by a call to
the generic function dbDisconnect. Use dbDriver("Oracle"), dbdDriver("PostgreSQL")
or dbDriver("SQLite") with those DBMSs and packages ROracle, PostgreSQL or RSQLite
respectively.
SQL queries can be sent by either dbSendQuery or dbGetQuery. dbGetquery sends the
query and retrieves the results as a data frame. dbSendQuery sends the query and returns
an object of class inheriting from "DBIResult" which can be used to retrieve the results,
and subsequently used in a call to dbClearResult to remove the result.
Function fetch is used to retrieve some or all of the rows in the query result, as a list. The
function dbHasCompleted indicates if all the rows have been fetched, and dbGetRowCount
returns the number of rows in the result.
These are convenient interfaces to read/write/test/delete tables in the database.
dbReadTable and dbWriteTable copy to and from an R data frame, mapping the row
names of the data frame to the field row_names in the MySQL table.
> library(RMySQL) # will load DBI as well
## open a connection to a MySQL database
> con <- dbConnect(dbDriver("MySQL"), dbname = "test")
## list the tables in the database
> dbListTables(con)
## load a data frame into the database, deleting any existing copy
> data(USArrests)
> dbWriteTable(con, "arrests", USArrests, overwrite = TRUE)
TRUE
> dbListTables(con)
[1] "arrests"
## get the whole table
> dbReadTable(con, "arrests")
Murder Assault UrbanPop Rape
Alabama
13.2
236
58 21.2
Alaska
10.0
263
48 44.5
Arizona
8.1
294
80 31.0
Arkansas
8.8
190
50 19.5
...
## Select from the loaded table
> dbGetQuery(con, paste("select row_names, Murder from arrests",
Chapter 4: Relational databases
18
"where Rape > 30 order by Murder"))
row_names Murder
1
Colorado
7.9
2
Arizona
8.1
3 California
9.0
4
Alaska
10.0
5 New Mexico
11.4
6
Michigan
12.1
7
Nevada
12.2
8
Florida
15.4
> dbRemoveTable(con, "arrests")
> dbDisconnect(con)
4.3.2 Package RODBC
Package RODBC on CRAN provides an interface to database sources supporting an ODBC
interface. This is very widely available, and allows the same R code to access different
database systems. RODBC runs on Unix/Linux, Windows and Mac OS X, and almost all
database systems provide support for ODBC. We have tested Microsoft SQL Server, Access,
MySQL, PostgreSQL, Oracle and IBM DB2 on Windows and MySQL, Oracle, PostgreSQL
and SQLite on Linux.
ODBC is a client-server system, and we have happily connected to a DBMS running on
a Unix server from a Windows client, and vice versa.
On Windows ODBC support is normally installed, and current versions are available
from http://www.microsoft.com/data/odbc/ as part of MDAC. On Unix/Linux you will
need an ODBC Driver Manager such as unixODBC (http://www.unixODBC.org) or iOBDC
(http://www.iODBC.org: this is pre-installed in Mac OS X) and an installed driver for your
database system.
Windows provides drivers not just for DBMSs but also for Excel (‘.xls’) spreadsheets,
DBase (‘.dbf’) files and even text files. (The named applications do not need to be installed.
Which file formats are supported depends on the the versions of the drivers.) There are
versions for Excel 2007 and Access 2007 (go to http://download.microsoft.com, and
search for ‘Office ODBC’, which will lead to ‘AccessDatabaseEngine.exe’), the ‘2007 Office
System Driver’.
On Mac OS X the Actual Technologies (http://www.actualtechnologies.com/product_
access.php) drivers provide ODBC interfaces to Access databases (including Access 2007)
and to Excel spreadsheets.
Many simultaneous connections are possible.
A connection is opened by a call to
odbcConnect or odbcDriverConnect (which on the Windows GUI allows a database to
be selected via dialog boxes) which returns a handle used for subsequent access to the data-
base. Printing a connection will provide some details of the ODBC connection, and calling
odbcGetInfo will give details on the client and server.
A connection is closed by a call to close or odbcClose, and also (with a warning) when
not R object refers to it and at the end of an R session.
Details of the tables on a connection can be found using sqlTables.
Function sqlSave copies an R data frame to a table in the database, and sqlFetch
copies a table in the database to an R data frame.
