Re: [R] Is there some way to customize colours for the View output?
Hi all, I've just could test your suggestions on using dataedit... entries now, and indeed they work... partially. See, please, the next screenshot: https://ibb.co/Dkn2pVs dataedituser modifies the red borders dataedittext the yellow text dataeditfg... I do not know, specified to green the output of View(mtcars) does not change from that of the screenshot dataeditbg is the (almost) black background, but in the column and row names. I tried the modifying the different colours through the GUI preferences, and the background colour for column and row names did not change. May this be a bug? Thank you for your help. Best regards, Iago De: Rolf Turner Enviat el: dimarts, 7 de maig de 2024 23:58 Per a: Duncan Murdoch A/c: Iago Gin� V�zquez ; r-help@r-project.org ; Achim Zeileis Tema: Re: [R] Is there some way to customize colours for the View output? On Tue, 7 May 2024 06:34:50 -0400 Duncan Murdoch wrote: > On 07/05/2024 6:31 a.m., Iago Gin� V�zquez wrote: > > Thanks Duncan. > > > > I am currently on Windows. Is there any solution for it? > > Switch to Linux or MacOS? Fortune nomination! cheers, Rolf Turner -- Honorary Research Fellow Department of Statistics University of Auckland Stats. Dep't. (secretaries) phone: +64-9-373-7599 ext. 89622 Home phone: +64-9-480-4619 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] Is there some way to customize colours for the View output?
Thanks Duncan. I am currently on Windows. Is there any solution for it? Best regards, Iago De: Duncan Murdoch Enviat el: dimarts, 7 de maig de 2024 12:24 Per a: Iago Gin� V�zquez ; r-help@r-project.org Tema: Re: [R] Is there some way to customize colours for the View output? If you are using X11, then the paragraph on X resources is relevant. Create a file named .Xresources in your home directory, and put a line like R_dataentry.background: green in it. On my Mac, this has to be in place before Xquartz is started. There is probably a similar restriction on other platforms. Colour names (used for foreground and background) can be words or hex colors like #ff . I don't know the format for "geometry", but I'd guess it's like the -geometry argument to X11 apps, e.g. 1000x1000+0+0. If you are on Windows, none of this is relevant. Duncan Murdoch On 07/05/2024 5:51 a.m., Iago Gin� V�zquez wrote: > Hi all, > > As the email subject tells, I write to ask if there is the chance to > customize the colours (and in particular the background) of the `View` output > window. > > > In the View help, it is told that: > > On Windows, the initial size of the data viewer window is taken from the > default dimensions of a pager (see Rconsole), but adjusted downwards to show > a whole number of rows and columns. > > So if it works for the sizes, it could work for the colours. But after > modifying > > ## Colours for console and pager(s) > # (see rw/etc/rgb.txt for the known colours). > background = gray9 > normaltext = yellow > usertext = YellowGreen > highlight = golderod > > I did not have success. > > On the other hand, in the data.entry it is told that > > The data entry window responds to X resources of class R_dataentry. > Resources foreground, background and geometry are utilized. > > But I do not know if this is related and how to modify those resources. > > Can someone help me? > > If this is not possible, is there any chance of making a feature request of > this to R-devel? (I mean, I could write to R-devel list, but do you think > there would be any interest in developing this?) > > Thanks! > Best regards, > > Iago > >[[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] Is there some way to customize colours for the View output?
Hi all, As the email subject tells, I write to ask if there is the chance to customize the colours (and in particular the background) of the `View` output window. In the View help, it is told that: On Windows, the initial size of the data viewer window is taken from the default dimensions of a pager (see Rconsole), but adjusted downwards to show a whole number of rows and columns. So if it works for the sizes, it could work for the colours. But after modifying ## Colours for console and pager(s) # (see rw/etc/rgb.txt for the known colours). background = gray9 normaltext = yellow usertext = YellowGreen highlight = golderod I did not have success. On the other hand, in the data.entry it is told that The data entry window responds to X resources of class R_dataentry. Resources foreground, background and geometry are utilized. But I do not know if this is related and how to modify those resources. Can someone help me? If this is not possible, is there any chance of making a feature request of this to R-devel? (I mean, I could write to R-devel list, but do you think there would be any interest in developing this?) Thanks! Best regards, Iago [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] Debugging functions defined (locally) inside another functions
Thanks a lot both Duncan and Ivan,
I will keep that example in mind, Duncan, great!
