This has nothing to do with RSPerl, instead it has to do what kind of
object you obtain and how these are print():ed. Typing the name of an
object, say, 'res', at R prompt and pressing ENTER;
> res
is equivalent as typing
> print(res)
This is for convenience to the user. Basically, this is why you can do
> 1+1
[1] 2
without having to do
> print(1+1)
[1] 2
When you "transfer" the object from R to Perl you will, as expect, only
receive the value of 'res', not the output from 'print(res)'. Here is an
example illustrating the behavior in R:
> res <- t.test(1:10,y=c(7:20))
> length(res)
[1] 9
> str(res)
List of 9
$ statistic : Named num -5.43
..- attr(*, "names")= chr "t"
$ parameter : Named num 22
..- attr(*, "names")= chr "df"
$ p.value : num 1.86e-05
$ conf.int : atomic [1:2] -11.05 -4.95
..- attr(*, "conf.level")= num 0.95
$ estimate : Named num [1:2] 5.5 13.5
..- attr(*, "names")= chr [1:2] "mean of x" "mean of y"
$ null.value : Named num 0
..- attr(*, "names")= chr "difference in means"
$ alternative: chr "two.sided"
$ method : chr "Welch Two Sample t-test"
$ data.name : chr "1:10 and c(7:20)"
- attr(*, "class")= chr "htest"
> print(res)
Welch Two Sample t-test
data: 1:10 and c(7:20)
t = -5.4349, df = 21.982, p-value = 1.855e-05
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-11.052802 -4.947198
sample estimates:
mean of x mean of y
5.5 13.5
In your case, to capture what print(res) is outputting, you may want to
look at ?capture.out, that is
> output <- capture.output(res)
> output # ...that is, print(output)
[1] ""
[2] "\tWelch Two Sample t-test"
[3] ""
[4] "data: 1:10 and c(7:20) "
[5] "t = -5.4349, df = 21.982, p-value = 1.855e-05"
[6] "alternative hypothesis: true difference in means is not equal to 0 "
[7] "95 percent confidence interval:"
[8] " -11.052802 -4.947198 "
[9] "sample estimates:"
[10] "mean of x mean of y "
[11] " 5.5 13.5 "
[12] ""
and transfer 'output' to Perl.
Cheers
Henrik
Wagle, Mugdha wrote:
> Hi,
>
> I've just started using R and RSPerl. I have some code as follows:
>
> &R::initR("--no-save");
> &R::call("t.test", ([EMAIL PROTECTED], [EMAIL PROTECTED]));
>
> where @array1 and @array2 are both 1-dimensional arrays in Perl having 54675
> elements each. On execution the output is as follows:
>
> Calling R function name `t.test', # arguments: 3
> 1) Arg type 3
> Got a reference to a value 10
> Here now!2) Arg type 3
> Got a reference to a value 10
> Here now!Calling R
> t.test(c(0, 6.24280675278087, 6.35175793656943, 5.76925805661511,
> 7.0789316246711, 7.4636498661157, 8.13730810691084, 8.78203131644273,
> 9.64502765609435, 9.95631242346133, 5.83129579495516, 6.8798700754926,
> 7.31814159140937.......(REST OF THE ARRAY ELEMENTS).....
> 4.91632461462501, 3.38099467434464,
> 3.91800507710569, 3.23867845216438, 3.38439026334577, 4.64918707140487,
> 3.23474917402449, 3.62966009445396, 3.36729582998647, 3.91999117507732
> ))
> Performed the call, result has length 9
>
> My question is : with other functions such as sum and log10, the actual
> values of the result are displayed. Here the call seems to have worked but
> the output is not what you get when running t.test directly on the R command
> prompt..
>
> data: data4[2] and data4[3]
> t = 0.2186, df = 109.847, p-value = 0.8274
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> -3722.830 4645.723
> sample estimates:
> mean of x mean of y
> 6185.139 5723.693
>
> which is what I had expected, after seeing the outputs in the case of simpler
> functions like sum. Could anyone please tell me how I can obtain the output I
> expect(i.e. the same as the command line output....giving values of t,
> p-value and the means)?
>
> Thank you very much for the help!!
>
> Sincerely,
> Mugdha Wagle
> Hartwell Center for Bioinformatics and Biotechnology,
> St.Jude Children's Research Hospital, Memphis TN 38105
>
> ______________________________________________
> [email protected] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
>
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