Chapter 4: Relational databases
19
An SQL query can be sent to the database by a call to sqlQuery. This returns the
result in an R data frame. (sqlCopy sends a query to the database and saves the result as
a table in the database.) A finer level of control is attained by first calling odbcQuery and
then sqlGetResults to fetch the results. The latter can be used within a loop to retrieve
a limited number of rows at a time, as can function sqlFetchMore.
Here is an example using PostgreSQL, for which the ODBC driver maps column and
data frame names to lower case. We use a database testdb we created earlier, and had
the DSN (data source name) set up in ‘~/.odbc.ini’ under unixODBC. Exactly the same
code worked using MyODBC to access a MySQL database under Linux or Windows (where
MySQL also maps names to lowercase). Under Windows, DSNs are set up in the ODBC
applet in the Control Panel (‘Data Sources (ODBC)’ in the ‘Administrative Tools’ section).
> library(RODBC)
## tell it to map names to l/case
> channel <- odbcConnect("testdb", uid="ripley", case="tolower")
## load a data frame into the database
> data(USArrests)
> sqlSave(channel, USArrests, rownames = "state", addPK = TRUE)
> rm(USArrests)
## list the tables in the database
> sqlTables(channel)
TABLE_QUALIFIER TABLE_OWNER TABLE_NAME TABLE_TYPE REMARKS
1
usarrests
TABLE
## list it
> sqlFetch(channel, "USArrests", rownames = "state")
murder assault urbanpop rape
Alabama
13.2
236
58 21.2
Alaska
10.0
263
48 44.5
...
## an SQL query, originally on one line
> sqlQuery(channel, "select state, murder from USArrests
where rape > 30 order by murder")
state murder
1 Colorado
7.9
2 Arizona
8.1
3 California
9.0
4 Alaska
10.0
5 New Mexico
11.4
6 Michigan
12.1
7 Nevada
12.2
8 Florida
15.4
## remove the table
> sqlDrop(channel, "USArrests")
## close the connection
> odbcClose(channel)
As a simple example of using ODBC under Windows with a Excel spreadsheet, we can
read from a spreadsheet by
> library(RODBC)
> channel <- odbcConnectExcel("bdr.xls")
## list the spreadsheets
> sqlTables(channel)
TABLE_CAT TABLE_SCHEM
TABLE_NAME
TABLE_TYPE REMARKS
1 C:\\bdr
NA
Sheet1$ SYSTEM TABLE
NA
2 C:\\bdr
NA
Sheet2$ SYSTEM TABLE
NA
Chapter 4: Relational databases
20
3 C:\\bdr
NA
Sheet3$ SYSTEM TABLE
NA
4 C:\\bdr
NA Sheet1$Print_Area
TABLE
NA
## retrieve the contents of sheet 1, by either of
> sh1 <- sqlFetch(channel, "Sheet1")
> sh1 <- sqlQuery(channel, "select * from [Sheet1$]")
Notice that the specification of the table is different from the name returned by sqlTables:
sqlFetch is able to map the differences.
Chapter 5: Binary files
21
5 Binary files
Binary connections (Chapter 6 [Connections], page 22) are now the preferred way to handle
binary files.
5.1 Binary data formats
Packages
hdf5,
RNetCDF
and
ncdf
on
CRAN
provide
interfaces
to
NASA’s
HDF5
(Hierarchical
Data
Format,
see
http://hdf.ncsa.uiuc.edu/HDF5/)
and
to
UCAR’s
netCDF
data
files
(network
Common
Data
Form,
see
http://www.unidata.ucar.edu/packages/netcdf/).
Both of these are systems to store scientific data in array-oriented ways, including de-
scriptions, labels, formats, units, . . . . HDF5 also allows groups of arrays, and the R interface
maps lists to HDF5 groups, and can write numeric and character vectors and matrices.
Package ncvar on CRAN provides a higher-level R interface to netCDF data files via
RNetCDF.
There is also a package rhdf5 available from http://www.bioconductor.org.
5.2 dBase files (DBF)
dBase was a DOS program written by Ashton-Tate and later owned by Borland which
has a binary flat-file format that became popular, with file extension ‘.dbf’.
It has
been adopted for the ’Xbase’ family of databases, covering dBase, Clipper, FoxPro
and their Windows equivalents Visual dBase, Visual Objects and Visual FoxPro (see
http://www.e-bachmann.dk/docs/xbase.htm). A dBase file contains a header and then
a series of fields and so is most similar to an R data frame. The data itself is stored in
text format, and can include character, logical and numeric fields, and other types in later
versions (see http://clicketyclick.dk/docs/data_types.html).
