Re: [R] how to send text output to its own window

2012-03-06 Thread Robert Kinley
many thanks for the response.

Rstudio seems to be a very clever  robust tool and i suspect that if R 
can 
do it (ie send text output to its own window) then Rstudio would probably 
handle it.

Can it be done in 'vanilla' R   ?

cheers  Bob






Uwe Ligges lig...@statistik.tu-dortmund.de 
05/03/2012 18:39

To
Robert Kinley kinley_rob...@lilly.com
cc
r-help@r-project.org
Subject
Re: [R] how to send text output to its own window






Sounds like a question for the RStudion people?

Uwe Ligges




On 05.03.2012 12:35, Robert Kinley wrote:
 platform:  R 2.14.2   -Windows XP -  Rstudio

 When I use cat()  or print()  in a script, the output text is of course
 mixed up with the lines of the script.

 I can  sink()  the output to a textfile and then play the file back at 
the
 end of the script, but that's not really what I'm after.

 It would be nice if the lines of text output could appear in a separate
 window,  in the same sort of way that you'd use  windows() for graphical
 output.

 Apologies if I'm missing something obvious.

  Bob Kinley








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[R] how to send text output to its own window

2012-03-05 Thread Robert Kinley
platform:  R 2.14.2   -Windows XP -  Rstudio

When I use cat()  or print()  in a script, the output text is of course 
mixed up with the lines of the script.

I can  sink()  the output to a textfile and then play the file back at the 
end of the script, but that's not really what I'm after.

It would be nice if the lines of text output could appear in a separate 
window,  in the same sort of way that you'd use  windows() for graphical 
output.

Apologies if I'm missing something obvious.

Bob Kinley








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[R] Rstudio question

2011-03-04 Thread Robert Kinley
 I really like RStudio ...

... but I wish it wouldn't automatically reload the last .RData it had.

Anyone know how to fix this ... ?

Also - does anyone know is there an Rstudio-user email-list forum thingy 
out there ?

ta.
 
 Robert Kinley
 
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Re: [R] RWinEdt difficulties

2011-03-02 Thread Robert Kinley
try  RStudio  instead   :o)


http://www.rstudio.org/
 
 Robert Kinley
 
 

 
 




Uwe Ligges lig...@statistik.tu-dortmund.de 
Sent by: r-help-boun...@r-project.org
02/03/2011 15:00

To
John Seers john.se...@googlemail.com
cc
r-help@r-project.org
Subject
Re: [R] RWinEdt difficulties








On 01.03.2011 11:01, John Seers wrote:
 Hello Everyone

 I have just upgraded my PC to Windows 7 (64 bit) and I have installed R
 2.12.2. R seems to be working fine.

 I am having problems getting RWinEdt working with it though.

 I have tried installing WinEdt 6.0 and WinEdt 5.5. But both fail with 
the
 same error using R as 64 bit or 32 bit. I install the package using
 Administrator rights.


 library(RWinEdt)
 Warning message:
 In shell(paste(\\, .gW$InstallRoot, \\WinEdt.exe\ -C=\R-WinEdt\
 -E=,  :
'C:\Program Files (x86)\WinEdt Team\WinEdt 6\WinEdt.exe 
-C=R-WinEdt
 -E=C:\Program Files (x86)\WinEdt Team\WinEdt 6\R.ini' execution 
failed
 with error code 1


One installing RWinEdt the first time, please run R with Administrator 
privileges (right click to do so). Then installation should work 
smoothly with WinEdt  6.0.

 Does it matter if you are using 64 bit R and the 32 bit WinEdt? (I have
 tried 32 bit R).

 Does RWinEdt work with WinEdt 6.0?


No, not yet, unfortunately. But some free time is scheduled for this in 
April.

Uwe Ligges


 Can anybody suggest a solution?




 Thanks for any help.

 Regards

 John Seers


 
**
 
**

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[R] problems formulating arguments to lme()

2010-12-01 Thread Robert Kinley
this is a clearer (I hope) version of an earlier post  -

My problem is formulating the  random = argument to give estimates
of all 9 random components for this kind of setup where there are
(I think) 9  variance/covariance components ...

 Study.1Study.2   ...  Study.5
 Treatment T1: subject:  1  2  3  4  5  6   ...  13 14 15
 
 Treatment T2: subject: 16 17 18   19 20 21   ...  28 29 30 
 
 A variable is measured at the same 2 fixed sites (a and b) on each 
subject

{ Toy example data at end of email }

so fixed effects are :-
 between-Treatments ( T1 and T2 )
 between-sites   ( a and b )
 Treatment*site interaction

and random effects are :-
 study effects at site a 
 study effects at site b
 correlation between site a and site b study effects 

 study*treatment interaction effects at site a 
 study*treatment interaction effects at site b
 correlation between site a and b study*treatment interaction effects 
 
 residual (between-subject) effects at site a 
 residual (between-subject) effects at site b
 correlation between site a and b residuals (between-subject) effects 

I'm having trouble seeing how to formulate this correctly in  lme()

Hope someone can help ...

