[babel] multiple result outputs from function

[babel] multiple result outputs from function

[Graham Smith]

Below is a function that I am trying to run in orgmode/babel.

It seems to run OK, but instead of printing out three values, its only
printing the final result.

Once again, i would appreciate some help with what I am missing.

Thanks,

Graham


#+srcname: CI_function
#+begin_src R :session daf
summary.ci<-function(x){
xbar<-mean(x)
sigma<-sd(x)
n<-length(x)
sem<-sigma/sqrt(n)
lower.ci<-xbar+sem*qnorm(0.025)
upper.ci<-xbar+sem*qnorm(0.975)
print (xbar)
print  (lower.ci)
print  (upper.ci)
}
#+end_src

#+srcname: SumFlowering2005
#+begin_src R :session daf
summary.ci(daf$Flower[daf$YEAR=="2005"])
#+end_src

#+results: SumFlowering2005
: 1.97860201016947

Re: [babel] multiple result outputs from function

[Dan Davison]

Graham Smith <myotisone@gmail.com> writes:

> Below is a function that I am trying to run in orgmode/babel.
>
> It seems to run OK, but instead of printing out three values, its only
> printing the final result.
>
> Once again, i would appreciate some help with what I am missing.

Hi Graham,

Use ':results output' to get the printed output. The default mode
is ':results value' which returns the value of the last expression in
the block.

#+srcname: CI_function
#+begin_src R :session daf
  summary.ci<-function(x){
      print ("value 1")
      print  ("value 2")
      print  ("value 3")
  }
#+end_src

#+begin_src R :session daf :results output
summary.ci()
#+end_src

#+results:
: [1] "value 1"
: [1] "value 2"
: [1] "value 3"


#+begin_src R :session daf
summary.ci()
#+end_src

#+results:
: value 3


Dan

>
> Thanks,
>
> Graham
>
>
> #+srcname: CI_function
> #+begin_src R :session daf
> summary.ci<-function(x){
> xbar<-mean(x)
> sigma<-sd(x)
> n<-length(x)
> sem<-sigma/sqrt(n)
> lower.ci<-xbar+sem*qnorm(0.025)
> upper.ci<-xbar+sem*qnorm(0.975)
> print (xbar)
> print  (lower.ci)
> print  (upper.ci)
> }
> #+end_src
>
> #+srcname: SumFlowering2005
> #+begin_src R :session daf
> summary.ci(daf$Flower[daf$YEAR=="2005"])
> #+end_src
>
> #+results: SumFlowering2005
> : 1.97860201016947
>
>
> _______________________________________________
> Emacs-orgmode mailing list
> Please use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode

Re: [babel] multiple result outputs from function

[Graham Smith]

Dan

> Use ':results output' to get the printed output. The default mode
> is ':results value' which returns the value of the last expression in
> the block.

Thanks, that's great.

At least I managed to sort out my other two problems today on my own !!

Graham

Re: [babel] multiple result outputs from function

[Erik Iverson]

Graham -

Graham Smith wrote:
> Below is a function that I am trying to run in orgmode/babel.
> 
> It seems to run OK, but instead of printing out three values, its only
> printing the final result.
> 
> Once again, i would appreciate some help with what I am missing.
> 
> Thanks,
> 
> Graham
> 
> 
> #+srcname: CI_function
> #+begin_src R :session daf
> summary.ci<-function(x){
> xbar<-mean(x)
> sigma<-sd(x)
> n<-length(x)
> sem<-sigma/sqrt(n)
> lower.ci<-xbar+sem*qnorm(0.025)
> upper.ci<-xbar+sem*qnorm(0.975)
> print (xbar)
> print  (lower.ci)
> print  (upper.ci)
> }
> #+end_src
> 
> #+srcname: SumFlowering2005
> #+begin_src R :session daf
> summary.ci(daf$Flower[daf$YEAR=="2005"])
> #+end_src
> 
> #+results: SumFlowering2005
> : 1.97860201016947
> 

 From org-babel docs...

The following options are mutually exclusive, and specify how the 
results should be collected from the source code block.

------------------------------------------------------
value
     This is the default. The result is the value of the last statement 
in the source code block. This header argument places Org-babel in 
functional mode. Note that in some languages, e.g., python, use of this 
result type requires that a return statement be included in the body of 
the source code block. E.g., :results value.

output
     The result is the collection of everything printed to stdout during 
the execution of the source code block. This header argument places 
Org-babel in scripting mode. E.g., :results output.
-------------------------------------------------------

So, add ":results output" to your source header block.

Or, you might want to define your R function to return a list of the 
three components you're after for further processing, and then not have 
to include ":results output"

Instead of the 3 print statements, which don't create objects, you could 
substitute

list(xbar, lower.ci, upper.ci)

--Erik

Re: [babel] multiple result outputs from function

[Graham Smith]

Erik

> So, add ":results output" to your source header block.

Dan beat you to it, but..

> list(xbar, lower.ci, upper.ci)

This is useful, but the output isn't exactly as I expected

#+results: SumFlowering2005
: [[1]]
: [1] 1.513333
:
: [[2]]
: [1] 1.048065
:
: [[3]]
: [1] 1.978602

is there a way of replacing the [1] [2] and [3] with the object names
(I know this is really an R question)

Thanks,

Graham

Re: [babel] multiple result outputs from function

[Dan Davison]

Graham Smith <myotisone@gmail.com> writes:

> Erik
>
>> So, add ":results output" to your source header block.
>
> Dan beat you to it, but..
>
>> list(xbar, lower.ci, upper.ci)
>
> This is useful, but the output isn't exactly as I expected
>
> #+results: SumFlowering2005
> : [[1]]
> : [1] 1.513333
> :
> : [[2]]
> : [1] 1.048065
> :
> : [[3]]
> : [1] 1.978602
>
> is there a way of replacing the [1] [2] and [3] with the object names

I think you meant replacing the [[1]], [[2]], [[3]]. That would be

list(myname1=xbar, myname2=lower.ci, myname3=upper.ci)

> (I know this is really an R question)

yep :)

Dan

>
> Thanks,
>
> Graham
>
>
> _______________________________________________
> Emacs-orgmode mailing list
> Please use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode

Re: [babel] multiple result outputs from function

[Graham Smith]

Dan,

>> is there a way of replacing the [1] [2] and [3] with the object names
>
> I think you meant replacing the [[1]], [[2]], [[3]]. That would be
>
> list(myname1=xbar, myname2=lower.ci, myname3=upper.ci)
>
>> (I know this is really an R question)

Thanks again :-)

Graham