Character string representing an SQL select statement or
character vector whose components each represent a successive SQL
statement to be executed.
The select statement syntax must conform to the particular database
being used. If x is missing then it establishes a connection
which subsequent sqldf statements access. In that case the database
is not destroyed until the next sqldf statement with no x.
stringsAsFactors
If TRUE then those columns output
from the database as "character" are
converted to "factor" if the heuristic is unable to determine
the class.
row.names
For TRUE the tables in the data base are given
a row_names column filled with the row names of the corresponding
data frames. Note that in SQLite a special rowid (or equivalently
oid or _rowid_) is available in any case.
envir
The environment where the data frames representing the tables
are to be found.
method
This argument is a list of two functions, keywords or character
vectors. If the second component of the list
is NULL (the default) then the first component
of the list can be specified without wrapping it in a list. The
first component
specifies a transformation of the data frame output from the database
and the second specifies a transformation to each data frame that is
passed to the data base just before it is read into the database.
The second component is less frequently used.
If the first component is NULL or not
specified that it defaults to "auto". If the second component is NULL
or not specified then no transformation is performed on the input.
The allowable keywords for the first components are (1) "auto"
which is the default and automatically assigns the class of each
column using the heuristic described later, (2) "auto.factor" which is
the same as "auto" but does not assign "factor" and
"ordered" classes,
(3) "raw" or NULL which means use
whatever classes are returned by the database with no automatic processing
and (4) "name__class" which
means that columns names that end in __class
with two underscores
where class is an R class (such as Date) are converted to
that class and the __class portion is removed from the column name.
For example,
sqldf("select a as x__Date from DF", method = "name__class")
would cause
column a to be coerced to class Date and have the column name
x.
The first component of method
can also be a character vector of classes to assign to the
returned data.frame. The example just given could alternately be implemented
using
sqldf("select a as x from DF", method = "Date")
Note that when Date is used in this way it assumes the database
contains the number of days since January 1, 1970. If the date is in
the format yyyy-mm-dd then use Date2 as the class.
file.format
A list whose components are passed to
sqliteImportFile. Components may include sep,
header, row.names, skip, eol and filter.
Except for filter they are passed to
sqliteImportFile and have the same default values as
in sqliteImportFile (except for eol which defaults
to the end of line character(s) for the operating system in use – note
that
if the file being read does not have the line endings for the platform
being used then eol will have to be specified. In particular,
certain UNIX-like tools on Windows may produce files with UNIX line endings
in which case eol="\n" should be specified).
filter may optionally contain a batch/shell command through which the
input file is piped prior to reading it in. Alternately filter
may be a list whose first component is a batch/shell command containing
names which correspond to the names of the subsequent list components.
These subsequent components should each be a character
vector which sqldf will read into a temporary file. The name of
the temporary file will be replaced into the command. For example,
filter = list("gawk -f prog", prog = '{ print gensub(/,/, ".", "g") }') .
command line quoting which may vary among shells and Windows.
Note that if the filter produces files with UNIX line endings on Windows
then eol must be specified, as discussed above.
file.format may be set to NULL in order not to search
for input file objects at all. The file.format can also
be specified as an attribute in each file object itself in which case
such specification overrides any given through the argument list. There
is further discussion of file.format below.
dbname
Name of the database. For SQLite and h2 data bases this
defaults to
":memory:" which results in an embedded database. For MySQL this
defaults to getOption("RMysql.dbname") and if that is not specified
then "test" is used.
For RPostgreSQL this
defaults to getOption("sqldf.RPostgreSQL.dbname") and if that is
not specified then "test" is used.
drv
"SQLite", "MySQL", "h2",
"PostgreSQL" or "pgSQL" or any of those names prefaced with
"R".
If not specified then
the "dbDriver" option is checked and if that is not set then
sqldf checks whether RPostgreSQL,
RMySQL or RH2
is loaded in that order and the driver corresponding to the first one
found is used. If none are loaded then "SQLite" is used.
dbname=NULL causes the default to be used.
user
user name. Not needed for embedded databases.
