The following examples try to follow “An Introduction to R” which can be found at http://cran.r-project.org/doc/manuals/R-intro.html .
EXAMPLES:
Simple manipulations; numbers and vectors
The simplest data structure in R is the numeric vector which
consists of an ordered collection of numbers. To create a
vector named using the R interface in Sage, you pass the
R interpreter object a list or tuple of numbers:
sage: x = r([10.4,5.6,3.1,6.4,21.7]); x
[1] 10.4 5.6 3.1 6.4 21.7
You can invert elements of a vector x in R by using the invert operator or by doing 1/x:
sage: ~x
[1] 0.09615385 0.17857143 0.32258065 0.15625000 0.04608295
sage: 1/x
[1] 0.09615385 0.17857143 0.32258065 0.15625000 0.04608295
The following assignment creates a vector with 11 entries which
consists of two copies of
with a 0 in between:
sage: y = r([x,0,x]); y
[1] 10.4 5.6 3.1 6.4 21.7 0.0 10.4 5.6 3.1 6.4 21.7
Vector Arithmetic
The following command generates a new vector of length 11 constructed
by adding together (element by element)
repeated 2.2 times,
repeated just once, and 1 repeated 11 times:
sage: v = 2*x+y+1; v
[1] 32.2 17.8 10.3 20.2 66.1 21.8 22.6 12.8 16.9 50.8 43.5
One can compute the sum of the elements of an R vector in the following two ways:
sage: sum(x)
[1] 47.2
sage: x.sum()
[1] 47.2
One can calculate the sample variance of a list of numbers:
sage: ((x-x.mean())^2/(x.length()-1)).sum()
[1] 53.853
sage: x.var()
[1] 53.853
sage: x.sort()
[1] 3.1 5.6 6.4 10.4 21.7
sage: x.min()
[1] 3.1
sage: x.max()
[1] 21.7
sage: x
[1] 10.4 5.6 3.1 6.4 21.7
sage: r(-17).sqrt()
[1] NaN
sage: r('-17+0i').sqrt()
[1] 0+4.123106i
Generating an arithmetic sequence:
sage: r('1:10')
[1] 1 2 3 4 5 6 7 8 9 10
Because from is a keyword in Python, it can’t be used as a keyword argument. Instead, from_ can be passed, and R will recognize it as the correct thing:
sage: r.seq(length=10, from_=-1, by=.2)
[1] -1.0 -0.8 -0.6 -0.4 -0.2 0.0 0.2 0.4 0.6 0.8
sage: x = r([10.4,5.6,3.1,6.4,21.7]);
sage: x.rep(2)
[1] 10.4 5.6 3.1 6.4 21.7 10.4 5.6 3.1 6.4 21.7
sage: x.rep(times=2)
[1] 10.4 5.6 3.1 6.4 21.7 10.4 5.6 3.1 6.4 21.7
sage: x.rep(each=2)
[1] 10.4 10.4 5.6 5.6 3.1 3.1 6.4 6.4 21.7 21.7
Missing Values:
sage: na = r('NA')
sage: z = r([1,2,3,na])
sage: z
[1] 1 2 3 NA
sage: ind = r.is_na(z)
sage: ind
[1] FALSE FALSE FALSE TRUE
sage: zero = r(0)
sage: zero / zero
[1] NaN
sage: inf = r('Inf')
sage: inf-inf
[1] NaN
sage: r.is_na(inf)
[1] FALSE
sage: r.is_na(inf-inf)
[1] TRUE
sage: r.is_na(zero/zero)
[1] TRUE
sage: r.is_na(na)
[1] TRUE
sage: r.is_nan(inf-inf)
[1] TRUE
sage: r.is_nan(zero/zero)
[1] TRUE
sage: r.is_nan(na)
[1] FALSE
Character Vectors:
sage: labs = r.paste('c("X","Y")', '1:10', sep='""'); labs
[1] "X1" "Y2" "X3" "Y4" "X5" "Y6" "X7" "Y8" "X9" "Y10"
Index vectors; selecting and modifying subsets of a data set:
sage: na = r('NA')
sage: x = r([10.4,5.6,3.1,6.4,21.7,na]); x
[1] 10.4 5.6 3.1 6.4 21.7 NA
sage: x['!is.na(self)']
[1] 10.4 5.6 3.1 6.4 21.7
sage: x = r([10.4,5.6,3.1,6.4,21.7,na]); x
[1] 10.4 5.6 3.1 6.4 21.7 NA
sage: (x+1)['(!is.na(self)) & self>0']
[1] 11.4 6.6 4.1 7.4 22.7
sage: x = r([10.4,-2,3.1,-0.5,21.7,na]); x
[1] 10.4 -2.0 3.1 -0.5 21.7 NA
sage: (x+1)['(!is.na(self)) & self>0']
[1] 11.4 4.1 0.5 22.7
Distributions:
sage: r.options(width="60");
$width
[1] 100
