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From |
Daniel Becker <daniel.becker@uni-rostock.de> |

To |
statalist@hsphsun2.harvard.edu |

Subject |
Re: st: RE: Stata code to run R code from within Stata and returncertain pieces of the results as Stata macros |

Date |
Sat, 31 May 2008 09:16:22 +0200 |

Hallo -

Thanks for this thread. I hope someone is trying to write that smart peace of software! But isn't rsource (findit rsource) already pretty smart?

Am 31.05.2008 um 02:20 schrieb Salah Mahmud:

I think a smart solution is possible

My understanding of the help of rsource is that the transfer of a dataset from stata to R is already possible. So no hard work here.1. Export a subset/all the data into a csv file and construct the necessary R code to import that data into R.

IN the rsource package, the R code is stored in a file that needs to be specified:2. The Stata user specifies the R library that need to be loaded-- eg library(cmprsk) -- and the exact R code needed to perform the specific calculations. These could be stored in an *.R file or for simple tasks could be passed directly to Rbridge. So Rbridge could have 2 mutually exclusive options: i) Rcommand ("out<-crr(ftime,fstatus,cov,failcode=2) ") ii) Rcmdfilename( "mycode.R")

rsource using R_source_filename [ , noloutput lsource rpath(R_pathname) roptions(R_options) ]

This seems perfectly ok to me.

it seems like this is the tricky part. rsource can already list the output of the R-code executed in the stata results window, but that's it. It is not yet possible to have the results produced by R in a r() macro.3. The user also specifies the result object returned by R (eg the out object in the out<-crr(ftime,fstatus,cov,failcode=2) that she would like Rbridge to return as global macros or r() macros. R is object-oriented so instead unlike Stata commands which return individual pieces of information, R functions typically return an object that contain all these pieces of information. So the object "out" in the call "out<-crr(ftime,fstatus,cov,failcode=2) " above stores all the info returned from calling the function crr. Things like out$coef , out$loglik etc which some call class members. Version 1 of Rbridge could return a specific class member (eg out$loglik). A more advanced implementation will parse (within R) the target object and extract all the members' names and values (contents) into a text file which would include info on each member's name, data type and value. The necessary commands are added to source.R. This may include calls to custom R functions that facilitate the parsing and extraction of the members of the result object. But as I said this is not essential for version 1.

Hm - isn't this already possible? If the R-code contains the necessary commands, the result of the execution of r could be that text file. Hence the ral work is to get the proper R-code that contains all results such that they can be imported back into stata.4. Stata runs R and pass along source.R for execution which results in the above results text file.

Once the textfile contains the information, this must be possible? Is there an example of reading a text file and putting something written there in a stata-macro?4. Stata reads the text file and generates macros with the same name, data type and values which Rbridge could also leave behind as r() macros.

Wouldn't the easy check be: Stata, please white until the file /file/ that/is/the/result/of/executing/R/ exists?I'm sure the devil is in the details (eg there are issues with coordinating the running of Stata and R). For instance, Stata may have to go to sleep until R signals that the code execution is over etc. But the above does not seem any more daunting than the average ado out there.

A variant of the pause command? How about an option waitfor(/file/that/ is/the/result/of/executing/R/results.txt) for rsource?

It is my impression that most things you want are already present in rsource and that the real hard work is to write the necessary R-code and then get the information back into stata. And for this, it very much depends on what exactly you want to do in R.

Best,

Daniel

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**Follow-Ups**:**Re: st: RE: Stata code to run R code from within Stata and returncertain pieces of the results as Stata macros***From:*Daniel Becker <daniel.becker@uni-rostock.de>

**References**:**st: Stata code to run R code from within Stata and return certain pieces of the results as Stata macros***From:*"Salah Mahmud" <salah.mahmud@gmail.com>

**st: RE: Stata code to run R code from within Stata and return certain pieces of the results as Stata macros***From:*"Nick Cox" <n.j.cox@durham.ac.uk>

**Re: st: RE: Stata code to run R code from within Stata and return certain pieces of the results as Stata macros***From:*"Salah Mahmud" <salah.mahmud@gmail.com>

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