For RPostgreSQL
the default is taken from option sqldf.RPostgreSQL.user and
if that is not specified either then "postgres" is used.
password
password. Not needed for embedded databases.
For RPostgreSQL
the default is taken from option sqldf.RPostgreSQL.password and
if that is not specified then "postgres" is used.
host
host. Default of "localhost" is normally sufficient.
For RPostgreSQL
the default is taken from option sqldf.RPostgreSQL.host and
if that is not specified then "test" is used.
port
port. For RPostgreSQL the default
is taken from the option sqldf.RPostgreSQL.port and if that is not
specified then 5432 is used.
dll
Name of an SQLite loadable extension to automatically load.
If found on PATH then it is
automatically loaded and the SQLite functions it in will be accessible.
connection
If this is NULL then a connection is created;
otherwise the indicated connection is used. The default is
the value of the option sqldf.connection. If neither
connection nor sqldf.connection are specified a connection
is automatically generated on-the-fly and closed on exit of the call to
sqldf. If this argument is not NULL then the specified
connection is left open on termination of the sqldf call. Usually
this argument is left unspecified. It can be used to make repeated calls
to a database without reloading it.
verbose
If TRUE then verboe output shown. Anything else
suppresses verbose output. Can be set globally using option
"sqldf.verbose".
Details
The typical action of sqldf is to
create a database
in memory
read in the data frames and files
used in the select statement.
This is done by scanning the select statement to see which words in
the select statement are of class "data.frame" or "file" in the parent frame, or the
specified environment if envir is used, and for each object
found by reading it into the database if it is a data frame. Note
that this heuristic usually reads in the wanted data frames and files
but on occasion may harmlessly reads in extra ones too.
run the select statement
getting the result as a data frame
assign the classes
of the returned data frame's columns if
method = "auto". This is done by checking all the column
names in the read-in data frames and if any are the same
as a column output from the data base then that column is coerced to the
class of the column whose name matched.
If the class of the column is "factor" or "ordered" or if the
column is not matched then the column is returned
as is. If method = "auto.factor" then processing is similar except
that "factor" and "ordered" classes and their levels will be
assigned as well. The "auto.factor" heuristic
is less reliable than the "auto" heuristic.
If method = "raw" then the classes are returned
as is from the database.
cleanup
If the database was created by sqldf then it is deleted;
otherwise, all tables that were created are dropped in order to leave
the database in the same state that it was before. The database
connection is terminated.
sqldf supports the following R options for RPostgreSQL:
"sqldf.RPostgreSQL.dbname",
"sqldf.RPostgreSQL.user",
"sqldf.RPostgreSQL.password",
"sqldf.RPostgreSQL.host" and
"sqldf.RPostgreSQL.port" which have defaults "test",
"postgres", "postgres", "localhost" and 5432,
respectively. It also supports
"sqldf.RPostgreSQL.other" which is a list of named parameters. These
may include
dbname,
user,
password,
host and
port.
Individually these take precdence over otherwise specified connection
arguments.
Warning. Although sqldf is usually used with on-the-fly databases
which it automatically sets up and destroys if you wish to use it
with existing databases be sure to back up your database prior to
using it since incorrect operation could destroy the entire
database.
Value
The result of the specified select statement is output as a data frame.
If a vector of sql statements is given as x then the result of
the last one is returned. If the x and connection
arguments are missing then it returns a new connection and also places
this connection in the option sqldf.connection.
Note
If row.names = TRUE is used then
any NATURAL JOIN will make use of it which may not be what was
intended.
3/2 and 3.0/2 are the same in R but in SQLite the first one
causes integer arithmetic to be used whereas the second using floating point.
Thus both evaluate to
1.5 in R but they evaluate to 1 and 1.5 respectively in SQLite.
