Re: [R] open source and R
Liaw, Andy wrote: However code readability can not be over-emphasized. I must admit to have written R code in such a supposedly `clever' way that I can't figure out what I was trying to do (or how I did it) a week later... The solution to that is to make sure this sort of code is adequately commented! Be as clever as you like - make your R look like a runner-up in the obfuscated perl programming contest if you want - but a well-placed comment will hopefully prevent that stupid feeling a week later. Baz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] open source and R
On Tue, 2005-11-15 at 09:54 +, Barry Rowlingson wrote: Liaw, Andy wrote: However code readability can not be over-emphasized. I must admit to have written R code in such a supposedly `clever' way that I can't figure out what I was trying to do (or how I did it) a week later... The solution to that is to make sure this sort of code is adequately commented! Be as clever as you like - make your R look like a runner-up in the obfuscated perl programming contest if you want - but a well-placed comment will hopefully prevent that stupid feeling a week later. Unfortunately the comments don't stick well with the R code. They would if you always edit the source code, but not with my preferred toolbox. For me the most natural way to work on a function is to install the package with the function, and then use Emacs+ESS to edit, test and debug the the function within an R session. That really ruins all decent commenting: comments may be misplaced, and the default formatting of comments is really bad in ESS. So my choice is to uncomment R code, but comment C (and Fortran). cheers, jari oksanen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] open source and R
Jari == Jari Oksanen [EMAIL PROTECTED] on Tue, 15 Nov 2005 12:25:17 +0200 writes: Jari On Tue, 2005-11-15 at 09:54 +, Barry Rowlingson wrote: Liaw, Andy wrote: However code readability can not be over-emphasized. I must admit to have written R code in such a supposedly `clever' way that I can't figure out what I was trying to do (or how I did it) a week later... Baz The solution to that is to make sure this sort of code Baz is adequately commented! Be as clever as you like - Baz make your R look like a runner-up in the obfuscated Baz perl programming contest if you want - but a Baz well-placed comment will hopefully prevent that stupid Baz feeling a week later. Exactly! Jari Unfortunately the comments don't stick well with the R Jari code. They would if you always edit the source code, Jari but not with my preferred toolbox. For me the most Jari natural way to work on a function is to install the Jari package with the function, and then use Emacs+ESS to Jari edit, test and debug the the function within an R Jari session. But why? Why on earth are you not working with the *.R files in your pkg/R/ directory? Or make a copy of these and work with the copy? Also, you can use library(, keep.source = TRUE) and this helps for all those packages that did *not* use lazy-loading or saved images at their installation time; unfortunately, that excludes many packages. Once you've seen the light, i.e. ESS :-) , using edit() , fix() and all those abominations is just plainly wrong in my (biased) view! Jari session. That really ruins all decent commenting: Jari comments may be misplaced, and the default formatting Jari of comments is really bad in ESS. Huh?? I'd have expected you to say the contrary here. I assume you have never heard of the difference between #, ## and ### in comments. Most of the R core developers adhere to it which you can see when browsing the R source files. Since one version of the ESS manual is online, look here: http://ESS.R-project.org/Manual/ess.html#index-comments-in-S-154 Jari So my choice is to uncomment R code, but comment C Jari (and Fortran). ooh; I hope you can be convinced to use comments in R code... and maybe adapt to the ## vs # (or ###) scheme. Regards, Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] open source and R
On 14-Nov-05 Prof Brian Ripley wrote: On Sun, 13 Nov 2005 [EMAIL PROTECTED] wrote: [...] There is one aspect though where R users are in the cold when it comes to C and FORTAN. If you want to understand the function 'eigen', say, then you can ?eigen to learn about its usage. You can enter eigen to see the R code, and indeed that is not too imcomprehensible. But then you find .Fortran(ch, n, n, xr, xi, values = dbl.n, !only.values, vectors = xr, ivectors = xi, dbl.n, dbl.n, double(2 * n), ierr = integer(1), PACKAGE = base) and similar for rs, cg and rg. Where's the help for these? Nowhere obvious! In fact you have to go to the source code, locate the FORTRAN routines, and study these, hoping that enough helpful comments have been included to steer your study. So it is a much more formidable task, especially if you are having to learn the language at the same time. That is an unfair comment. The help page for eigen explains what routines are used and gives you references to books describing them. So the help _is_ in the most obvious place. Apologies for misleading wording. This was not meant as a criticism of R in any way, but as an illustration of the theme that, sooner or later, you drop through the floor of what R can provide in the way of explicit explanation. So, while R's help is indeed helpful in this case in indicating an orientation for your travels in that outside world, out in the cold as it were, users are then on their own as far as R is concerned. This is of course inevitable, and the comment was intended as part of the general response to Robert that if you want to study how R does things you are led to study how other software, on which R depends, does things. Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 14-Nov-05 Time: 08:55:35 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] open source and R
