Comments on: The basics of…R http://www.programming4scientists.com/2008/12/08/the-basics-ofr/ Software development wisdom and common-sense for the scientist-programmer Sun, 28 Feb 2010 19:34:26 +0000 http://wordpress.org/?v=2.8.4 hourly 1 By: Rich http://www.programming4scientists.com/2008/12/08/the-basics-ofr/comment-page-1/#comment-249 Rich Fri, 20 Mar 2009 12:34:39 +0000 http://www.programming4scientists.com/?p=364#comment-249 Thanks to Heather for leaving the following useful info on multi-threading in R, at one of our other posts: http://epub.ub.uni-muenchen.de/8991/1/parallelR_techRep.pdf (http://www.programming4scientists.com/2009/02/the-basics-ofidl/) Thanks to Heather for leaving the following useful info on multi-threading in R, at one of our other posts:

http://epub.ub.uni-muenchen.de/8991/1/parallelR_techRep.pdf

(http://www.programming4scientists.com/2009/02/the-basics-ofidl/)

]]> By: Steve Lianoglou http://www.programming4scientists.com/2008/12/08/the-basics-ofr/comment-page-1/#comment-191 Steve Lianoglou Wed, 04 Mar 2009 16:15:49 +0000 http://www.programming4scientists.com/?p=364#comment-191 Hi, A few notes for you and your readers: (1) I've (relatively) recently stumbled on this handy PDF called "The R Inferno", by Patrick Burns. It highlights many/some of the idiosyncrasies that might trip you up as you get accustomed to R (especially if you have experience w/ other programming languages): http://www.burns-stat.com/pages/Tutor/R_inferno.pdf It's very helpful, and really an enjoyable read at the same time. Just take a look at its abstract: If you are using R and you think you're in hell, this is a map for you. :-) He has other tutorials on his site which might be worth checking out as well. (2) @gioby: If, by testing frameworks, you mean unit testing and the like, check out: * RUnit: http://cran.r-project.org/web/packages/RUnit/index.html * Some hints on debugging with R : http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/ Hi,

A few notes for you and your readers:

(1) I’ve (relatively) recently stumbled on this handy PDF called “The R Inferno”, by Patrick Burns. It highlights many/some of the idiosyncrasies that might trip you up as you get accustomed to R (especially if you have experience w/ other programming languages):

http://www.burns-stat.com/pages/Tutor/R_inferno.pdf

It’s very helpful, and really an enjoyable read at the same time. Just take a look at its abstract: If you are using R and you think you’re in hell, this is a map for you. :-)

He has other tutorials on his site which might be worth checking out as well.

(2) @gioby: If, by testing frameworks, you mean unit testing and the like, check out:

* RUnit: http://cran.r-project.org/web/packages/RUnit/index.html
* Some hints on debugging with R : http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/

]]> By: Rich http://www.programming4scientists.com/2008/12/08/the-basics-ofr/comment-page-1/#comment-186 Rich Wed, 04 Mar 2009 11:43:38 +0000 http://www.programming4scientists.com/?p=364#comment-186 Hi Roland, Thanks for your comments! To address them: - yes, you're right. What we meant to say was that people often use variable/function names that look like "data.input". - Ah yes. What we meant was that if you encounter (in R) something called myObject.someMethod, it *could* be something other than the method "someMethod" associated with the object "myObject". The language definition doesn't stop you using confusing naming conventions for unrelated variables, functions etc. Thanks again for the feedback! Tweaks now applied to the article :-) Hi Roland,

Thanks for your comments! To address them:

– yes, you’re right. What we meant to say was that people often use variable/function names that look like “data.input”.

– Ah yes. What we meant was that if you encounter (in R) something called myObject.someMethod, it *could* be something other than the method “someMethod” associated with the object “myObject”. The language definition doesn’t stop you using confusing naming conventions for unrelated variables, functions etc.