Best regards,
Iago
De: Duncan Murdoch
Enviat el: divendres, 12 d�abril de 2024 15:36
Per a: Iago Gin� V�zquez ; r-help@r-project.org
Tema: Re: [R] Debugging functions defined (locally) inside another functions
On 12/04/2024 8:15 a.m., Iago Gin� V�zquez wrote:
> Hi all, I am trying to debug an error of a function g defined and used inside
> another function f of a package.
> So I have
>
> f <- function(whatever){
> ...
> g <- function(whatever2){
> ...
> }
> ...
> }
>
> If I wanted to debug some thing directly inside f I would do debug(f). But
> this does not go inside g code. On the other hand, debug(g) does not work as
> g is not a defined function in the namespace of the package.
>
> Is there some way to debug errors inside g?
The easiest case is if you have access to the source code. Just put a
browser() statement at the start of g, i.e. change it to
g <- function(whatever2){
browser()
...
}
and it will break very similarly to what happens if you have set debug(g).
Another possibility if you have the source but don't want to edit it is
to use trace. Suppose that the definition of g is in source.R at lines
100 to 120. Then you can run
setBreakpoint("source.R#101")
to set a breakpoint via trace() just before line 101 runs. trace() has
lots of options; it can just print things, or call browser(), etc. They
are available in setBreakpoint().
If you are executing code from a package and you don't have the source
handy it's a bit tedious, but you can still do the search that
setBreakpoint() does to find the source. For example, let's set a
breakpoint just before the print statement in g in this example:
f <- function() {
g <- function() {
print("this is g")
}
print("this is f")
g()
}
You need to find the location of that line in f. Look at as.list(body(f)):
> as.list(body(f))
[[1]]
`{`
[[2]]
g <- function() {
print("this is g")
}
[[3]]
print("this is f")
[[4]]
g()
So we need to look within entry 2:
> as.list(body(f)[[2]])
[[1]]
`<-`
[[2]]
g
[[3]]
function() {
print("this is g")
}
Continue drilling down:
> as.list(body(f)[[c(2,3)]])
[[1]]
`function`
[[2]]
NULL
[[3]]
{
print("this is g")
}
[[4]]
function() {
print("this is g")
}
> as.list(body(f)[[c(2,3, 3)]])
[[1]]
`{`
[[2]]
print("this is g")
So now we know the print statement is at location c(2,3,3,2). Set a
browser call there:
> trace(f, at=list(c(2,3,3,2)), tracer = quote(browser()))
[1] "f"
> body(f)
{
g <- function() {
{
.doTrace(browser(), "step 2,3,3,2")
print("this is g")
}
}
print("this is f")
g()
}
Note that the "at" argument needs to be a list to drill down; if you
just said at=c(2,3,3,2) it would set breakpoints at step 2 and 3.
Duncan Murdoch
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Re: [R] Debugging functions defined (locally) inside another functions
Thank you Ivan, your example solves my issue this time through
debug(environment(Adder$add)$add)
Just for the future, you say
Moreover, `g` doesn't exist at all until f() is evaluated and reaches
this point. If `f` was a function, it would be possible to trace() it,
inserting a call to debug(g) after it's created.
How should I call trace() if f was a function?
Best regards,
Iago
De: Ivan Krylov
Enviat el: divendres, 12 d��abril de 2024 14:38
Per a: Iago Gin�� V��zquez
A/c: r-help@r-project.org
Tema: Re: [R] Debugging functions defined (locally) inside another functions
�� Fri, 12 Apr 2024 12:15:07 +
Iago Gin�� V��zquez ��ڧ�֧�:
> f <- function(whatever){
>...
>g <- function(whatever2){
> ...
>}
>...
> }
>
> If I wanted to debug some thing directly inside f I would do
> debug(f). But this does not go inside g code. On the other hand,
> debug(g) does not work as g is not a defined function in the
> namespace of the package.
Moreover, `g` doesn't exist at all until f() is evaluated and reaches
this point. If `f` was a function, it would be possible to trace() it,
inserting a call to debug(g) after it's created.
> f <- ggplot2::ggproto(...)