Here comes a not-so-nice one: Sorry to be blunt, but I think the current reality is that one's effectiveness in scientific computing is not likely to be high if s/he can't read C for Fortran code. The mode of development for new methods, I believe, should be: - Write it in R (or S-PLUS or Matlab or ...) because one can usually do that quite quickly. - Check and make sure the code produces correct result. - See if the code can be improved for efficiency. Use the profiling facility in R to see where the bottlenecks really are, and try to improve those parts. - If no significant improvement is possible in R, move only the time-consuming part of the computation to C/Fortran/C++. The above mode is not always followed, because many of the packages on CRAN are simply R interfaces to _existing_ C/Fortran code. One would be happy to be able to use them at the R level, but to rewrite the whole thing in R, one better have _very_ good reason! For some algorithms, efficient code can be written in pure R, but the resulting code can be less readable than one written more legibly in C for Fortran. Just my $0.02... Andy From: Robert Thanks for all the nice discussions. Though different users have various needs from R, It's always good to stand on the shoulders of giants (as roger said). How far we will see depends our ability to understand what have been done by other languages. The package written in pure R might be good for education in starting OOP in research but not effective in scientific computing as suggested. [EMAIL PROTECTED] wrote: On 13-Nov-05 Roger Bivand wrote: On Sun, 13 Nov 2005, Robert wrote: If I do not know C or FORTRAN, how can I fully understand the package or possibly improve it? By learning enough to see whether that makes a difference for your purposes. Life is hard, but that's what makes life interesting ... Robert. Roger Bivand wrote: On Sun, 13 Nov 2005, Robert wrote: Roger Bivand wrote: On Sun, 13 Nov 2005, Robert wrote: It uses FORTRAN code and not in pure R. The same applies to deldir - it also includes Fortran. So the answer seems to be no, there is no voronoi function only written in R. Robert wrote: I am curious about one thing: since the reason for using r is r is a easy-to-learn language and it is good for getting more people involved. Why most of the packages written in r use other languages such as FORTRAN's code? I understand some functions have already been written in other language or it is faster to be implemented in other language. But my understanding is if the user does not know that language (for example, FORTRAN), the package is still a black box to him because he can not improve the package and can not be involved in the development. When I searched the packages of R, I saw many packages with duplicated or similar functions. the main difference among them are the different functions implemented using other languages, which are always a black box to the users. So it is very hard for users to believe the package will run something they need, let alone getting involved in the development. My comments are not to disregard these efforts. But it is good to see the packages written in pure R. Although surprisingly much of R is written in R, quite a lot is written in Fortran and C. One very good reason, apart from efficiency, is code re-use - BLAS and LAPACK among many others are excellent implementations of what we need for numerical linear algebra. R is very typical of good scientific software, it tries to avoid re-implementing functions that are used by the community, are well-supported by the community, and work. Packages by and large do the same - if existing software does the required job, package authors attempt to port that software to R, providing interfaces to underlying C or Fortran libraries. It's about standing on the shoulders of giants. Those are very strong points. Some comments: It would be possible to implement in pure R a matrix inversion or eigenvalue/vector function, for instance, and I'm sure it would be done (if it were done) to very high quality. However, it would run like an elephant in quicksands. BLAS and LAPACK have, over the years, become highly optimised not just for accuracy and robustness, but for speed and efficiency. Also, you will hit the other language problem sooner or later. Robert's complaint is that he does not like black boxes. But R itself is a black box. You cannot write R in R, all the way down to the bottom. At the bottom is machine code, and languages like assember, C, C++, FORTRAN and their compilers provide black box wrappers for this. That is not a whimsical comment either -- all those discussions about why 2 - sqrt(2)^2 is not equal to 0 come down to this sort of issue. Sooner or later, if
Re: [R] open source and R
However code readability can not be over-emphasized. I must admit to have written R code in such a supposedly `clever' way that I can't figure out what I was trying to do (or how I did it) a week later... Andy From: Ernesto Jardim Hi, One single comment about the subject of this message. Open source is about making the code _available_ for all, not making the code _understandable_ for all. Regards EJ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] open source and R
