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please recommend an editor
20 messages · Hai Lin, Randall C Johnson [Contr.], Kasper Daniel Hansen +10 more
Hi Kevin, I prefer Emacs with ESS. It is fairly easy to install, and includes syntax highlighting and interfacing with R. The keyboard shortcuts are a little awkward at first, but make life *much* easier in the long run. I've only been using it for a few months, and I'm very happy with it. Best, Randy
On 12/5/05 5:07 PM, "Hai Lin" <kevinvol2002 at yahoo.com> wrote:
Hi R-Mac users: I am using R in Mac OS 10.3.8 and I am trying to find an editor which is compatible with R in Mac. I recently bumped into Xcode for a few times in Mac when I directly opened scripts. Would Xcode be a good editor to learn? Are there a lot people use it? I don't know what you use to edit your files. Can you recommend? Thanks for any information. Kevin --------------------------------- Single? There's someone we'd like you to meet. [[alternative HTML version deleted]]
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Randall C Johnson Bioinformatics Analyst SAIC-Frederick, Inc (Contractor) Laboratory of Genomic Diversity NCI-Frederick P.O. Box B 1050 Boyles Street Bldg 560, Rm 11-85 Frederick, MD 21702 Phone: (301) 846-1304 Fax: (301) 846-1686 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Kevin,
On Dec 5, 2005, at 5:07 PM, Hai Lin wrote:
I am using R in Mac OS 10.3.8 and I am trying to find an editor which is compatible with R in Mac. I recently bumped into Xcode for a few times in Mac when I directly opened scripts. Would Xcode be a good editor to learn? Are there a lot people use it?
Xcode is nice, but the R support is limited to some syntax highlighting (which was posted on this list some time ago). Personally I use either the integrated editor in the R GUI or Emacs (Carbon Emacs 22.0.50 to be more precise). Both have good R integration (i.e. not just syntax highlighting, but also auto- completion of functions, objects and argument lookup). The integrated R GUI editor is more suitable for beginners, Emacs is ... well, Emacs :) powerful if you know how to use it (and it's the only one with Rd mode AFAIK). I have also heard that SubEthaEdit is a really good editor with R syntax highlighting support, but never used it myself. Cheers, Simon
One nice feature of the R GUI integrated editor is the ability to run an R command from within the editor. It also looks and feels like the App itself, which is nice. I have found that Emacs does a better job with auto-indentation, and have also made use of Emac's backup automation features. Emacs can probably do the "run a command from the editor trick" (it unclogged my toilet the other day); I just haven't figured out how to make it happen yet.
On Tuesday, December 06, 2005, at 09:10AM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
Kevin, On Dec 5, 2005, at 5:07 PM, Hai Lin wrote:
I am using R in Mac OS 10.3.8 and I am trying to find an editor which is compatible with R in Mac. I recently bumped into Xcode for a few times in Mac when I directly opened scripts. Would Xcode be a good editor to learn? Are there a lot people use it?
Xcode is nice, but the R support is limited to some syntax highlighting (which was posted on this list some time ago). Personally I use either the integrated editor in the R GUI or Emacs (Carbon Emacs 22.0.50 to be more precise). Both have good R integration (i.e. not just syntax highlighting, but also auto- completion of functions, objects and argument lookup). The integrated R GUI editor is more suitable for beginners, Emacs is ... well, Emacs :) powerful if you know how to use it (and it's the only one with Rd mode AFAIK). I have also heard that SubEthaEdit is a really good editor with R syntax highlighting support, but never used it myself. Cheers, Simon
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As several people have replied, Emacs is by far the preferred choice for most serious R developers. Using the ESS package with Emacs provides you with an interface to R which goes beyond just syntax highlightning. An example (which Simon has already described): you can press a key combination to start looking up in the help system. Typing plot. and pressing TAB will then give you alist of help pages for functions starting with plot. amongst the loaded packages. This is extremely useful. There are other features such as the ability to send a single line of code or a single function to R (instead of sourcing the whole script). For package writes there are also nice modes for .Rd files and (in case you use it) saved transcript files (you can eg. say you entire transcript from an R session and remove all the output, leaving only the commands as a sourcable R script.). Ess supports Sweave documents as well. Emacs has other advantages: * it is truly cross-platform, a big advantage if you are also using *NIX servers and/or windows * it supports basically any kind of language out there, so if you write in a set of different language, it makes sense to use a single editor * One small lifesaver for statisticians (and others): it supports rectangular cut and paste: imagine being able to cut out a column from a table... Other editors does the same, but the functionality of the ESS package is to my knowledge not present in any other editor, making Emacs a first choice for R users. Having said all of that, Emacs is a big program (which btw. is older than dos), with some learning curve. It will take you a long time before you feel totally at home in it. And you will spend the first couple of months cursing about the strange key combinations and the small quirks. So do not even think of using it unless you plan to do more than write 10 lines of R code. As Jan has said: you do not in any way need to run X11 to run Emacs, although it makes sense to use x11 to plot graphics. Other people have suggested other editors for the causal user. /Kasper