>
> So debug(f) produces
> Error in debug(f) : argument must be a function
Can you show more information about the call that produces `f`? Where
does `g` come into play? Following ?ggplot2::ggproto, I can trigger the
browser if I reach into the environment of the publicly available
method:
Adder <- ggproto(...) # from the example
debug(environment(Adder$add)$add)
Adder$add(1234)
# debugging in: add(..., self = self)
# debug �ߧ� #3: {
# self$x <- self$x + n
# self$x
# }
--
Best regards,
Ivan
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Re: [R] Debugging functions defined (locally) inside another functions
To be precise, in the case I am looking this time f is not a function, but
f <- ggplot2::ggproto(...)
So debug(f) produces
Error in debug(f) : argument must be a function
Iago
De: R-help de part de Iago Gin� V�zquez
Enviat el: divendres, 12 d�abril de 2024 14:15
Per a: r-help@r-project.org
Tema: [R] Debugging functions defined (locally) inside another functions
Hi all, I am trying to debug an error of a function g defined and used inside
another function f of a package.
So I have
f <- function(whatever){
...
g <- function(whatever2){
...
}
...
}
If I wanted to debug some thing directly inside f I would do debug(f). But this
does not go inside g code. On the other hand, debug(g) does not work as g is
not a defined function in the namespace of the package.
Is there some way to debug errors inside g?
Thank you in advance.
All the best,
Iago
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
[R] Debugging functions defined (locally) inside another functions
Hi all, I am trying to debug an error of a function g defined and used inside
another function f of a package.
So I have
f <- function(whatever){
...
g <- function(whatever2){
...
}
...
}
If I wanted to debug some thing directly inside f I would do debug(f). But this
does not go inside g code. On the other hand, debug(g) does not work as g is
not a defined function in the namespace of the package.
Is there some way to debug errors inside g?
Thank you in advance.
All the best,
Iago
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[ESS] Where does ESS saves ESSR environment information
Hi all,
I have included a line such as the following in my .emacs file:
(add-hook 'ess-r-post-run-hook (lambda () (ess-load-file "~/startR.r")))
I have restarted Emacs, tried to start R and get an error due to that R did not
find the file. I realized that I put ~ thinking in home path for Emacs, not
home path for R, so I updated the path address to the correct one in my .emacs
file:
(add-hook 'ess-r-post-run-hook (lambda () (ess-load-file
"C:/Users/.../startR.r")))
Again, restarted Emacs, tried starting R..., but I got the same error, which
through a traceback I get
base::as.environment("ESSR")$.ess.source("~/startR.r", visibly = FALSE,
output = TRUE)
So, at some point the address "~/startR.r" was saved, but I cannot find it. How
may I remove it and update the ESS configuration?
Thank you for your help.
Best regards,
Iago
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Re: [R] gsub issue with consecutive pattern finds
Hi Iris,
Thank you. Further, very nice solution.
Best,
Iago
On 01/03/2024 12:49, Iris Simmons wrote:
> Hi Iago,
>
>
> This is not a bug. It is expected. Patterns may not overlap. However, there
> is a way to get the result you want using perl:
>
> ```R
> gsub("([aeiouAEIOU])(?=[aeiouAEIOU])", "\\1_", "aerioue", perl = TRUE)
> ```
>
> The specific change I made is called a positive lookahead, you can read
> more about it here:
>
> https://www.regular-expressions.info/lookaround.html
>
> It's a way to check for a piece of text without consuming it in the match.
>
> Also, since you don't care about character case, it might be more legible
> to add ignore.case = TRUE and remove the upper case characters:
>
> ```R
> gsub("([aeiou])(?=[aeiou])", "\\1_", "aerioue", perl = TRUE, ignore.case =
> TRUE)
>
> ## or
>
> gsub("(?i)([aeiou])(?=[aeiou])", "\\1_", "aerioue", perl = TRUE)
> ```
>
> I hope this helps!
>
>
> On Fri, Mar 1, 2024, 06:37 Iago Giné Vázquez wrote:
>
>> Hi all,
>>
>> I tested next command:
>>
>> gsub("([aeiouAEIOU])([aeiouAEIOU])", "\\1_\\2", "aerioue")
>>
>> with the following output:
>>
>> [1] "a_eri_ou_e"
>>
>> So, there are two consecutive vowels where an underscore is not added.
>>
>> May it be a bug? Is it expected (bug or not)? Is there any chance to get
>> what I want (an underscore between each pair of consecutive vowels)?