Andy: Ah, don't feel bad, Andy; this is a universal problem in programming that despite all kinds of efforts in lucid programming, OOP, etc. no one has figured out. So while code readability cannot be overemphasized, what this actually means also apparently cannot be defined. From: http://www.jeffgainer.com/lucid_code/lc_cover.html If you are a software professional, you know how software is created. Surely you recognize it. Chances are you live it: chaos. ;-) -- Bert -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy Sent: Monday, November 14, 2005 2:46 PM To: 'Ernesto Jardim' Cc: [EMAIL PROTECTED]; r-help@stat.math.ethz.ch Subject: Re: [R] open source and R However code readability can not be over-emphasized. I must admit to have written R code in such a supposedly `clever' way that I can't figure out what I was trying to do (or how I did it) a week later... Andy From: Ernesto Jardim Hi, One single comment about the subject of this message. Open source is about making the code _available_ for all, not making the code _understandable_ for all. Regards EJ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] open source and R
Roger Bivand [EMAIL PROTECTED] wrote: On Sun, 13 Nov 2005, Robert wrote: It uses FORTRAN code and not in pure R. The same applies to deldir - it also includes Fortran. So the answer seems to be no, there is no voronoi function only written in R. I am curious about one thing: since the reason for using r is r is a easy-to-learn language and it is good for getting more people involved. Why most of the packages written in r use other languages such as FORTRAN's code? I understand some functions have already been written in other language or it is faster to be implemented in other language. But my understanding is if the user does not know that language (for example, FORTRAN), the package is still a black box to him because he can not improve the package and can not be involved in the development. When I searched the packages of R, I saw many packages with duplicated or similar functions. the main difference among them are the different functions implemented using other languages, which are always a black box to the users. So it is very hard for users to believe the package will run something they need, let alone getting involved in the development. My comments are not to disregard these efforts. But it is good to see the packages written in pure R. - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] open source and R
On Sun, 13 Nov 2005, Robert wrote: Roger Bivand [EMAIL PROTECTED] wrote: On Sun, 13 Nov 2005, Robert wrote: It uses FORTRAN code and not in pure R. The same applies to deldir - it also includes Fortran. So the answer seems to be no, there is no voronoi function only written in R. Robert wrote: I am curious about one thing: since the reason for using r is r is a easy-to-learn language and it is good for getting more people involved. Why most of the packages written in r use other languages such as FORTRAN's code? I understand some functions have already been written in other language or it is faster to be implemented in other language. But my understanding is if the user does not know that language (for example, FORTRAN), the package is still a black box to him because he can not improve the package and can not be involved in the development. When I searched the packages of R, I saw many packages with duplicated or similar functions. the main difference among them are the different functions implemented using other languages, which are always a black box to the users. So it is very hard for users to believe the package will run something they need, let alone getting involved in the development. My comments are not to disregard these efforts. But it is good to see the packages written in pure R. Please indent your replies, they are very difficult to read sensibly. Although surprisingly much of R is written in R, quite a lot is written in Fortran and C. One very good reason, apart from efficiency, is code re-use - BLAS and LAPACK among many others are excellent implementations of what we need for numerical linear algebra. R is very typical of good scientific software, it tries to avoid re-implementing functions that are used by the community, are well-supported by the community, and work. Packages by and large do the same - if existing software does the required job, package authors attempt to port that software to R, providing interfaces to underlying C or Fortran libraries. It's about standing on the shoulders of giants. -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] open source and R
If I do not know C or FORTRAN, how can I fully understand the package or possibly improve it? Robert. Roger Bivand [EMAIL PROTECTED] wrote: On Sun, 13 Nov 2005, Robert wrote: Roger Bivand wrote: On Sun, 13 Nov 2005, Robert wrote: It uses FORTRAN code and not in pure R. The same applies to deldir - it also includes Fortran. So the answer seems to be no, there is no voronoi function only written in R. Robert wrote: I am curious about one thing: since the reason for using r is r is a easy-to-learn language and it is good for getting more people involved. Why most of the packages written in r use other languages such as FORTRAN's code? I understand some functions have already been written in other language or it is faster to be implemented in other language. But my understanding is if the user does not know that language (for example, FORTRAN), the package is still a black box to him because he can not improve the package and can not be involved in the development. When I searched the packages of R, I saw many packages with duplicated or similar functions. the main difference among them are the different functions implemented using other languages, which are always a black box to the users. So it is very hard for users to believe the package