On Dec 5, 2005, at 2:07 PM, Hai Lin wrote:
Hi R-Mac users: I am using R in Mac OS 10.3.8 and I am trying to find an editor which is compatible with R in Mac. I recently bumped into Xcode for a few times in Mac when I directly opened scripts. Would Xcode be a good editor to learn? Are there a lot people use it? I don't know what you use to edit your files. Can you recommend? Thanks for any information. Kevin --------------------------------- Single? There's someone we'd like you to meet. [[alternative HTML version deleted]]
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This is a related remark to this topic and the icon topic of last week. I'm not sure how file associations work between OS X apps and their extensions, however R.app doesn't appear to "own" any file extensions when it is installed, and they have generic or blank icons. Perhaps the individual keen on making icons from the email discussion last week could make new icons for "*.R" files, which might look like R-code with the R logo; an icon for "*.RData" which could look like those DB cylinders with the R logo; and another icon for "*.Rd" files (document-like text with the R logo?). I forget if I had to manually get the "*.RData" extension to "Open with..." R.app, but this should be an automatic association after install; same goes for the "*.R" files. The default behavior for double-clicking an "*.R" file should not open XCode, and should not be associated with an XCode "*.r" Resource Manager file icon. (I'm defiantly not sure if app file ownership in OS X is case sensitive, because in an ideal UNIX world "*.r" extensions and "*.R" are different, which they are in this case.) Anyways, just a thought. +mt
Simon Urbanek wrote:
Kevin, On Dec 5, 2005, at 5:07 PM, Hai Lin wrote:
I am using R in Mac OS 10.3.8 and I am trying to find an editor
which is compatible with R in Mac. I recently bumped into Xcode for
a few times in Mac when I directly opened scripts. Would Xcode be a
good editor to learn? Are there a lot people use it?
Xcode is nice, but the R support is limited to some syntax highlighting (which was posted on this list some time ago). Personally I use either the integrated editor in the R GUI or Emacs (Carbon Emacs 22.0.50 to be more precise). Both have good R integration (i.e. not just syntax highlighting, but also auto- completion of functions, objects and argument lookup). The integrated R GUI editor is more suitable for beginners, Emacs is ... well, Emacs :) powerful if you know how to use it (and it's the only one with Rd mode AFAIK). I have also heard that SubEthaEdit is a really good editor with R syntax highlighting support, but never used it myself. Cheers, Simon
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Appreciate you all for kind replys. With others, I am getting incrediable amount of Info. It really really helps. Thanks again. Kevin --- Kasper Daniel Hansen <khansen at stat.Berkeley.EDU> wrote:
As several people have replied, Emacs is by far the preferred choice for most serious R developers. Using the ESS package with Emacs provides you with an interface to R which goes beyond just syntax highlightning. An example (which Simon has already described): you can press a key combination to start looking up in the help system. Typing plot. and pressing TAB will then give you alist of help pages for functions starting with plot. amongst the loaded packages. This is extremely useful. There are other features such as the ability to send a single line of code or a single function to R (instead of sourcing the whole script). For package writes there are also nice modes for .Rd files and (in case you use it) saved transcript files (you can eg. say you entire transcript from an R session and remove all the output, leaving only the commands as a sourcable R script.). Ess supports Sweave documents as well. Emacs has other advantages: * it is truly cross-platform, a big advantage if you are also using *NIX servers and/or windows * it supports basically any kind of language out there, so if you write in a set of different language, it makes sense to use a single editor * One small lifesaver for statisticians (and others): it supports rectangular cut and paste: imagine being able to cut out a column from a table... Other editors does the same, but the functionality of the ESS package is to my knowledge not present in any other editor, making Emacs a first choice for R users. Having said all of that, Emacs is a big program (which btw. is older than dos), with some learning curve. It will take you a long time before you feel totally at home in it. And you will spend the first couple of months cursing about the strange key combinations and the small quirks. So do not even think of using it unless you plan to do more than write 10 lines of R code. As Jan has said: you do not in any way need to run X11 to run Emacs, although it makes sense to use x11 to plot graphics. Other people have suggested other editors for the causal user. /Kasper On Dec 5, 2005, at 2:07 PM, Hai Lin wrote:
Hi R-Mac users: I am using R in Mac OS 10.3.8 and I am trying to
find an editor
which is compatible with R in Mac. I recently
bumped into Xcode for
a few times in Mac when I directly opened scripts.