>>
>>
>> Thank you!
>>
>> Best regards,
>>
>> Iago
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>>
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] gsub issue with consecutive pattern finds
Hi all,
I tested next command:
gsub("([aeiouAEIOU])([aeiouAEIOU])", "\\1_\\2", "aerioue")
with the following output:
[1] "a_eri_ou_e"
So, there are two consecutive vowels where an underscore is not added.
May it be a bug? Is it expected (bug or not)? Is there any chance to get
what I want (an underscore between each pair of consecutive vowels)?
Thank you!
Best regards,
Iago
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Avoiding Delete key function as 'Quit R' in Rterm when there are no characters in cursor line
Thanks to both, Duncan and Thomas. Best, Iago De: Tomas Kalibera Enviat el: dilluns, 12 de febrer de 2024 11:18 Per a: Iago Giné Vázquez ; CALUM POLWART ; Duncan Murdoch A/c: r-help@r-project.org Tema: Re: [R] Avoiding Delete key function as 'Quit R' in Rterm when there are no characters in cursor line On 2/9/24 21:39, Iago Giné Vázquez wrote: > Duncan, do you think it's worth to comment this in R-devel list? Duncan filed a bug report via R bugzilla (thanks). There is no way to disable this functionality and it has existed for very long time, I tested that at least in R 3.0. Optionally ending the session was I believe intentional with Ctrl+D, when the input is empty, and it is also how Unix terminals work. But ending the session with DEL was probably an implementation compromise and I've changed that in R-devel. Thanks for the report. More implementation details in the bugzilla report: https://bugs.r-project.org/show_bug.cgi?id=18666 Best Tomas > Iago > > > De: CALUM POLWART > Enviat el: divendres, 9 de febrer de 2024 18:28 > Per a: Duncan Murdoch > A/c: Iago Giné Vázquez ; r-help@r-project.org > > Tema: Re: [R] Avoiding Delete key function as 'Quit R' in Rterm when there > are no characters in cursor line > > I don't use term, but I've just tested it and this is reproducable. > > Is it a bug? Not sure. If you hit c after getting the message it will cancel > the q() request. > > > On Fri, 9 Feb 2024, 17:21 Duncan Murdoch, > mailto:murdoch.dun...@gmail.com>> wrote: > That looks to me like a bug, but I don't use Windows any more, so I > won't offer to try to fix it for you. In fact I don't think Rterm has > many users at all: most Windows users probably use RStudio or one of > the other graphical front ends (Visual Studio, Emacs, Rgui, etc.) > > So maybe you can track down the issue, or someone else will try. Or > maybe you'll just have to avoid triggering the bug (if it really is one). > > Duncan Murdoch > > On 09/02/2024 10:03 a.m., Iago Giné Vázquez wrote: >> Yes, indeed, I am talking about Rterm in Windows. >> >> Iago >> >> *De:* Duncan Murdoch >> mailto:murdoch.dun...@gmail.com>> >> *Enviat el:* divendres, 9 de febrer de 2024 13:50 >> *Per a:* Iago Giné Vázquez mailto:iago.g...@sjd.es>> >> *Tema:* Re: [R] Avoiding Delete key function as 'Quit R' in Rterm when >> there are no characters in cursor line >> On 09/02/2024 6:25 a.m., Iago Giné Vázquez wrote: >>> Hi all, >>> >>> I cite from README.Rterm >>> >>> ^D, DEL : Delete the character under the cursor. >>> >>> That is the general behaviour, but when there is no character (neither >>> under the cursor nor at its left), pressing the Delete key suggests closing >>> the R terminal. Is there any (configurable) way to avoid this behaviour? >> Are you talking about rterm in Windows, or which front end? >> >> Duncan Murdoch >> > __ > R-help@r-project.org<mailto:R-help@r-project.org> mailing list -- To > UNSUBSCRIBE and more, see > 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]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] Avoiding Delete key function as 'Quit R' in Rterm when there are no characters in cursor line
Duncan, do you think it's worth to comment this in R-devel list? Iago De: CALUM POLWART Enviat el: divendres, 9 de febrer de 2024 18:28 Per a: Duncan Murdoch A/c: Iago Giné Vázquez ; r-help@r-project.org Tema: Re: [R] Avoiding Delete key function as 'Quit R' in Rterm when there are no characters in cursor line I don't use term, but I've just tested it and this is reproducable. Is it a bug? Not sure. If you hit c after getting the message it will cancel the q() request. On Fri, 9 Feb 2024, 17:21 Duncan Murdoch, mailto:murdoch.dun...@gmail.com>> wrote: That looks to me like a bug, but I don't use Windows any more, so I won't offer to try to fix it for you. In fact I don't think Rterm has many users at all: most Windows users probably use RStudio or one of the other graphical front ends (Visual Studio, Emacs, Rgui, etc.) So maybe you can track down the issue, or someone else will try. Or maybe you'll just have to avoid triggering the bug (if it really is one). Duncan Murdoch On 09/02/2024 10:03 a.m., Iago Giné Vázquez wrote: > Yes, indeed, I am talking about Rterm in Windows. > > Iago > > *De:* Duncan Murdoch > mailto:murdoch.dun...