The dbWriteTable/sqliteImportFile routines that sqldf uses to transfer files to the data base are intended for speed and they are not as flexible as read.table. Also they have slightly different defaults. (If more flexible input is needed use the slower read.table to read the data into a data frame instead of reading directly from a file.) The default for sep is sep = ",". If the first row of the file has one fewer entry than subsequent ones then it is assumed that header <- row.names <- TRUE and otherwise that header <- row.names <- FALSE. The header can be forced to header <- TRUE by specifying file.format = list(header = TRUE) as an argument to sqldf.sep and row.names are other file.format subarguments. Also, one limitation with .csv files is that quotes are not regarded as special within files so a comma within a data field such as "Smith, James" would be regarded as a field delimiter and the quotes would be entered as part of the data which probably is not what is intended.
Typically the SQL result will have the same data as the analogous
non-database R code manipulations using data frames
but may differ in row names and other attributes. In the
examples below we use identical in those cases where the two
results are the same in all respects or set the row names to NULL
if they would have otherwise differed only in row names or use
all.equal if the data portion is the same but attributes aside
from row names differ.
On MySQL the database must pre-exist. Create a c:my.ini
or %MYSQL_HOME%my.ini file on Windows or a /etc/my.cnf
file on UNIX to contain information about the database. This file may
specify the username, password and port. The password
can be omitted if one has not been set. If using a standard port
setup then the port can be omitted as well.
The database is taken from the dbname argument of the sqldf
command or if not set from getOption("sqldf.dbname") or if that option
is not set it is assumed to be "test".
Note that MySQL does not use the user, password, host
and codeport arguments of sqldf.
See http://dev.mysql.com/doc/refman/5.6/en/option-files.html for
additional locations that the configuration files can be placed as well
as other information.
If getOption("sqldf.dll") is specified
then the named dll will be loaded as an SQLite loadable extension.
This is in addition to the extension functions included with RSQLite.
References
The sqldf home page http://sqldf.googlecode.com contains
more examples as well as links to SQLite pages that may be helpful in
formulating queries. It also containers pointers to using sqldf with H2
and PostgreSQL.
Examples
#
# These examples show how to run a variety of data frame manipulations
# in R without SQL and then again with SQL
#
# head
a1r <- head(warpbreaks)
a1s <- sqldf("select * from warpbreaks limit 6")
identical(a1r, a1s)
# subset
a2r <- subset(CO2, grepl("^Qn", Plant))
a2s <- sqldf("select * from CO2 where Plant like 'Qn%'")
all.equal(as.data.frame(a2r), a2s)
data(farms, package = "MASS")
a3r <- subset(farms, Manag %in% c("BF", "HF"))
a3s <- sqldf("select * from farms where Manag in ('BF', 'HF')")
row.names(a3r) <- NULL
identical(a3r, a3s)
a4r <- subset(warpbreaks, breaks >= 20 & breaks <= 30)
a4s <- sqldf("select * from warpbreaks where breaks between 20 and 30",
row.names = TRUE)
identical(a4r, a4s)
a5r <- subset(farms, Mois == 'M1')
a5s <- sqldf("select * from farms where Mois = 'M1'", row.names = TRUE)
identical(a5r, a5s)
a6r <- subset(farms, Mois == 'M2')
a6s <- sqldf("select * from farms where Mois = 'M2'", row.names = TRUE)
identical(a6r, a6s)
# rbind
a7r <- rbind(a5r, a6r)
a7s <- sqldf("select * from a5s union all select * from a6s")