Would Xcode be a
good editor to learn? Are there a lot people use
it?
I don't know what you use to edit your files.
Can you recommend?
Thanks for any information. Kevin --------------------------------- Single? There's someone we'd like you to meet. [[alternative HTML version deleted]]
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I have found that Emacs does a better job with auto-indentation, and have also made use of Emac's backup automation features. Emacs can probably do the "run a command from the editor trick" (it unclogged my toilet the other day); I just haven't figured out how to make it happen yet.
ctr-c ctr-j runs the line ctr-c ctr-r runs the region - mark the beginning of the region with ctr-spc ctr-c ctr-b runs the buffer Best, Randy ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Randall C Johnson Bioinformatics Analyst SAIC-Frederick, Inc (Contractor) Laboratory of Genomic Diversity NCI-Frederick P.O. Box B 1050 Boyles Street Bldg 560, Rm 11-85 Frederick, MD 21702 Phone: (301) 846-1304 Fax: (301) 846-1686 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Furthermore, if I ever got around to doing anything else with the Xcode stuff, it would be aimed towards the package developer and not the R user. In my copious spare time, of course.
On Dec 6, 2005, at 8:08 AM, Simon Urbanek wrote:
Kevin, On Dec 5, 2005, at 5:07 PM, Hai Lin wrote:
I am using R in Mac OS 10.3.8 and I am trying to find an editor which is compatible with R in Mac. I recently bumped into Xcode for a few times in Mac when I directly opened scripts. Would Xcode be a good editor to learn? Are there a lot people use it?
Xcode is nice, but the R support is limited to some syntax highlighting (which was posted on this list some time ago). Personally I use either the integrated editor in the R GUI or Emacs (Carbon Emacs 22.0.50 to be more precise). Both have good R integration (i.e. not just syntax highlighting, but also auto- completion of functions, objects and argument lookup). The integrated R GUI editor is more suitable for beginners, Emacs is ... well, Emacs :) powerful if you know how to use it (and it's the only one with Rd mode AFAIK). I have also heard that SubEthaEdit is a really good editor with R syntax highlighting support, but never used it myself. Cheers, Simon
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--- Byron Ellis (ellis at stat.harvard.edu) "Oook" -- The Librarian
This is a really important feature but BBEdit and Alpha also support it (option-click-drag)
On Dec 6, 2005, at 12:29 , Kasper Daniel Hansen wrote:
* One small lifesaver for statisticians (and others): it supports rectangular cut and paste: imagine being able to cut out a column from a table...
since this topic is pretty popular, let me mention a problem i have found with the integrated editor from R.app: the "undo typing" command seems to remove an arbitrary number of keystrokes. at times, i will make a mistake, then when i go to undo it, i find the editor has undone not only my mistake but a significant amount of prior work. it is difficult to produce a replicable example, because i am not sure whether the number of keystrokes that are undone is a function of time between the keystrokes, or some other grouping mechanism. i apologize for not including one. just wondering, has anyone else experienced this? is it a bug, or a setting?
On Dec 6, 2005, at 12:02 PM, Randall C. Johnson [Contr] wrote:
I have found that Emacs does a better job with auto-indentation, and have also made use of Emac's backup automation features. Emacs can probably do the "run a command from the editor trick" (it unclogged my toilet the other day); I just haven't figured out how to make it happen yet.
ctr-c ctr-j runs the line ctr-c ctr-r runs the region - mark the beginning of the region with ctr-spc ctr-c ctr-b runs the buffer Best, Randy ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Randall C Johnson Bioinformatics Analyst SAIC-Frederick, Inc (Contractor) Laboratory of Genomic Diversity NCI-Frederick P.O. Box B 1050 Boyles Street Bldg 560, Rm 11-85 Frederick, MD 21702 Phone: (301) 846-1304 Fax: (301) 846-1686 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3 days later
On Dec 7, 2005, at 8:06 AM, Jan de Leeuw wrote:
This is a really important feature but BBEdit and Alpha also support it (option-click-drag)
Good to know - we could build it into the integrated Mac GUI editor as well - any other wishes? The Xmas shall be jolly, so I could put in a feature or two ;) .. Cheers, Simon
On Dec 8, 2005, at 5:21 AM, Parlamis Franklin wrote:
since this topic is pretty popular, let me mention a problem i have found with the integrated editor from R.app: the "undo typing" command seems to remove an arbitrary number of keystrokes. at times, i will make a mistake, then when i go to undo it, i find the editor has undone not only my mistake but a significant amount of prior work.