@gmail.com>> > *Enviat el:* divendres, 9 de febrer de 2024 13:50 > *Per a:* Iago Giné Vázquez mailto:iago.g...@sjd.es>> > *Tema:* Re: [R] Avoiding Delete key function as 'Quit R' in Rterm when > there are no characters in cursor line > On 09/02/2024 6:25 a.m., Iago Giné Vázquez wrote: >> Hi all, >> >> I cite from README.Rterm >> >> ^D, DEL : Delete the character under the cursor. >> >> That is the general behaviour, but when there is no character (neither under >> the cursor nor at its left), pressing the Delete key suggests closing the R >> terminal. Is there any (configurable) way to avoid this behaviour? > > Are you talking about rterm in Windows, or which front end? > > Duncan Murdoch > __ R-help@r-project.org<mailto:R-help@r-project.org> mailing list -- To UNSUBSCRIBE and more, see 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]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] Avoiding Delete key function as 'Quit R' in Rterm when there are no characters in cursor line
Yes, indeed, I am talking about Rterm in Windows. Iago De: Duncan Murdoch Enviat el: divendres, 9 de febrer de 2024 13:50 Per a: Iago Giné Vázquez Tema: Re: [R] Avoiding Delete key function as 'Quit R' in Rterm when there are no characters in cursor line On 09/02/2024 6:25 a.m., Iago Giné Vázquez wrote: > Hi all, > > I cite from README.Rterm > > ^D, DEL : Delete the character under the cursor. > > That is the general behaviour, but when there is no character (neither under > the cursor nor at its left), pressing the Delete key suggests closing the R > terminal. Is there any (configurable) way to avoid this behaviour? Are you talking about rterm in Windows, or which front end? Duncan Murdoch [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] Avoiding Delete key function as 'Quit R' in Rterm when there are no characters in cursor line
Hi all, I cite from README.Rterm ^D, DEL : Delete the character under the cursor. That is the general behaviour, but when there is no character (neither under the cursor nor at its left), pressing the Delete key suggests closing the R terminal. Is there any (configurable) way to avoid this behaviour? Thanks! Best regards, Iago [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] Why Rprofile.site is not built with manual installation of R devel in linux?
Hi all, I downloaded R-devel as explicited in https://developer.r-project.org/SVNtips.html Then, I tried to install it through instructions in https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installation (taking into account also https://stat.ethz.ch/pipermail/r-devel/2016-May/072777.html) So: export REPOS=https://svn.r-project.org/R export RTOP=~ #adjust as necessary cd $RTOP svn co $REPOS/trunk r-devel/R cd r-devel/R tools/rsync-recommended mkdir ../build-R cd ../build-R ../R/configure --prefix=/where/you/want/R/to/go make make check make install make install-tests cd tests ## followed by one of ../bin/R CMD make check ../bin/R CMD make check-devel And here I get the following error checking package 'base' Error in file(filename, "r", encoding = encoding) : cannot open the connection Calls: source -> file In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file '.../etc/Rprofile.site': No such file or directory Execution halted where the dots ... specify the path to the build-R folder where R-devel was built. And I check the etc folder and indeed there is no the Rprofile.site -rw-r--r-- 1 iago iago 209 Nov 9 08:27 javaconf -rw-r--r-- 1 iago iago 770 Nov 9 08:35 ldpaths -rw-r--r-- 1 iago iago 6672 Nov 9 08:35 Makeconf -rw-r--r-- 1 iago iago 3336 Nov 9 08:27 Makefile -rw-r--r-- 1 iago iago 1853 Nov 9 08:27 Renviron -rw-r--r-- 1 iago iago 1173 Nov 9 08:32 repositories I note that make install installed R in the path I specified in ../R/configure --prefix=/where/you/want/R/to/go however 1. make install-tests installed the tests folder in build-R . 2. In the installed R in /where/you/want/R/to/go, there is no even etc folder, there are only the folders bin, lib and share. Am I skipping some step? I am on Debain 12. Thank you! Iago [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] aggregate formula - differing results
It seems that the issue are the missings. If in #1 you use the dataset
na.omit(my_data) instead of my_data, you get the same output that in #2 and in
#4, where all observations with missing data are removed since you are
including all the variables.