sage: rr = r.dnorm(r.seq(-3,3,0.1))
sage: rr
[1] 0.004431848 0.005952532 0.007915452 0.010420935
[5] 0.013582969 0.017528300 0.022394530 0.028327038
[9] 0.035474593 0.043983596 0.053990967 0.065615815
[13] 0.078950158 0.094049077 0.110920835 0.129517596
[17] 0.149727466 0.171368592 0.194186055 0.217852177
[21] 0.241970725 0.266085250 0.289691553 0.312253933
[25] 0.333224603 0.352065327 0.368270140 0.381387815
[29] 0.391042694 0.396952547 0.398942280 0.396952547
[33] 0.391042694 0.381387815 0.368270140 0.352065327
[37] 0.333224603 0.312253933 0.289691553 0.266085250
[41] 0.241970725 0.217852177 0.194186055 0.171368592
[45] 0.149727466 0.129517596 0.110920835 0.094049077
[49] 0.078950158 0.065615815 0.053990967 0.043983596
[53] 0.035474593 0.028327038 0.022394530 0.017528300
[57] 0.013582969 0.010420935 0.007915452 0.005952532
[61] 0.004431848
Convert R Data Structures to Python/Sage:
sage: rr = r.dnorm(r.seq(-3,3,0.1))
sage: sum(rr._sage_())
9.9772125168981...
Or you get a dictionary to be able to access all the information:
sage: rs = r.summary(r.c(1,4,3,4,3,2,5,1))
sage: rs
Min. 1st Qu. Median Mean 3rd Qu. Max.
1.000 1.750 3.000 2.875 4.000 5.000
sage: d = rs._sage_()
sage: d['DATA']
[1, 1.75, 3, 2.875, 4, 5]
sage: d['_Names']
['Min.', '1st Qu.', 'Median', 'Mean', '3rd Qu.', 'Max.']
sage: d['_r_class']
['summaryDefault', 'table']
It is also possible to access the plotting capabilities of R through Sage. For more information see the documentation of r.plot() or r.png().
AUTHORS:
Bases: sage.interfaces.expect.Expect
An interface to the R interpreter.
R is a comprehensive collection of methods for statistics, modelling, bioinformatics, data analysis and much more. For more details, see http://www.r-project.org/about.html
Resources:
EXAMPLES:
sage: r.summary(r.c(1,2,3,111,2,3,2,3,2,5,4))
Min. 1st Qu. Median Mean 3rd Qu. Max.
1.00 2.00 3.00 12.55 3.50 111.00
TESTS:
sage: r == loads(dumps(r))
True
Returns a list of all available R package names.
This list is not necessarily sorted.
OUTPUT: list of strings
Note
This requires an internet connection. The CRAN server is that is checked is defined at the top of sage/interfaces/r.py.
EXAMPLES:
sage: ap = r.available_packages() # optional - internet
sage: len(ap) > 20 #optional
True
This is an alias for function_call().
EXAMPLES:
sage: r.call('length', [1,2,3])
[1] 3
Changes the working directory to dir
INPUT:
EXAMPLES:
sage: import tempfile
sage: tmpdir = tempfile.mkdtemp()
sage: r.chdir(tmpdir)
Check that tmpdir and r.getwd() refer to the same directory. We need to use realpath() in case $TMPDIR (by default /tmp) is a symbolic link (see trac ticket #10264).
sage: os.path.realpath(tmpdir) == sageobj(r.getwd()) # known bug (:trac:`9970`)
True
Return all commands names that complete the command starting with the string s. This is like typing s[Ctrl-T] in the R interpreter.
INPUT:
OUTPUT: list – a list of strings
EXAMPLES:
sage: dummy = r.trait_names(use_disk_cache=False) #clean doctest
sage: r.completions('tes')
['testInheritedMethods', 'testPlatformEquivalence', 'testVirtual']
Runs the R console as a separate new R process.
EXAMPLES:
sage: r.console() # not tested
R version 2.6.1 (2007-11-26)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
...
Converts an R list to a Python list.