will run something they need, let alone getting involved in the development. My comments are not to disregard these efforts. But it is good to see the packages written in pure R. Please indent your replies, they are very difficult to read sensibly. Although surprisingly much of R is written in R, quite a lot is written in Fortran and C. One very good reason, apart from efficiency, is code re-use - BLAS and LAPACK among many others are excellent implementations of what we need for numerical linear algebra. R is very typical of good scientific software, it tries to avoid re-implementing functions that are used by the community, are well-supported by the community, and work. Packages by and large do the same - if existing software does the required job, package authors attempt to port that software to R, providing interfaces to underlying C or Fortran libraries. It's about standing on the shoulders of giants. -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [EMAIL PROTECTED] - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] open source and R
On Sun, 13 Nov 2005, Robert wrote: If I do not know C or FORTRAN, how can I fully understand the package or possibly improve it? By learning enough to see whether that makes a difference for your purposes. Life is hard, but that's what makes life interesting ... Robert. Roger Bivand [EMAIL PROTECTED] wrote: On Sun, 13 Nov 2005, Robert wrote: Roger Bivand wrote: On Sun, 13 Nov 2005, Robert wrote: It uses FORTRAN code and not in pure R. The same applies to deldir - it also includes Fortran. So the answer seems to be no, there is no voronoi function only written in R. Robert wrote: I am curious about one thing: since the reason for using r is r is a easy-to-learn language and it is good for getting more people involved. Why most of the packages written in r use other languages such as FORTRAN's code? I understand some functions have already been written in other language or it is faster to be implemented in other language. But my understanding is if the user does not know that language (for example, FORTRAN), the package is still a black box to him because he can not improve the package and can not be involved in the development. When I searched the packages of R, I saw many packages with duplicated or similar functions. the main difference among them are the different functions implemented using other languages, which are always a black box to the users. So it is very hard for users to believe the package will run something they need, let alone getting involved in the development. My comments are not to disregard these efforts. But it is good to see the packages written in pure R. Please indent your replies, they are very difficult to read sensibly. Although surprisingly much of R is written in R, quite a lot is written in Fortran and C. One very good reason, apart from efficiency, is code re-use - BLAS and LAPACK among many others are excellent implementations of what we need for numerical linear algebra. R is very typical of good scientific software, it tries to avoid re-implementing functions that are used by the community, are well-supported by the community, and work. Packages by and large do the same - if existing software does the required job, package authors attempt to port that software to R, providing interfaces to underlying C or Fortran libraries. It's about standing on the shoulders of giants. -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] open source and R
On Nov 13, 2005, at 3:24 PM, Robert wrote: I am curious about one thing: since the reason for using r is r is a easy-to-learn language and it is good for getting more people involved. Why most of the packages written in r use other languages such as FORTRAN's code? I understand some functions have already been written in other language or it is faster to be implemented in other language. But my understanding is if the user does not know that language (for example, FORTRAN), the package is still a black box to him because he can not improve the package and can not be involved in the development. When I searched the packages of R, I saw many packages with duplicated or similar functions. the main difference among them are the different functions implemented using other languages, which are always a black box to the users. So it is very hard for users to believe the package will run something they need, let alone getting involved in the development. No, the box is not black, it is utterly transparent. Of course, what you can recognize and understand inside depends on you,. Just say no to linguistic chauvinism -- even R-ism. url:www.econ.uiuc.edu/~rogerRoger Koenker email [EMAIL PROTECTED] Department of Economics vox:217-333-4558University of Illinois fax:217-244-6678Champaign, IL 61820 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] open source and R
On Sun, 13 Nov 2005, Roger Bivand wrote: On Sun, 13 Nov 2005, Robert wrote: If I do not know C or FORTRAN, how can I fully understand the package or possibly improve it? By learning enough to see whether that makes a difference for your purposes. Life is hard, but that's what makes life interesting ... None of us fully understands what we are doing with computer software. If you understand R code, that's great, but then there is the R interpreter -- do you understand how it works? That interpreter was written in another language that was then compiled by a compiler which was written by someone else for some other purpose -- do you understand the compiler? Then it all gets processed by some very complex hardware that practically none of us *fully* understands. We have to accept that we can't have a complete grasp of what R is doing, but we can still read the R docs and test R in many ways. When functions are written in R, they may be easier for you to read, but they may run much slower than code written in C, C++ or FORTRAN. I don't think it is wise to forgo the speed improvement so that people who don't know FORTRAN can enjoy contributing to R development. The contribution of FORTRAN libraries R functionality and efficiency is probably much greater than the contributions would be from any group of people who could code in R but could't code in C or FORTRAN. That said, I appreciate the sentiment and I think we should prefer straight R code for many functions, but some things just run too slowly when written that way. Mike __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] open source and R