The second dataset has no issue since it has no missing data.
Iago
De: R-help de part de Ivan Calandra
Enviat el: dilluns, 4 de setembre de 2023 11:44
Per a: R-help
Tema: [R] aggregate formula - differing results
Dear useRs,
I have just stumbled across a behavior in aggregate() that I cannot
explain. Any help would be appreciated!
Sample data:
my_data <- structure(list(ID = c("FLINT-1", "FLINT-10", "FLINT-100",
"FLINT-101", "FLINT-102", "HORN-10", "HORN-100", "HORN-102", "HORN-103",
"HORN-104"), EdgeLength = c(130.75, 168.77, 142.79, 130.1, 140.41,
121.37, 70.52, 122.3, 71.01, 104.5), SurfaceArea = c(1736.87, 1571.83,
1656.46, 1247.18, 1177.47, 1169.26, 444.61, 1791.48, 461.15, 1127.2),
Length = c(44.384, 29.831, 43.869, 48.011, 54.109, 41.742, 23.854,
32.075, 21.337, 35.459), Width = c(45.982, 67.303, 52.679, 26.42,
25.149, 33.427, 20.683, 62.783, 26.417, 35.297), PLATWIDTH = c(38.84,
NA, 15.33, 30.37, 11.44, 14.88, 13.86, NA, NA, 26.71), PLATTHICK =
c(8.67, NA, 7.99, 11.69, 3.3, 16.52, 4.58, NA, NA, 9.35), EPA = c(78,
NA, 78, 54, 72, 49, 56, NA, NA, 56), THICKNESS = c(10.97, NA, 9.36, 6.4,
5.89, 11.05, 4.9, NA, NA, 10.08), WEIGHT = c(34.3, NA, 25.5, 18.6, 14.9,
29.5, 4.5, NA, NA, 23), RAWMAT = c("FLINT", "FLINT", "FLINT", "FLINT",
"FLINT", "HORNFELS", "HORNFELS", "HORNFELS", "HORNFELS", "HORNFELS")),
row.names = c(1L, 2L, 3L, 4L, 5L, 111L, 112L, 113L, 114L, 115L), class =
"data.frame")
1) Simple aggregation with 2 variables:
aggregate(cbind(Length, Width) ~ RAWMAT, data = my_data, FUN = mean,
na.rm = TRUE)
2) Using the dot notation - different results:
aggregate(. ~ RAWMAT, data = my_data[-1], FUN = mean, na.rm = TRUE)
3) Using dplyr, I get the same results as #1:
group_by(my_data, RAWMAT) %>%
summarise(across(c("Length", "Width"), ~ mean(.x, na.rm = TRUE)))
4) It gets weirder: using all columns in #1 give the same results as in
#2 but different from #1 and #3
aggregate(cbind(EdgeLength, SurfaceArea, Length, Width, PLATWIDTH,
PLATTHICK, EPA, THICKNESS, WEIGHT) ~ RAWMAT, data = my_data, FUN = mean,
na.rm = TRUE)
So it seems it is not only due to the notation (cbind() vs. dot). Is it
a bug? A peculiar thing in my dataset? I tend to think this could be due
to some variables (or their names) as all notations seem to agree when I
remove some variables (although I haven't found out which variable(s) is
(are) at fault), e.g.:
my_data2 <- structure(list(ID = c("FLINT-1", "FLINT-10", "FLINT-100",
"FLINT-101", "FLINT-102", "HORN-10", "HORN-100", "HORN-102", "HORN-103",
"HORN-104"), EdgeLength = c(130.75, 168.77, 142.79, 130.1, 140.41,
121.37, 70.52, 122.3, 71.01, 104.5), SurfaceArea = c(1736.87, 1571.83,
1656.46, 1247.18, 1177.47, 1169.26, 444.61, 1791.48, 461.15, 1127.2),
Length = c(44.384, 29.831, 43.869, 48.011, 54.109, 41.742, 23.854,
32.075, 21.337, 35.459), Width = c(45.982, 67.303, 52.679, 26.42,
25.149, 33.427, 20.683, 62.783, 26.417, 35.297), RAWMAT = c("FLINT",
"FLINT", "FLINT", "FLINT", "FLINT", "HORNFELS", "HORNFELS", "HORNFELS",
"HORNFELS", "HORNFELS")), row.names = c(1L, 2L, 3L, 4L, 5L, 111L, 112L,
113L, 114L, 115L), class = "data.frame")
aggregate(cbind(EdgeLength, SurfaceArea, Length, Width) ~ RAWMAT, data =
my_data2, FUN = mean, na.rm = TRUE)
aggregate(. ~ RAWMAT, data = my_data2[-1], FUN = mean, na.rm = TRUE)