EXAMPLES:
sage: s = 'c(".GlobalEnv", "package:stats", "package:graphics", "package:grDevices", \n"package:utils", "package:datasets", "package:methods", "Autoloads", \n"package:base")'
sage: r.convert_r_list(s)
['.GlobalEnv',
'package:stats',
'package:graphics',
'package:grDevices',
'package:utils',
'package:datasets',
'package:methods',
'Autoloads',
'package:base']
Evaluates a command inside the R interpreter and returns the output as a string.
EXAMPLES:
sage: r.eval('1+1')
'[1] 2'
Return the result of calling an R function, with given args and keyword args.
OUTPUT: RElement – an object in R
EXAMPLES:
sage: r.function_call('length', args=[ [1,2,3] ])
[1] 3
Returns the string representation of the variable var.
INPUT:
OUTPUT: string
EXAMPLES:
sage: r.set('a', 2)
sage: r.get('a')
'[1] 2'
Returns help string for a given command.
INPUT: - command – a string
OUTPUT: HelpExpression – a subclass of string whose __repr__ method is __str__, so it prints nicely
EXAMPLES:
sage: r.help('print.anova')
anova package:stats R Documentation
...
Chambers, J. M. and Hastie, T. J. (1992) _Statistical Models in
S_, Wadsworth & Brooks/Cole.
...
Note
This is similar to typing r.command?.
Install an R package into Sage’s R installation.
EXAMPLES:
sage: r.install_packages('aaMI') # not tested
...
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
...
Please restart Sage in order to use 'aaMI'.
Load the library library_name into the R interpreter.
This function raises an ImportError if the given library is not known.
INPUT:
EXAMPLES:
sage: r.library('grid')
sage: 'grid' in r.eval('(.packages())')
True
sage: r.library('foobar')
Traceback (most recent call last):
...
ImportError: ...
Returns the NA in R.
OUTPUT: RElement – an element of R
EXAMPLES:
sage: r.na()
[1] NA
The R plot function. Type r.help(‘plot’) for much more extensive documentation about this function. See also below for a brief introduction to more plotting with R.
If one simply wants to view an R graphic, using this function is is sufficient (because it calls dev.off() to turn off the device).
However, if one wants to save the graphic to a specific file, it should be used as in the example below to write the output.
EXAMPLES:
This example saves a plot to the standard R output, usually a filename like Rplot001.png - from the command line, in the current directory, and in the cell directory in the notebook:
sage: d=r.setwd('"%s"'%SAGE_TMP) # for doctesting only; ignore if you are trying this;
sage: r.plot("1:10") # optional -- rgraphics
null device
1
To save to a specific file name, one should use png() to set the output device to that file. If this is done in the notebook, it must be done in the same cell as the plot itself:
sage: filename = tmp_filename() + '.png'
sage: r.png(filename='"%s"'%filename) # Note the double quotes in single quotes!; optional -- rgraphics
NULL
sage: x = r([1,2,3])
sage: y = r([4,5,6])
sage: r.plot(x,y) # optional -- rgraphics
null device
1
sage: import os; os.unlink(filename) # For doctesting, we remove the file; optional -- rgraphics
Please note that for more extensive use of R’s plotting capabilities (such as the lattices package), it is advisable to either use an interactive plotting device or to use the notebook. The following examples are not tested, because they differ depending on operating system:
sage: r.X11() # not tested - opens interactive device on systems with X11 support
sage: r.quartz() # not tested - opens interactive device on OSX
sage: r.hist("rnorm(100)") # not tested - makes a plot
sage: r.library("lattice") # not tested - loads R lattice plotting package
sage: r.histogram(x = "~ wt | cyl", data="mtcars") # not tested - makes a lattice plot
sage: r.dev_off() # not tested, turns off the interactive viewer
In the notebook, one can use r.png() to open the device, but would need to use the following since R lattice graphics do not automatically print away from the command line:
sage: filename = tmp_filename() + '.png' # Not needed in notebook, used for doctesting
sage: r.png(filename='"%s"'%filename) # filename not needed in notebook, used for doctesting; optional -- rgraphics
NULL
sage: r.library("lattice")
sage: r("print(histogram(~wt | cyl, data=mtcars))") # plot should appear; optional -- rgraphics
sage: import os; os.unlink(filename) # We remove the file for doctesting, not needed in notebook; optional -- rgraphics
Creates an R PNG device.
This should primarily be used to save an R graphic to a custom file. Note that when using this in the notebook, one must plot in the same cell that one creates the device. See r.plot() documentation for more information about plotting via R in Sage.
These examples won’t work on the many platforms where R still gets built without graphics support.