Functions read.dbf and write.dbf provide ways to read and write basic DBF files on
all R platforms. For Windows users odbcConnectDbase in package RODBC provides more
comprehensive facilities to read DBF files via Microsoft’s dBase ODBC driver (and the
Visual FoxPro driver can also be used via odbcDriverConnect).
Chapter 6: Connections
22
6 Connections
Connections are used in R in the sense of Chambers (1998), a set of functions to replace
the use of file names by a flexible interface to file-like objects.
6.1 Types of connections
The most familiar type of connection will be a file, and file connections are created by
function file. File connections can (if the OS will allow it for the particular file) be opened
for reading or writing or appending, in text or binary mode. In fact, files can be opened for
both reading and writing, and R keeps a separate file position for reading and writing.
Note that by default a connection is not opened when it is created. The rule is that
a function using a connection should open a connection (needed) if the connection is not
already open, and close a connection after use if it opened it. In brief, leave the connection
in the state you found it in. There are generic functions open and close with methods to
explicitly open and close connections.
Files compressed via the algorithm used by gzip can be used as connections created by
the function gzfile, whereas files compressed by bzip2 can be used via bzfile.
Unix programmers are used to dealing with special files stdin, stdout and stderr.
These exist as terminal connections in R. They may be normal files, but they might also
refer to input from and output to a GUI console. (Even with the standard Unix R interface,
stdin refers to the lines submitted from readline rather than a file.)
The three terminal connections are always open, and cannot be opened or closed. stdout
and stderr are conventionally used for normal output and error messages respectively. They
may normally go to the same place, but whereas normal output can be re-directed by a
call to sink, error output is sent to stderr unless re-directed by sink, type="message").
Note carefully the language used here: the connections cannot be re-directed, but output
can be sent to other connections.
Text connections are another source of input. They allow R character vectors to be read
as if the lines were being read from a text file. A text connection is created and opened by
a call to textConnection, which copies the current contents of the character vector to an
internal buffer at the time of creation.
Text connections can also be used to capture R output to a character vector.
textConnection can be asked to create a new character object or append to an existing
one, in both cases in the user’s workspace.
The connection is opened by the call to
textConnection, and at all times the complete lines output to the connection are available
in the R object. Closing the connection writes any remaining output to a final element of
the character vector.
Pipes are a special form of file that connects to another process, and pipe connections
are created by the function pipe. Opening a pipe connection for writing (it makes no sense
to append to a pipe) runs an OS command, and connects its standard input to whatever
R then writes to that connection. Conversely, opening a pipe connection for input runs an
OS command and makes its standard output available for R input from that connection.
URLs of types ‘http://’, ‘ftp://’ and ‘file://’ can be read from using the function
url. For convenience, file will also accept these as the file specification and call url.
Chapter 6: Connections
23
Sockets can also be used as connections via function socketConnection on platforms
which support Berkeley-like sockets (most Unix systems, Linux and Windows). Sockets can
be written to or read from, and both client and server sockets can be used.
6.2 Output to connections
We have described functions cat, write, write.table and sink as writing to a file, possibly
appending to a file if argument append = TRUE, and this is what they did prior to R version
1.2.0.
The current behaviour is equivalent, but what actually happens is that when the file
argument is a character string, a file connection is opened (for writing or appending) and
closed again at the end of the function call. If we want to repeatedly write to the same file,
it is more efficient to explicitly declare and open the connection, and pass the connection
object to each call to an output function. This also makes it possible to write to pipes,
which was implemented earlier in a limited way via the syntax file = "|cmd" (which can
still be used).
There is a function writeLines to write complete text lines to a connection.
Some simple examples are
zz <- file("ex.data", "w")
# open an output file connection
cat("TITLE extra line", "2 3 5 7", "", "11 13 17",
file = zz, sep = "\n")
cat("One more line\n", file = zz)
close(zz)
## convert decimal point to comma in output, using a pipe (Unix)
## both R strings and (probably) the shell need \ doubled
zz <- pipe(paste("sed s/\\\\./,/ >", "outfile"), "w")
cat(format(round(rnorm(100), 4)), sep = "\n", file = zz)
close(zz)
## now look at the output file:
file.show("outfile", delete.file = TRUE)
## capture R output: use examples from help(lm)
zz <- textConnection("ex.lm.out", "w")
sink(zz)
example(lm, prompt.echo = "> ")
sink()
close(zz)
## now ‘ex.lm.out’ contains the output for futher processing.
## Look at it by, e.g.,
cat(ex.lm.out, sep = "\n")
6.3 Input from connections
The basic functions to read from connections are scan and readLines.