group_by(my_data2, RAWMAT) %>%
summarise(across(where(is.numeric), ~ mean(.x, na.rm = TRUE)))
Thank you in advance for any hint.
Best wishes,
Ivan
*LEIBNIZ-ZENTRUM*
*F�R ARCH�OLOGIE*
*Dr. Ivan CALANDRA*
**Head of IMPALA (IMaging Platform At LeizA)
*MONREPOS* Archaeological Research Centre, Schloss Monrepos
56567 Neuwied, Germany
T: +49 2631 9772 243
T: +49 6131 8885 543
ivan.calan...@leiza.de
leiza.de
ResearchGate
LEIZA is a foundation under public law of the State of
Rhineland-Palatinate and the City of Mainz. Its headquarters are in
Mainz. Supervision is carried out by the Ministry of Science and Health
of the State of Rhineland-Palatinate. LEIZA is a research museum of the
Leibniz Association.
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Re: [R] Help/documentation on Rgui
Thank you Petr, great! Best, Iago De: PIKAL Petr Enviat: Dilluns, 3-juliol 3e000 2023 9:42 Per a: Iago Gin� V�zquez; r-help@r-project.org Assumpte: RE: Help/documentation on Rgui Hi I am not sure about opening Rgui in terminal but for customising Rgui appearance you can modify Rconsole and Rprofile or Rprofile.site which you should find in etc folder of your R installation. https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rconsole.html https://rdrr.io/r/utils/Rconsole.html and "Initialization at Start of an R Session" in R help ?Rprofile Cheers Petr > -Original Message- > From: R-help On Behalf Of Iago Gin� > V�zquez > Sent: Monday, July 3, 2023 8:36 AM > To: r-help@r-project.org > Subject: [R] Help/documentation on Rgui > > Hi all, > > Where can I find a detailed document(ation) on the use of Rgui.exe. The most > detailed I found is https://cran.r-project.org/doc/manuals/r-release/R- > ints.html#GUI-consoles, where there is almost nothing. > > Actually I want to know how to open Rgui.exe (let's say, from a terminal > [mainly in Windows], even better, through the ViM plugin NVim-R) with a set > of specific preferences, like a dark background or specific text colour and size, > which I see I can modify once it is open. > > Thank you for your help. > > Iago > > >[[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] Help/documentation on Rgui
Hi all, Where can I find a detailed document(ation) on the use of Rgui.exe. The most detailed I found is https://cran.r-project.org/doc/manuals/r-release/R-ints.html#GUI-consoles, where there is almost nothing. Actually I want to know how to open Rgui.exe (let's say, from a terminal [mainly in Windows], even better, through the ViM plugin NVim-R) with a set of specific preferences, like a dark background or specific text colour and size, which I see I can modify once it is open. Thank you for your help. Iago [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] Matrix scalar operation that saves memory?
You may take a look at the bigmemory package or other which deal with large
memory data in
https://cran.r-project.org/web/views/HighPerformanceComputing.html#large-memory-and-out-of-memory-data
Some extra explanation is in https://stackoverflow.com/a/11127229/997979
Iago
De: R-help de part de Eric Berger
Enviat el: dimecres, 12 d’abril de 2023 8:38
Per a: Bert Gunter
A/c: R-help
Tema: Re: [R] Matrix scalar operation that saves memory?