EXAMPLES:
sage: filename = tmp_filename() + '.png'
sage: r.png(filename='"%s"'%filename) # optional -- rgraphics
NULL
sage: x = r([1,2,3])
sage: y = r([4,5,6])
sage: r.plot(x,y) # This saves to filename, but is not viewable from command line; optional -- rgraphics
null device
1
sage: import os; os.unlink(filename) # We remove the file for doctesting; optional -- rgraphics
We want to make sure that we actually can view R graphics, which happens differently on different platforms:
sage: s = r.eval('capabilities("png")') # Should be on Linux and Solaris
sage: t = r.eval('capabilities("aqua")') # Should be on all supported Mac versions
sage: "TRUE" in s+t # optional -- rgraphics
True
Read filename into the R interpreter by calling R’s source function on a read-only file connection.
EXAMPLES:
sage: filename = tmp_filename()
sage: f = open(filename, 'w')
sage: f.write('a <- 2+2\n')
sage: f.close()
sage: r.read(filename)
sage: r.get('a')
'[1] 4'
Load the library library_name into the R interpreter.
This function raises an ImportError if the given library is not known.
INPUT:
EXAMPLES:
sage: r.library('grid')
sage: 'grid' in r.eval('(.packages())')
True
sage: r.library('foobar')
Traceback (most recent call last):
...
ImportError: ...
Set the variable var in R to what the string value evaluates to in R.
INPUT:
EXAMPLES:
sage: r.set('a', '2 + 3')
sage: r.get('a')
'[1] 5'
Display the R source (if possible) about the function named s.
INPUT:
OUTPUT: string – source code
EXAMPLES:
sage: print r.source("print.anova")
function (x, digits = max(getOption("digits") - 2L, 3L), signif.stars = getOption("show.signif.stars"),
...
Return list of all R functions.
INPUT:
OUTPUT: list – list of string
EXAMPLES:
sage: t = r.trait_names(verbose=False)
sage: len(t) > 200
True
Return the version of R currently running.
OUTPUT: tuple of ints; string
EXAMPLES:
sage: r.version() # not tested
((3, 0, 1), 'R version 3.0.1 (2013-05-16)')
sage: rint, rstr = r.version()
sage: rint[0] >= 3
True
sage: rstr.startswith('R version')
True
Bases: sage.interfaces.expect.ExpectElement
Implements the notation self . other.
INPUT:
OUTPUT: R element
EXAMPLES:
sage: c = r.c(1,2,3,4)
sage: c.dot_product(c.t())
[,1] [,2] [,3] [,4]
[1,] 1 2 3 4
[2,] 2 4 6 8
[3,] 3 6 9 12
[4,] 4 8 12 16
sage: v = r([3,-1,8])
sage: v.dot_product(v)
[,1]
[1,] 74
The tilde regression operator in R.
EXAMPLES:
sage: x = r([1,2,3,4,5])
sage: y = r([3,5,7,9,11])
sage: a = r.lm( y.tilde(x) ) # lm( y ~ x )
sage: d = a._sage_()
sage: d['DATA']['coefficients']['DATA'][1]
2
The tilde regression operator in R.
EXAMPLES:
sage: x = r([1,2,3,4,5])
sage: y = r([3,5,7,9,11])
sage: a = r.lm( y.tilde(x) ) # lm( y ~ x )
sage: d = a._sage_()
sage: d['DATA']['coefficients']['DATA'][1]
2
Return a list of all methods of this object.
Note
Currently returns all R commands.
EXAMPLES:
sage: a = r([1,2,3])
sage: t = a.trait_names()
sage: len(t) > 200
True
Bases: sage.interfaces.expect.ExpectFunction
A Function in the R interface.
INPUT:
EXAMPLES:
sage: length = r.length
sage: type(length)
<class 'sage.interfaces.r.RFunction'>
sage: loads(dumps(length))
length
Return True if x is an element in an R interface.
INPUT:
OUTPUT: bool
EXAMPLES:
sage: from sage.interfaces.r import is_RElement
sage: is_RElement(2)
False
sage: is_RElement(r(2))
True
Spawn a new R command-line session.
EXAMPLES:
sage: r.console() # not tested
R version 2.6.1 (2007-11-26)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
...
Return the R version.
EXAMPLES:
sage: r_version() # not tested
((3, 0, 1), 'R version 3.0.1 (2013-05-16)')
sage: rint, rstr = r_version()
sage: rint[0] >= 3
True
sage: rstr.startswith('R version')
True
Used for reconstructing a copy of the R interpreter from a pickle.
EXAMPLES:
sage: from sage.interfaces.r import reduce_load_R
sage: reduce_load_R()
R Interpreter