These take a
character string argument and open a file connection for the duration of the function call,
Chapter 6: Connections
24
but explicitly opening a file connection allows a file to be read sequentially in different
formats.
Other functions that call scan can also make use of connections, in particular
read.table.
Some simple examples are
## read in file created in last examples
readLines("ex.data")
unlink("ex.data")
## read listing of current directory (Unix)
readLines(pipe("ls -1"))
# remove trailing commas from an input file.
# Suppose we are given a file ‘data’ containing
450, 390, 467, 654,
30, 542, 334, 432, 421,
357, 497, 493, 550, 549, 467, 575, 578, 342,
446, 547, 534, 495, 979, 479
# Then read this by
scan(pipe("sed -e s/,$// data"), sep=",")
For convenience, if the file argument specifies a FTP or HTTP URL, the URL is opened
for reading via url. Specifying files via ‘file://foo.bar’ is also allowed.
6.3.1 Pushback
C programmers may be familiar with the ungetc function to push back a character onto a
text input stream. R connections have the same idea in a more powerful way, in that an
(essentially) arbitrary number of lines of text can be pushed back onto a connection via a
call to pushBack.
Pushbacks operate as a stack, so a read request first uses each line from the most recently
pushbacked text, then those from earlier pushbacks and finally reads from the connection
itself. Once a pushbacked line is read completely, it is cleared. The number of pending lines
pushed back can be found via a call to pushBackLength.
A simple example will show the idea.
> zz <- textConnection(LETTERS)
> readLines(zz, 2)
[1] "A" "B"
> scan(zz, "", 4)
Read 4 items
[1] "C" "D" "E" "F"
> pushBack(c("aa", "bb"), zz)
> scan(zz, "", 4)
Read 4 items
[1] "aa" "bb" "G"
"H"
> close(zz)
Pushback is only available for connections opened for input in text mode.
Chapter 6: Connections
25
6.4 Listing and manipulating connections
A summary of all the connections currently opened by the user can be found by
showConnections(), and a summary of all connections, including closed and terminal
connections, by showConnections(all = TRUE)
The generic function seek can be used to read and (on some connections) reset the
current position for reading or writing. Unfortunately it depends on OS facilities which
may be unreliable (e.g. with text files under Windows). Function isSeekable reports if
seek can change the position on the connection given by its argument.
The function truncate can be used to truncate a file opened for writing at its current
position. It works only for file connections, and is not implemented on all platforms.
6.5 Binary connections
Functions readBin and writeBin read to and write from binary connections. A connection
is opened in binary mode by appending "b" to the mode specification, that is using mode
"rb" for reading, and mode "wb" or "ab" (where appropriate) for writing. The functions
have arguments
readBin(con, what, n = 1, size = NA, endian = .Platform$endian)
writeBin(object, con, size = NA, endian = .Platform$endian)
In each case con is a connection which will be opened if necessary for the duration of
the call, and if a character string is given it is assumed to specify a file name.
It is slightly simpler to describe writing, so we will do that first. object should be an
atomic vector object, that is a vector of mode numeric, integer, logical, character,
complex or raw, without attributes. By default this is written to the file as a stream of
bytes exactly as it is represented in memory.
readBin reads a stream of bytes from the file and interprets them as a vector of mode
given by what. This can be either an object of the appropriate mode (e.g. what=integer())
or a character string describing the mode (one of the five given in the previous paragraph
or "double" or "int"). Argument n specifies the maximum number of vector elements to
read from the connection: if fewer are available a shorter vector will be returned. Argument
signed allows 1-byte and 2-byte integers to be read as signed (the default) or unsigned
integers.
The remaining two arguments are used to write or read data for interchange with another
program or another platform. By default binary data is transferred directly from memory to
the connection or vice versa. This will not suffice if the file is to be transferred to a machine
with a different architecture, but between almost all R platforms the only change needed
is that of byte-order. Common PCs (‘ix86’-based and ‘x86_64’-based machines), Compaq
Alpha and Vaxen are little-endian, whereas Sun Sparc, mc680x0 series, IBM R6000, Apple
Macintosh, SGI and most others are big-endian. (Network byte-order (as used by XDR,
eXternal Data Representation) is big-endian.) To transfer to or from other programs we
may need to do more, for example to read 16-bit integers or write single-precision real
numbers. This can be done using the size argument, which (usually) allows sizes 1, 2, 4,
8 for integers and logicals, and sizes 4, 8 and perhaps 12 or 16 for reals. Transferring at
different sizes can lose precision, and should not be attempted for vectors containing NA’s.