One possibility might be to use Rcpp.
An R matrix is stored in contiguous memory, which can be considered as a
vector.
Define a C++ function which operates on a vector in place, as in the
following:
library(Rcpp)
cppFunction(
'void subtractConst(NumericVector x, double c) {
for ( int i = 0; i < x.size(); ++i)
x[i] = x[i] - c;
}')
Try this function out on a matrix. Here we define a 5x2 matrix
m <- matrix(150.5 + 1:10, nrow=5)
print(m)
[,1] [,2]
[1,] 151.5 156.5
[2,] 152.5 157.5
[3,] 153.5 158.5
[4,] 154.5 159.5
[5,] 155.5 160.5
Now call the C++ function
subtractConst(m,100.0)
print(m)
[,1] [,2]
[1,] 51.5 56.5
[2,] 52.5 57.5
[3,] 53.5 58.5
[4,] 54.5 59.5
[5,] 55.5 60.5
HTH,
Eric
On Wed, Apr 12, 2023 at 7:34 AM Bert Gunter wrote:
> I doubt that R's basic matrix capabilities can handle this, but have a look
> at the Matrix package, especially if your matrix is some special form.
>
> Bert
>
> On Tue, Apr 11, 2023, 19:21 Shunran Zhang <
> szh...@ngs.gen-info.osaka-u.ac.jp>
> wrote:
>
> > Hi all,
> >
> > I am currently working with a quite large matrix that takes 300G of
> > memory. My computer only has 512G of memory. I would need to do a few
> > arithmetic on it with a scalar value. My current code looks like this:
> >
> > mat <- 100 - mat
> >
> > However such code quickly uses up all of the remaining memory and got
> > the R script killed by OOM killer.
> >
> > Are there any more memory-efficient way of doing such operation?
> >
> > Thanks,
> >
> > S. Zhang
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
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> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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Re: [R] Importing data with value labels into R
Hello Maryam,
The haven function for reading Stata files is read_dta (not read.dta!!!). May
this be your issue?
Iago
De: R-help de part de Maryam Iraniparast
Enviat el: dilluns, 14 de novembre de 2022 19:07
Per a: r-help@r-project.org
Tema: [R] Importing data with value labels into R
Hello!
I want to read SPSS data into R and I want to carry the value labels with my
dataset.
Based on my research, only Stata file can transfer the value labels to R (It is
easy to save SPSS data with Stata format).
The last time I did that successfully, I was using R4.2.1 and the following
code. But it does not work anymore.
install.packages("tidyverse")
install.packages("haven")
library(tidyverse)
library(haven)
df=file.choose() *Note: Select the STATA file from the folder where it is saved.
dataset=read.dta(df)
I appreciate any thoughts or suggestion.
Thanks,
Mary
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[R] Rare behaviour for nlme::reStruct example and question about ?lmeObject
Dear developers, When I run the example code in the help of reStruct, I get > library(nlme) > rs1 <- reStruct(list(Dog = ~day, Side = ~1), data = Pixel) > rs1 Uninitialized random effects structure > str(rs1) List of 2 $ Side:Error in pdMatrix.pdSymm(x) : cannot extract matrix from an uninitialized object Is it expected? In addition to that I would like to ask if shouldn't be `terms` documented in `?lmeObject`. Kind regards, Iago [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] Is it possible to set a default working directory for all R consoles?
Hi all, Is there some way to set a default working directory each time R.exe is opened? I ask this because Always that I open R 4.2.o in Windows 10 I get the next warning messages Warning message: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is denied Warning message: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is denied Warning message: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is denied Warning message: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is denied Even from cmd.exe in a C: location C:\Users\me>R Warning message: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is denied Warning message: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is denied Warning message: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is denied Warning message: In normalizePath(path.expand(path), winslash, mustWork) : path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is denied Reading https://cran.r-project.org/bin/windows/base/rw-FAQ.html#What-are-HOME-and-working-directories_003f, first I cannot apply the suggested solution (I cannot see such "shortcut�s properties"), and second, I am not interested just in Rgui, or even RStudio, but other terminals running R (like VSCode-radian or SublimeText-Terminus) Thanks in advance. Best wishes, Iago [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