On 13-Nov-05 Roger Bivand wrote: On Sun, 13 Nov 2005, Robert wrote: If I do not know C or FORTRAN, how can I fully understand the package or possibly improve it? By learning enough to see whether that makes a difference for your purposes. Life is hard, but that's what makes life interesting ... Robert. Roger Bivand [EMAIL PROTECTED] wrote: On Sun, 13 Nov 2005, Robert wrote: Roger Bivand wrote: On Sun, 13 Nov 2005, Robert wrote: It uses FORTRAN code and not in pure R. The same applies to deldir - it also includes Fortran. So the answer seems to be no, there is no voronoi function only written in R. Robert wrote: I am curious about one thing: since the reason for using r is r is a easy-to-learn language and it is good for getting more people involved. Why most of the packages written in r use other languages such as FORTRAN's code? I understand some functions have already been written in other language or it is faster to be implemented in other language. But my understanding is if the user does not know that language (for example, FORTRAN), the package is still a black box to him because he can not improve the package and can not be involved in the development. When I searched the packages of R, I saw many packages with duplicated or similar functions. the main difference among them are the different functions implemented using other languages, which are always a black box to the users. So it is very hard for users to believe the package will run something they need, let alone getting involved in the development. My comments are not to disregard these efforts. But it is good to see the packages written in pure R. Although surprisingly much of R is written in R, quite a lot is written in Fortran and C. One very good reason, apart from efficiency, is code re-use - BLAS and LAPACK among many others are excellent implementations of what we need for numerical linear algebra. R is very typical of good scientific software, it tries to avoid re-implementing functions that are used by the community, are well-supported by the community, and work. Packages by and large do the same - if existing software does the required job, package authors attempt to port that software to R, providing interfaces to underlying C or Fortran libraries. It's about standing on the shoulders of giants. Those are very strong points. Some comments: It would be possible to implement in pure R a matrix inversion or eigenvalue/vector function, for instance, and I'm sure it would be done (if it were done) to very high quality. However, it would run like an elephant in quicksands. BLAS and LAPACK have, over the years, become highly optimised not just for accuracy and robustness, but for speed and efficiency. Also, you will hit the other language problem sooner or later. Robert's complaint is that he does not like black boxes. But R itself is a black box. You cannot write R in R, all the way down to the bottom. At the bottom is machine code, and languages like assember, C, C++, FORTRAN and their compilers provide black box wrappers for this. That is not a whimsical comment either -- all those discussions about why 2 - sqrt(2)^2 is not equal to 0 come down to this sort of issue. Sooner or later, if you really want to understand what is going on, you have to get beneath the shiny smooth surface and swim amongst the molecules! So, Robert, try to be positive about C and FORTRAN etc., rather than feeling put off by the fact that they are yet more things to learn and seem to get in the way of understanding how the functions work. C and FORTRAN are your friends, as well as the R langauge itself, and great deal more friemdly than the raw machine code. There is one aspect though where R users are in the cold when it comes to C and FORTAN. If you want to understand the function 'eigen', say, then you can ?eigen to learn about its usage. You can enter eigen to see the R code, and indeed that is not too imcomprehensible. But then you find .Fortran(ch, n, n, xr, xi, values = dbl.n, !only.values, vectors = xr, ivectors = xi, dbl.n, dbl.n, double(2 * n), ierr = integer(1), PACKAGE = base) and similar for rs, cg and rg. Where's the help for these? Nowhere obvious! In fact you have to go to the source code, locate the FORTRAN routines, and study these, hoping that enough helpful comments have been included to steer your study. So it is a much more formidable task, especially if you are having to learn the language at the same time. Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 13-Nov-05 Time: 23:13:58 -- XFMail -- __ R-help@stat.math.ethz.ch
Re: [R] open source and R