Thanks again for the feedback! Tweaks now applied to the article :-)

]]> By: Roland http://www.programming4scientists.com/2008/12/08/the-basics-ofr/comment-page-1/#comment-184 Roland Wed, 04 Mar 2009 10:44:56 +0000 http://www.programming4scientists.com/?p=364#comment-184 Nice article. Just two comments, both related to your "‘Period’ (.) is just a character." section: - as far as I know, it is not a convention to use data.input, data.processed, ... - the remark about object oriented programming is not exactly correct. Have a look at the R Language Definition, in particular Section 5. http://cran.r-project.org/doc/manuals/R-lang.html Nice article. Just two comments, both related to your “‘Period’ (.) is just a character.” section:
- as far as I know, it is not a convention to use data.input, data.processed, …
- the remark about object oriented programming is not exactly correct. Have a look at the R Language Definition, in particular Section 5.
http://cran.r-project.org/doc/manuals/R-lang.html

]]> By: scriptworld.com.au » The basics of…R http://www.programming4scientists.com/2008/12/08/the-basics-ofr/comment-page-1/#comment-143 scriptworld.com.au » The basics of…R Tue, 20 Jan 2009 12:53:05 +0000 http://www.programming4scientists.com/?p=364#comment-143 [...] Ben wrote an interesting post today onHere’s a quick excerpt [...] [...] Ben wrote an interesting post today onHere’s a quick excerpt [...]

]]> By: List of programming languages used by programmer scientists | Programming for Scientists http://www.programming4scientists.com/2008/12/08/the-basics-ofr/comment-page-1/#comment-111 List of programming languages used by programmer scientists | Programming for Scientists Tue, 23 Dec 2008 04:45:52 +0000 http://www.programming4scientists.com/?p=364#comment-111 [...] R. A statistical programming language.  It has loads of statistical libraries that are either built-in or downloadable.  R is open source and has a community that develops new code for it; for example, the Bioconductor toolbox for analysing gene expression data is very widely used.  It can be slow to run big jobs, unless you use the built-in functions (written in C and hence v. fast) or attach your own C or C++ code to speed up the critical bottlenecks.  Interfacing C/C++ to R in this way take a bit of care, but can be very powerful (See Basics of … R). [...] [...] R. A statistical programming language.  It has loads of statistical libraries that are either built-in or downloadable.  R is open source and has a community that develops new code for it; for example, the Bioconductor toolbox for analysing gene expression data is very widely used.  It can be slow to run big jobs, unless you use the built-in functions (written in C and hence v. fast) or attach your own C or C++ code to speed up the critical bottlenecks.  Interfacing C/C++ to R in this way take a bit of care, but can be very powerful (See Basics of … R). [...]

]]> By: Rich http://www.programming4scientists.com/2008/12/08/the-basics-ofr/comment-page-1/#comment-106 Rich Tue, 16 Dec 2008 17:33:05 +0000 http://www.programming4scientists.com/?p=364#comment-106 There may well be, but I've not come across any (please let us know if you find some!). The FOR loops issue can be a real killer, but can be worked around (sometimes thinking in vector operations is a bit...challenging :-) ). I know from experience that Matlab and IDL suffer from exactly the same issue, which is why they also provide vectorised operations. That said, I have found all three languages extremely useful! There may well be, but I’ve not come across any (please let us know if you find some!).

The FOR loops issue can be a real killer, but can be worked around (sometimes thinking in vector operations is a bit…challenging :-) ). I know from experience that Matlab and IDL suffer from exactly the same issue, which is why they also provide vectorised operations. That said, I have found all three languages extremely useful!

]]> By: gioby http://www.programming4scientists.com/2008/12/08/the-basics-ofr/comment-page-1/#comment-105 gioby Tue, 16 Dec 2008 17:21:30 +0000 http://www.programming4scientists.com/?p=364#comment-105 Thank you for the article. I am also a newbie to R and I should start studying it already. I didn't know of this 'for' loops problem. Are there any testing frameworks for R programs? Thank you for the article.
I am also a newbie to R and I should start studying it already.
I didn’t know of this ‘for’ loops problem. Are there any testing frameworks for R programs?

]]> By: Ben http://www.programming4scientists.com/2008/12/08/the-basics-ofr/comment-page-1/#comment-104 Ben Thu, 11 Dec 2008 22:40:34 +0000 http://www.programming4scientists.com/?p=364#comment-104 Glad you found it useful. Please get back to us on how you get along and what you think we should add to the article. Glad you found it useful. Please get back to us on how you get along and what you think we should add to the article.

]]> By: James P. http://www.programming4scientists.com/2008/12/08/the-basics-ofr/comment-page-1/#comment-103 James P. Thu, 11 Dec 2008 22:35:08 +0000 http://www.programming4scientists.com/?p=364#comment-103 Thanks for this, I am about to dive into R as a new graduate student, this provided some good perspective. Thanks for this, I am about to dive into R as a new graduate student, this provided some good perspective.

]]>