Chapter 6: Connections
26
Character strings are read and written in C format, that is as a string of bytes terminated
by a zero byte. Functions readChar and writeChar provide greater flexibility.
6.5.1 Special values
Functions readBin and writeBin will pass missing and special values, although this should
not be attempted if a size change is involved.
The missing value for R logical and integer types is INT_MIN, the smallest representable
int defined in the C header ‘limits.h’, normally corresponding to the bit pattern
0x80000000.
The representation of the special values for R numeric and complex types is machine-
dependent, and possibly also compiler-dependent. The simplest way to make use of them is
to link an external application against the standalone Rmath library which exports double
constants NA_REAL, R_PosInf and R_NegInf, and include the header ‘Rmath.h’ which defines
the macros ISNAN and R_FINITE.
If that is not possible, on all common platforms IEC 60559 (aka IEEE 754) arithmetic
is used, so standard C facilities can be used to test for or set Inf, -Inf and NaN values. On
such platforms NA is represented by the NaN value with low-word 0x7a2 (1954 in decimal).
Character missing values are written as NA, and there are no provision to recognize
character values as missing (as this can be done by re-assigning them once read).
Chapter 7: Network interfaces
27
7 Network interfaces
Some limited facilities are available to exchange data at a lower level across network con-
nections.
7.1 Reading from sockets
Base R comes with some facilities to communicate via BSD sockets on systems that support
them (including the common Linux, Unix and Windows ports of R). One potential problem
with using sockets is that these facilities are often blocked for security reasons or to force
the use of Web caches, so these functions may be more useful on an intranet than externally.
For new projects it is suggested that socket connections are used instead.
The earlier low-level interface is given by functions make.socket, read.socket,
write.socket and close.socket.
7.2 Using download.file
Function download.file is provided to read a file from a Web resource via FTP or HTTP
and write it to a file. Often this can be avoided, as functions such as read.table and
scan can read directly from a URL, either by explicitly using url to open a connection, or
implicitly using it by giving a URL as the file argument.
7.3 DCOM interface
DCOM is a Windows protocol for communicating between different programs, possibly on
different machines. Thomas Baier’s StatConnector program available from CRAN under
Software->Other->Non-standard provides an interface to the proxy DLL in package rscproxy
and makes an DCOM server. This can be used to pass simple objects (vectors and matrices)
to and from R and to submit commands to R. (It is not clear if this is still functional: there
is another version in the RExcelInstaller package.)
The program comes with a Visual Basic demonstration and an Excel plug-in by Erich
Neuwirth available. This interface is in the other direction to most of those considered here
in that it is another application (Excel, or written in Visual Basic) that is the client and R
is the server.
Another (D)COM server is available from http://www.omegahat.org/, which allows
R objects to be exported as COM values. That site also has packages RDCOMClient and
SWinTypeLibs which allow R to act as a (D)COM client.
7.4 CORBA interface
CORBA (Common Object Request Broker Architecture) is similar to DCOM, allowing
applications to call methods,
or operations,
in server objects running in other
applications, potentially programmed in different languages and running on different
machines.
There is a CORBA package available from the Omegahat project (at
http://www.omegahat.org/RSCORBA/), currently for Unix but a Windows version looks
to be possible.
This package allows R commands to be used to locate available CORBA servers, query
the methods they provide, and dynamically invoke methods on these objects. R values given
Chapter 7: Network interfaces
28
as arguments in these calls are exported in the call and made available to that operation
invocation. Primitive data types (vectors and lists) are exported by default, while more
complex objects are exported by reference. Examples of using this include communicating
with the Gnumeric (http://www.gnumeric.org) spreadsheet, and also interacting with the
data visualization system ggobi.
One can also create CORBA servers within R, allowing other applications to call these
methods. For example, one might offer access to a particular dataset or to some of R’s
modelling software. This is done dynamically by combining R data objects and functions.
This allows one to explicitly export data and functionality from R.