Thanks for all the nice discussions. Though different users have various needs from R, It's always good to stand on the shoulders of giants (as roger said). How far we will see depends our ability to understand what have been done by other languages. The package written in pure R might be good for education in starting OOP in research but not effective in scientific computing as suggested. [EMAIL PROTECTED] wrote: On 13-Nov-05 Roger Bivand wrote: On Sun, 13 Nov 2005, Robert wrote: If I do not know C or FORTRAN, how can I fully understand the package or possibly improve it? By learning enough to see whether that makes a difference for your purposes. Life is hard, but that's what makes life interesting ... Robert. Roger Bivand wrote: On Sun, 13 Nov 2005, Robert wrote: Roger Bivand wrote: On Sun, 13 Nov 2005, Robert wrote: It uses FORTRAN code and not in pure R. The same applies to deldir - it also includes Fortran. So the answer seems to be no, there is no voronoi function only written in R. Robert wrote: I am curious about one thing: since the reason for using r is r is a easy-to-learn language and it is good for getting more people involved. Why most of the packages written in r use other languages such as FORTRAN's code? I understand some functions have already been written in other language or it is faster to be implemented in other language. But my understanding is if the user does not know that language (for example, FORTRAN), the package is still a black box to him because he can not improve the package and can not be involved in the development. When I searched the packages of R, I saw many packages with duplicated or similar functions. the main difference among them are the different functions implemented using other languages, which are always a black box to the users. So it is very hard for users to believe the package will run something they need, let alone getting involved in the development. My comments are not to disregard these efforts. But it is good to see the packages written in pure R. Although surprisingly much of R is written in R, quite a lot is written in Fortran and C. One very good reason, apart from efficiency, is code re-use - BLAS and LAPACK among many others are excellent implementations of what we need for numerical linear algebra. R is very typical of good scientific software, it tries to avoid re-implementing functions that are used by the community, are well-supported by the community, and work. Packages by and large do the same - if existing software does the required job, package authors attempt to port that software to R, providing interfaces to underlying C or Fortran libraries. It's about standing on the shoulders of giants. Those are very strong points. Some comments: It would be possible to implement in pure R a matrix inversion or eigenvalue/vector function, for instance, and I'm sure it would be done (if it were done) to very high quality. However, it would run like an elephant in quicksands. BLAS and LAPACK have, over the years, become highly optimised not just for accuracy and robustness, but for speed and efficiency. Also, you will hit the other language problem sooner or later. Robert's complaint is that he does not like black boxes. But R itself is a black box. You cannot write R in R, all the way down to the bottom. At the bottom is machine code, and languages like assember, C, C++, FORTRAN and their compilers provide black box wrappers for this. That is not a whimsical comment either -- all those discussions about why 2 - sqrt(2)^2 is not equal to 0 come down to this sort of issue. Sooner or later, if you really want to understand what is going on, you have to get beneath the shiny smooth surface and swim amongst the molecules! So, Robert, try to be positive about C and FORTRAN etc., rather than feeling put off by the fact that they are yet more things to learn and seem to get in the way of understanding how the functions work. C and FORTRAN are your friends, as well as the R langauge itself, and great deal more friemdly than the raw machine code. There is one aspect though where R users are in the cold when it comes to C and FORTAN. If you want to understand the function 'eigen', say, then you can ?eigen to learn about its usage. You can enter eigen to see the R code, and indeed that is not too imcomprehensible. But then you find .Fortran(ch, n, n, xr, xi, values = dbl.n, !only.values, vectors = xr, ivectors = xi, dbl.n, dbl.n, double(2 * n), ierr = integer(1), PACKAGE = base) and similar for rs, cg and rg. Where's the help for these? Nowhere obvious! In fact you have to go to the source code, locate the FORTRAN routines, and study these, hoping that enough helpful comments have been included to steer your study. So it is a much more formidable task, especially if you are having to learn the language at the same time.
Re: [R] open source and R
On Sun, 13 Nov 2005 [EMAIL PROTECTED] wrote: [...] There is one aspect though where R users are in the cold when it comes to C and FORTAN. If you want to understand the function 'eigen', say, then you can ?eigen to learn about its usage. You can enter eigen to see the R code, and indeed that is not too imcomprehensible. But then you find .Fortran(ch, n, n, xr, xi, values = dbl.n, !only.values, vectors = xr, ivectors = xi, dbl.n, dbl.n, double(2 * n), ierr = integer(1), PACKAGE = base) and similar for rs, cg and rg. Where's the help for these? Nowhere obvious! In fact you have to go to the source code, locate the FORTRAN routines, and study these, hoping that enough helpful comments have been included to steer your study. So it is a much more formidable task, especially if you are having to learn the language at the same time. That is an unfair comment. The help page for eigen explains what routines are used and gives you references to books describing them. So the help _is_ in the most obvious place. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
