[R] working with environments to ensure code quality for long R scripts

[cberry at tajo.ucsd.edu]

Alexander,

If Tal's suggestion to use caching in Sweave doesn't appeal to you, you
might look at  'R.cache' and other packages mentioned in 

http://cran.r-project.org/web/views/ReproducibleResearch.html

under 'Caching of R Objects'.

However, an advantage of the Sweave-like approaches is that you can
generate a brief report that includes the versions of scripts used,
summarizes the data processing, and gives intermediate results for later
inspection and sanity checks.

HTH,

Chuck

Tal Galili <tal.galili at gmail.com> writes:

> Hi Alexander,
> Saving full environments is possible, but it is very easy to start loosing
> track on where each variable came from.
> You might want to use this process:
> http://www.r-bloggers.com/a-better-way-of-saving-and-loading-objects-in-r/
> It depends on how many variables you work with, but it might help.
>
> Another way is to do all of the work through Sweave, and combine it with
> caching:  http://cran.r-project.org/web/packages/cacheSweave/index.html
> This will ensure that every code chunk will keep the variables you created,
> without the need to re-run the code from scratch.
>
> For extracting data from outside sources, I would often use the first
> method, and for analysis I would use the later option.
>
> Good luck,
> Tal
>
>
> ----------------Contact
> Details:-------------------------------------------------------
> Contact me: Tal.Galili at gmail.com |  972-52-7275845
> Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
> www.r-statistics.com (English)
> ----------------------------------------------------------------------------------------------
>
>
>
>
> On Thu, Apr 19, 2012 at 11:15 AM, Alexander <juschitz_alexander at yahoo.de>wrote:
>
>> Hello, I am working under R2.11 Windows and currently I work on a big R
>> progjet which executes different R script in a row. Every R script
>> represents a module. As every module depends of the variables created in
>> the
>> modules previously executed, I want to be shure, that I don't create or
>> change a variable in a scriptwithout being aware that this affects the
>> results in a later executed script. Therefore, I was think to save all
>> important variables to keep in a seperate "backup" environment. Everytime a
>> script starts, it loads the variables of the "backup" environment in
>> .GlobalEnv. At the end of the script, I want to add all new obtained
>> variables to the "backup" environment (and check automaticaly if any
>> variables of "backup"environment is going to be overwritten) and clean the
>> workspace .GlobalEnv to start the next script neat and tidy. What do you
>> think of this solution? Does anyone have better ideas or experience to
>> share?
>>
>> Thank you in advance
>>
>> Alexander
>>
>> --
>> View this message in context:
>> http://r.789695.n4.nabble.com/working-with-environments-to-ensure-code-quality-for-long-R-scripts-tp4570195p4570195.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> 	[[alternative HTML version deleted]]
>

-- 
Charles C. Berry                            Dept of Family/Preventive Medicine
cberry at ucsd edu			    UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901