# sqldf drops the unused levels of Mois but rbind does not; however,
# all data is the same and the other columns are identical
row.names(a7r) <- NULL
identical(a7r[-1], a7s[-1])
# aggregate - avg conc and uptake by Plant and Type
a8r <- aggregate(iris[1:2], iris[5], mean)
a8s <- sqldf('select Species, avg("Sepal.Length") `Sepal.Length`,
avg("Sepal.Width") `Sepal.Width` from iris group by Species')
all.equal(a8r, a8s)
# by - avg conc and total uptake by Plant and Type
a9r <- do.call(rbind, by(iris, iris[5], function(x) with(x,
data.frame(Species = Species[1],
mean.Sepal.Length = mean(Sepal.Length),
mean.Sepal.Width = mean(Sepal.Width),
mean.Sepal.ratio = mean(Sepal.Length/Sepal.Width)))))
row.names(a9r) <- NULL
a9s <- sqldf('select Species, avg("Sepal.Length") `mean.Sepal.Length`,
avg("Sepal.Width") `mean.Sepal.Width`,
avg("Sepal.Length"/"Sepal.Width") `mean.Sepal.ratio` from iris
group by Species')
all.equal(a9r, a9s)
# head - top 3 breaks
a10r <- head(warpbreaks[order(warpbreaks$breaks, decreasing = TRUE), ], 3)
a10s <- sqldf("select * from warpbreaks order by breaks desc limit 3")
row.names(a10r) <- NULL
identical(a10r, a10s)
# head - bottom 3 breaks
a11r <- head(warpbreaks[order(warpbreaks$breaks), ], 3)
a11s <- sqldf("select * from warpbreaks order by breaks limit 3")
# attributes(a11r) <- attributes(a11s) <- NULL
row.names(a11r) <- NULL
identical(a11r, a11s)
# ave - rows for which v exceeds its group average where g is group
DF <- data.frame(g = rep(1:2, each = 5), t = rep(1:5, 2), v = 1:10)
a12r <- subset(DF, v > ave(v, g, FUN = mean))
Gavg <- sqldf("select g, avg(v) as avg_v from DF group by g")
a12s <- sqldf("select DF.g, t, v from DF, Gavg where DF.g = Gavg.g and v > avg_v")
row.names(a12r) <- NULL
identical(a12r, a12s)
# same but reduce the two select statements to one using a subquery
a13s <- sqldf("select g, t, v
from DF d1, (select g as g2, avg(v) as avg_v from DF group by g)
where d1.g = g2 and v > avg_v")
identical(a12r, a13s)
# same but shorten using natural join
a14s <- sqldf("select g, t, v
from DF
natural join (select g, avg(v) as avg_v from DF group by g)
where v > avg_v")
identical(a12r, a14s)
# table
a15r <- table(warpbreaks$tension, warpbreaks$wool)
a15s <- sqldf("select sum(wool = 'A'), sum(wool = 'B')
from warpbreaks group by tension")
all.equal(as.data.frame.matrix(a15r), a15s, check.attributes = FALSE)
# reshape
t.names <- paste("t", unique(as.character(DF$t)), sep = "_")
a16r <- reshape(DF, direction = "wide", timevar = "t", idvar = "g", varying = list(t.names))
a16s <- sqldf("select
g,
sum((t == 1) * v) t_1,
sum((t == 2) * v) t_2,
sum((t == 3) * v) t_3,
sum((t == 4) * v) t_4,
sum((t == 5) * v) t_5
from DF group by g")
all.equal(a16r, a16s, check.attributes = FALSE)
# order
a17r <- Formaldehyde[order(Formaldehyde$optden, decreasing = TRUE), ]
a17s <- sqldf("select * from Formaldehyde order by optden desc")
row.names(a17r) <- NULL
identical(a17r, a17s)
# centered moving average of length 7
set.seed(1)
DF <- data.frame(x = rnorm(15, 1:15))
s18 <- sqldf("select a.x x, avg(b.x) movavgx from DF a, DF b
where a.row_names - b.row_names between -3 and 3
group by a.row_names having count(*) = 7
order by a.row_names+0",
row.names = TRUE)
r18 <- data.frame(x = DF[4:12,], movavgx = rowMeans(embed(DF$x, 7)))
row.names(r18) <- NULL
all.equal(r18, s18)
# merge. a19r and a19s are same except row order and row names
A <- data.frame(a1 = c(1, 2, 1), a2 = c(2, 3, 3), a3 = c(3, 1, 2))
B <- data.frame(b1 = 1:2, b2 = 2:1)
a19s <- sqldf("select * from A, B")
a19r <- merge(A, B)
Sort <- function(DF) DF[do.call(order, DF),]
all.equal(Sort(a19s), Sort(a19r), check.attributes = FALSE)