One can also use the CORBA package to achieve distributed, parallel computing in
R. One R session acts as a manager and dispatches tasks to different servers running in
other R worker sessions.
This uses the ability to invoke asynchronous or background
CORBA calls in R. More information is available from the Omegahat project at
http://www.omegahat.org/RSCORBA/.
Chapter 8: Reading Excel spreadsheets
29
8 Reading Excel spreadsheets
The most common R data import/export question seems to be ‘how do I read an Excel
spreadsheet’. This chapter collects together advice and options given earlier. Note that
most of the advice is for pre-Excel 2007 spreadsheets: currently the only one of these
methods that reads the ‘.xlsx’ format is that via RODBC, but see also the Omegahat
package RExcelXML.
The first piece of advice is to avoid doing so if possible! If you have access to Ex-
cel, export the data you want from Excel in tab-delimited or comma-separated form, and
use read.delim or read.csv to import it into R. (You may need to use read.delim2
or read.csv2 in a continental European locale that uses comma as the decimal point.)
Exporting a DIF file and reading it using read.DIF is another possibility.
If
you
do
not
have
Excel,
many
other
programs
are
able
to
read
such
spreadsheets and export in a text format on both Windows and Unix, for ex-
ample
Gnumeric
(http://www.gnome.org/projects/gnumeric/)
and
OpenOffice
(http://www.openoffice.org).
You can also cut-and-paste between the display of a
spreadsheet in such a program and R: read.table will read from the R console or,
under Windows, from the clipboard (via file = "clipboard" or readClipboard). The
read.DIF function can also read from the clipboard.
Note that an Excel ‘.xls’ file is not just a spreadsheet: such files can contain many
sheets, and the sheets can contain formulae, macros and so on. Not all readers can read
other than the first sheet, and may be confused by other contents of the file.
Windows users can use odbcConnectExcel in package RODBC. This can select rows and
columns from any of the sheets in an Excel spreadsheet file (at least from Excel 97–2003,
depending on your ODBC drivers: by calling odbcConnect directly versions back to Excel
3.0 can be read). The version odbcConnectExcel2007 will read the Excel 2007 formats
as well as earlier ones (provided the drivers are installed: see Section 4.3.2 [RODBC],
page 18). Mac users can also use RODBC if they have a suitable driver (e.g. that from
Actual Technologies).
Perl users have contributed a module OLE::SpreadSheet::ParseExcel and a program
xls2csv.pl to convert Excel 95–2003 spreadsheets to CSV files. Package gdata provides a
basic wrapper in its read.xls function.
Windows-only package xlsReadWrite from http://treetron.googlepages.com/ has a
function read.xls to read ‘.xls’ files (based on a third-party non-Open Source Delphi
component).
Packages dataframes2xls and WriteXLS each contain a function to write one or more data
frames to an ‘.xls’ file, using Python and Perl respectively. Another version of write.xls
in available in package xlsReadWrite.
Appendix A: References
30
Appendix A References
R. A. Becker, J. M. Chambers and A. R. Wilks (1988) The New S Language. A Programming
Environment for Data Analysis and Graphics. Wadsworth & Brooks/Cole.
J. Bowman, S. Emberson and M. Darnovsky (1996) The Practical SQL Handbook. Using
Structured Query Language. Addison-Wesley.
J. M. Chambers (1998) Programming with Data. A Guide to the S Language. Springer-
Verlag.
P. Dubois (2000) MySQL. New Riders.
M. Henning and S. Vinoski (1999) Advanced CORBA Programming with C++. Addison-
Wesley.
K. Kline and D. Kline (2001) SQL in a Nutshell. O’Reilly.
B. Momjian (2000) PostgreSQL: Introduction and Concepts. Addison-Wesley. Also down-
loadable at http://www.postgresql.org/docs/awbook.html.
T. M. Therneau and P. M. Grambsch (2000) Modeling Survival Data. Extending the Cox
Model. Springer-Verlag.
E. J. Yarger, G. Reese and T. King (1999) MySQL & mSQL. O’Reilly.
Function and variable index
31
Function and variable index
.