The problem is to decide when to put in a checkpoint. Right now, we are forcing them only after <Enter> which is ok for usual work, but if you are only fixing a line here or there then those won't be checked in. Should we use some time-based limit? Cocoa's default is to place no checkpoints so it's not a help :P Cheers, Simon
On Dec 8, 2005, at 5:21 AM, Parlamis Franklin wrote:
since this topic is pretty popular, let me mention a problem i have found with the integrated editor from R.app: the "undo typing" command seems to remove an arbitrary number of keystrokes. at times, i will make a mistake, then when i go to undo it, i find the editor has undone not only my mistake but a significant amount of prior work.
The problem is to decide when to put in a checkpoint. Right now, we are forcing them only after <Enter> which is ok for usual work, but if you are only fixing a line here or there then those won't be checked in. Should we use some time-based limit? Cocoa's default is to place no checkpoints so it's not a help :P
Since you mentioned christmas - ideal might be a short time limit (10 s?) and multiple undos. Knowing how the checkpoint is set already helps a great deal. Cheers, Martin
i think time-based might be awkward because if you don't type for a while, your first several (potentially many) strokes of the undo command would have no effect. maybe a certain number of keystrokes? whatever aquamacs does works fine by me, so i would mimic if possible.
On Monday, December 12, 2005, at 01:50AM, Martin Renner <martin.renner at stonebow.otago.ac.nz> wrote:
On Dec 8, 2005, at 5:21 AM, Parlamis Franklin wrote:
since this topic is pretty popular, let me mention a problem i have found with the integrated editor from R.app: the "undo typing" command seems to remove an arbitrary number of keystrokes. at times, i will make a mistake, then when i go to undo it, i find the editor has undone not only my mistake but a significant amount of prior work.
The problem is to decide when to put in a checkpoint. Right now, we are forcing them only after <Enter> which is ok for usual work, but if you are only fixing a line here or there then those won't be checked in. Should we use some time-based limit? Cocoa's default is to place no checkpoints so it's not a help :P
Since you mentioned christmas - ideal might be a short time limit (10 s?) and multiple undos. Knowing how the checkpoint is set already helps a great deal. Cheers, Martin
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17 days later
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Use the application diff from the shell diff -c file1.R file2.R D.
Hai Lin wrote:
Dear R-Mac, I am using Mac OX 10.3 and I have Emacs+ESS installed. I try to find difference b/w two script files. I appreciate it if you could kindly tell me how do I achieve it, either by some kind of Mac applications or command in R. I did see someone running a statement on Unix. By the way, thanks for everyone's recommendation on the editor in R-Mac . I've installed Emacs on my machine. Kevin --------------------------------- [[alternative HTML version deleted]]
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Duncan Temple Lang duncan at wald.ucdavis.edu Department of Statistics work: (530) 752-4782 371 Kerr Hall fax: (530) 752-7099 One Shields Ave. University of California at Davis Davis, CA 95616, USA -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: not available Url : https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20051230/2ce4b659/attachment.bin
On 12/30/05 3:29 AM, "Duncan Temple Lang" <duncan at wald.ucdavis.edu> wrote:
Use the application diff from the shell diff -c file1.R file2.R D. Hai Lin wrote:
Dear R-Mac, I am using Mac OX 10.3 and I have Emacs+ESS installed. I try to find difference b/w two script files. I appreciate it if you could kindly tell me how do I achieve it, either by some kind of Mac applications or command in R. I did see someone running a statement on Unix. By the way, thanks for everyone's recommendation on the editor in R-Mac . I've installed Emacs on my machine.
Emacs has a diff built in. Sean
On 29 Dec 2005, kevinvol2002 at yahoo.com wrote:
I try to find difference b/w two script files. I appreciate it if you could kindly tell me how do I achieve it, either by some kind of Mac applications or command in R. I did see someone running a statement on Unix.
Since you are using Emacs already, you might try M-x ediff. But before you do that, you can read the help for it via C-h f ediff. + seth
Kevin,
On Dec 29, 2005, at 3:45 PM, Hai Lin wrote:
I am using Mac OX 10.3 and I have Emacs+ESS installed. I try to find difference b/w two script files. I appreciate it if you could kindly tell me how do I achieve it, either by some kind of Mac applications or command in R. I did see someone running a statement on Unix.
just for completeness, there is a very nice utility in Developer/ Applications/Utilities called "FileMerge". It is much nicer than diff and also allows you to create a resulting file by specifying which parts you want from which file. It is too intuitive and easy to use for Emacs users but I though I'll mention it anyway ;). Cheers, Simon