R

"R is a language and environment for statistical computing and graphics." -- http://www.r-project.org/

Sage includes R and is able to invoke it. It is possible to send lines of code, invoke commands in a standardized fashion, work with results of calculations as objects and convert those objects back into python data structures. The last point is essential to write native Sage commands that use R as backend.

Work

http://trac.sagemath.org/sage_trac/ticket/839

Command Completion

sage: r.k[TAB]
r.kappa          r.kappa_qr       r.kernel         r.knots          r.ks_test        
r.kappa_default  r.kappa_tri      r.kill           r.kronecker      r.ksmooth        
r.kappa_lm       r.kernapply      r.kmeans         r.kruskal_test

Examples

sequence

sage: r.seq(1,9)    

[1] 1 2 3 4 5 6 7 8 9

Matrix

Matrix m as Sage object and R printout - then a translation to a Sage matrix.

sage: m = r.matrix(r.seq(1,12),3)

sage: type(m)
<class 'sage.interfaces.r.RElement'>

sage: m

     [,1] [,2] [,3] [,4]
[1,]    1    4    7   10
[2,]    2    5    8   11
[3,]    3    6    9   12

argument byrow=True

sage: m = r.matrix(r.seq(1,12),3, byrow=True)
sage: m

     [,1] [,2] [,3] [,4]
[1,]    1    2    3    4
[2,]    5    6    7    8
[3,]    9   10   11   12

translation:

sage: sageobj(m)

sage: m._sage_()

[ 1  2  3  4]
[ 5  6  7  8]
[ 9 10 11 12]

sage: type(sageobj(m))
<type 'sage.matrix.matrix_integer_dense.Matrix_integer_dense'>

t-Test

sage: r.t_test(r.c(1,2,3,5),r.c(1,2,4,5))

or just

sage: r.t_test([1,2,3],[1,2,4])


        Welch Two Sample t-test

data:  sage6 and sage7
t = -0.2, df = 5.973, p-value = 0.8481
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -3.311938  2.811938
sample estimates:
mean of x mean of y
     2.75      3.00

and native

sage: t = ttest([1,2,3,4,5],[1,2,3,3.5,5.121])
sage: t

(0.941026372027427,
 {'DATA': {'alternative': 'two.sided',
           'conf_int': {'DATA': [-2.2140805547522402, 2.3656805547522399],
                        'conf_level': 0.94999999999999996},
           'data_name': 'sage5 and sage11',
           'estimate': {'DATA': [3, 2.9241999999999999],
                        '_Names': ['mean of x', 'mean of y']},
           'method': 'Welch Two Sample t-test',
           'null_value': {'DATA': 0, '_Names': 'difference in means'},
           'p_value': 0.941026372027427,
           'parameter': {'DATA': 7.9983864630024701, '_Names': 'df'},
           'statistic': {'DATA': 0.076336405881313296, '_Names': 't'}},
  '_Names': ['statistic',
             'parameter',
             'p.value',
             'conf.int',
             'estimate',
             'null.value',
             'alternative',
             'method',
             'data.name'],
  '_r_class': 'htest'})
sage: t[0]
0.941026372027427

sage: ttest([1,2,3,4,5],[1,2,3,3.5,5.121])[0] 
0.941026372027427

table

sage: rt = r.table(x = r.c(3,3,3,1,2,3,1), y = r.c(2,1,2,2,2,1,2))

sage: rt

   x
y   1 2 3
  1 0 0 2
  2 2 1 2

sage: rt.summary()

Number of cases in table: 7 
Number of factors: 2 
Test for independence of all factors:
        Chisq = 2.1, df = 2, p-value = 0.3499
        Chi-squared approximation may be incorrect

F. A. Q.

Q: "r" doesn't work!
A: You have probably assigned a new value to it - just assign it again: r = R() or any other variable you like!
Q: I cannot pass string to R function, getting errors like Error: object "sage1" not found or random output
A: Use double-quoted strings inside single-quoted strings, like r.paste(1, 2, sep='"+"') - maybe as you read this it's no longer needed, check http://trac.sagemath.org/sage_trac/ticket/2963