N
.dbf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
netCDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
.xls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18, 19
O
B
odbcClose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
odbcConnect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
bzfile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
odbcConnectDbase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
odbcConnectExcel . . . . . . . . . . . . . . . . . . . . . . . . . 19, 29
C
odbcConnectExcel2007 . . . . . . . . . . . . . . . . . . . . . . . . 29
odbcDriverConnect . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
cat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3, 23
odbcGetInfo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
close . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18, 22
odbcQuery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
close.socket . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
open . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
count.fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
D
P
pipe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
data.restore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
pushBack. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
dataframes2xls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
pushBackLength . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
dbClearResult . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
dbConnect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
dbDisconnect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
R
dbDriver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
read.csv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8, 29
dbExistsTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
read.csv2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
dbGetQuery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
read.dbf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
dbReadTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
read.delim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8, 29
dbRemoveTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
read.delim2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
dbSendQuery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
read.DIF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8, 29
dbWriteTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
read.dta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
read.epiinfo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
F
read.fortran . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
read.ftable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
fetch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
read.fwf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
read.mtp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
read.octave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
ftable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
read.S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
read.socket . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
G
read.spss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
read.systat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
gzfile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
read.table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6, 23, 29
read.xls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
read.xport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
H
readBin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
hdf5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
readChar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
readClipboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
readLines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9, 23
I
reshape . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
isSeekable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
S
M
scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2, 9, 23
make.socket . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
seek . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
showConnections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Function and variable index
32
sink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4, 23
url . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
socketConnection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
sqlCopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
sqlFetch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
W
sqlFetchMore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
write . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3, 23
sqlGetResults . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
sqlQuery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
write.csv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
sqlSave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
write.csv2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
sqlTables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
write.dbf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
stack . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
write.dta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
stderr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
write.foreign . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
stdin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
write.matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
stdout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
write.socket . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Sys.localeconv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
write.table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3, 23
writeBin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
T
writeChar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
writeLines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
textConnection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
WriteXLS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
truncate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
U
X
unstack. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
xlsReadWrite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Concept index
33
Concept index
A
MySQL database system . . . . . . . . . . . . . . . . . . . 17, 19
AWK . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
N
B
network Common Data Form . . . . . . . . . . . . . . . . . . 21
Binary files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21, 25
O
C
Octave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
comma separated values . . . . . . . . . . . . . . . . . . . . . . . . 3
ODBC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14, 18
Compressed files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Open Database Connectivity . . . . . . . . . . . . . . . 14, 18
Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22, 23, 25
CORBA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
P
CSV files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3, 8
perl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2, 8
Pipe connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
D
PostgreSQL database system . . . . . . . . . . . . . . . . . . 19
Data Interchange Format (DIF) . . . . . . . . . . . . . . . . . 8
Pushback on a connection . . . . . . . . . . . . . . . . . . . . . 24
dBase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Dbase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Q
DBF files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
DBMS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Quoting strings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4, 6
DCOM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
R
E
Re-shaping data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
EpiData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Relational databases . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
EpiInfo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Excel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18, 19
S
Exporting to a text file . . . . . . . . . . . . . . . . . . . . . . . . . 3
S-PLUS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
SAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
F
Sockets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22, 27
File connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Spreadsheet-like data . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Fixed-width-format files . . . . . . . . . . . . . . . . . . . . . . . . 8
SPSS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Flat contingency tables . . . . . . . . . . . . . . . . . . . . . . . . 11
SPSS Data Entry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
SQL queries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Stata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
H
Systat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Hierarchical Data Format . . . . . . . . . . . . . . . . . . . . . . 21
T
I
Terminal connections . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Importing from other statistical systems . . . . . . . 12
Text connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
L
U
locales . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Unix tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
URL connections . . . . . . . . . . . . . . . . . . . . . . . . . . . 22, 24
M
X
Minitab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Missing values. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4, 7
XML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Document Outline
- Acknowledgements
- Introduction
- Imports
- Export to text files
- XML
- Spreadsheet-like data
- Variations on read.table
- Fixed-width-format files
- Data Interchange Format (DIF)
- Using scan directly
- Re-shaping data
- Flat contingency tables
- Importing from other statistical systems
- EpiInfo, Minitab, S-PLUS, SAS, SPSS, Stata, Systat
- Octave
- Relational databases
- Why use a database?
- Overview of RDBMSs
- R interface packages
- Packages DBI and RMySQL
- Package RODBC
- Binary files
- Binary data formats
- dBase files (DBF)
- Connections
- Types of connections
- Output to connections
- Input from connections
- Listing and manipulating connections
- Binary connections
- Network interfaces
- Reading from sockets
- Using download.file
- DCOM interface
- CORBA interface
- Reading Excel spreadsheets
- References
- Function and variable index
- Concept index