# within Date, of the highest quality records list the one closest
# to noon. Note use of two sql statements in one call to sqldf.
Lines <- "DeployID Date.Time LocationQuality Latitude Longitude
STM05-1 2005/02/28 17:35 Good -35.562 177.158
STM05-1 2005/02/28 19:44 Good -35.487 177.129
STM05-1 2005/02/28 23:01 Unknown -35.399 177.064
STM05-1 2005/03/01 07:28 Unknown -34.978 177.268
STM05-1 2005/03/01 18:06 Poor -34.799 177.027
STM05-1 2005/03/01 18:47 Poor -34.85 177.059
STM05-2 2005/02/28 12:49 Good -35.928 177.328
STM05-2 2005/02/28 21:23 Poor -35.926 177.314
"
DF <- read.table(textConnection(Lines), skip = 1, as.is = TRUE,
col.names = c("Id", "Date", "Time", "Quality", "Lat", "Long"))
sqldf(c("create temp table DFo as select * from DF order by
Date DESC, Quality DESC,
abs(substr(Time, 1, 2) + substr(Time, 4, 2) /60 - 12) DESC",
"select * from DFo group by Date"))
## Not run:
# test of file connections with sqldf
# create test .csv file of just 3 records
write.table(head(iris, 3), "iris3.dat", sep = ",", quote = FALSE)
# look at contents of iris3.dat
readLines("iris3.dat")
# set up file connection
iris3 <- file("iris3.dat")
sqldf('select * from iris3 where "Sepal.Width" > 3')
# using a non-default separator
# file.format can be an attribute of file object or an arg passed to sqldf
write.table(head(iris, 3), "iris3.dat", sep = ";", quote = FALSE)
iris3 <- file("iris3.dat")
sqldf('select * from iris3 where "Sepal.Width" > 3', file.format = list(sep = ";"))
# same but pass file.format through attribute of file object
attr(iris3, "file.format") <- list(sep = ";")
sqldf('select * from iris3 where "Sepal.Width" > 3')
# copy file straight to disk without going through R
# and then retrieve portion into R
sqldf('select * from iris3 where "Sepal.Width" > 3', dbname = tempfile())
### same as previous example except it allows multiple queries against
### the database. We use iris3 from before. This time we use an
### in memory SQLite database.
sqldf() # open a connection
sqldf('select * from iris3 where "Sepal.Width" > 3')
# At this point we have an iris3 variable in both
# the R workspace and in the SQLite database so we need to
# explicitly let it know we want the version in the database.
# If we were not to do that it would try to use the R version
# by default and fail since sqldf would prevent it from
# overwriting the version already in the database to protect
# the user from inadvertent errors.
sqldf('select * from main.iris3 where "Sepal.Width" > 4')
sqldf('select * from main.iris3 where "Sepal_Width" < 4')
sqldf() # close connection
### another way to do this is a mix of sqldf and RSQLite statements
### In that case we need to fetch the connection for use with RSQLite
### and do not have to specifically refer to main since RSQLite can
### only access the database.
con <- sqldf()
# this iris3 refers to the R variable and file
sqldf('select * from iris3 where "Sepal.Width" > 3')
sqldf("select count(*) from iris3")
# these iris3 refer to the database table
dbGetQuery(con, 'select * from iris3 where "Sepal.Width" > 4')
dbGetQuery(con, 'select * from iris3 where "Sepal.Width" < 4')
sqldf()
## End(Not run)