cheers  Bob Kinley

 Toy
   Study Treatment Subject SiteResult
   1T1   1a  13.901820
   1T1   1b  19.158889
   1T1   2a  16.026299
   1T1   2b  15.545153
   1T1   3a  19.667706
   1T1   3b  21.945156
   1T2  16a   9.822498
   1T2  16b  13.271435
   1T2  17a  18.602909
   1T2  17b  15.679736
   1T2  18a  15.083195
   1T2  18b  18.012834
   2T1   4a  19.394835
   2T1   4b  13.537977
   2T1   5a  17.921014
   2T1   5b  12.070566
   2T1   6a  14.419953
   2T1   6b  16.990585
   2T2  19a  15.489600
   2T2  19b  21.721682
   2T2  20a  18.553789
   2T2  20b  16.628156
   2T2  21a  20.310238
   2T2  21b  18.604716
   3T1   7a  12.458706
   3T1   7b  17.279394
   3T1   8a  14.598512
   3T1   8b  17.024093
   3T1   9a  20.821720
   3T1   9b  22.051680
   3T2  22a  17.923521
   3T2  22b  11.690319
   3T2  23a  12.547144
   3T2  23b  15.051402
   3T2  24a  12.865087
   3T2  24b  13.451004
   4T1  10a  13.819201
   4T1  10b  18.375914
   4T1  11a  18.540972
   4T1  11b  15.741144
   4T1  12a  16.992064
   4T1  12b  16.964870
   4T2  25a  18.583896
   4T2  25b  19.920100
   4T2  26a  18.782343
   4T2  26b  15.095778
   4T2  27a  23.042282
   4T2  27b  19.296852
   5T1  13a  12.425960
   5T1  13b  12.865022
   5T1  14a  16.774604
   5T1  14b  15.540754
   5T1  15a  15.726991
   5T1  15b   8.089564
   5T2  28a  11.694392
   5T2  28b  24.740416
   5T2  29a  14.664904
   5T2  29b  16.348194
   5T2  30a  20.911168
   5T2  30b  15.394160
 
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[R] difficulty setting the random = argument to lme()

2010-11-25 Thread Robert Kinley
My small brain is having trouble getting to grips with lme()

I wonder if anyone can help me correctly set the   random = argument
to lme() for this kind of setup with  (I think) 9  variance/covariance
components ...

   Study.1  Study.2 ... 
Study.10
 Treatment.A:   subject:  1  2  3   4  5  6  etc. 28 29 30
 
 Treatment.B:   subject: 31 32 3334 35 36   58 59 60  
   A variable is measured at 2 fixed sites (A and B) on each subject

so we have fixed effects :-

 between-Treatments 
 between-sites (A and B)
 Treatment*site interaction


and we have random effects :-

 study effects at site A 
 study effects at site B
 correlation between site A and site B study effects 

 study*treatment interaction effects at site A 
 study*treatment interaction effects at site B
 correlation between site A and B study*treatment interaction effects 
 
 residual (between-subject) effects at site A 
 residual (between-subject) effects at site B
 correlation between site A and B residuals (between-subject) effects 

My problem is formulating the  random = argument to give estimates
of all 9 random components ...

Hope someone can help ...

  Robert Kinley 
 



Study:  Pos tissue VC, Neg tissue VC, Pos/Neg tissue 
correlation
Study*Group:Pos tissue VC, Neg tissue VC, Pos/Neg tissue 
correlation
Residual (animal):  Pos tissue VC, Neg tissue VC, Pos/Neg tissue 
correlation
 
 

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and provide commented, minimal, self-contained, reproducible code.


[R] code ok in unix R2.6 , fails in windows R 2.12

2010-11-09 Thread Robert Kinley
hello ...

Can anyone help me with this :


In R.exe 2.6 , Unix , :-

plot.data-model[[i]]$data$conc
newdata-seq(min(plot.data),max(plot.data),by=1)
model.pred-predict(model[[i]],data.frame(newdata),interval=prediction)
matpoints(newdata,model.pred[,c(Lower,Upper)],l,col=blue,lty=1)

works OK ... 


in Rgui  2.12 , Windows XP , same code 

 plot.data-model[[i]]$data$conc
 newdata-seq(min(plot.data),max(plot.data),by=1)
 
model.pred-predict(model[[i]],data.frame(newdata),interval=prediction)
Error in `[.data.frame`(newdata, , 2) : undefined columns selected
 
 

  Robert Kinley  ( 'baffled' of Berkshire )
 
 

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and provide commented, minimal, self-contained, reproducible code.


Re: [R] code ok in unix R2.6 , fails in windows R 2.12

2010-11-09 Thread Robert Kinley
apologies for omitting the data 


   conc  response curve
150 0.7533954 1
250 0.7755960 2
350 0.8001151 3
489 0.2858031 1
589 0.2883478 2
689 0.2954936 3
7   158 0.4296482 1
8   158 0.4406220 2
9   158 0.4567403 3
10  282 0.6484347 1
11  282 0.6555722 2
12  282 0.7361552 3
13  501 0.9768917 1
14  501 0.9809505 2
15  501 0.9952711 3
16  890 1.395 1
17  890 1.3262830 2
18  890 1.4754281 3
19 1582 2.2157078 1
20 1582 2.2918927 2
21 1582 2.5538562 3
22 2813 3.7403291 1
23 2813 4.0623972 2
24 2813 4.1439147 3
25 5000 5.1405423 1
26 5000 5.4242582 2
27 5000 5.4322730 3

also -

 model
[[1]]

A 'drc' model.

Call:
drm(formula = response ~ conc, data = assay.data, fct = l4())

Coefficients:
b:(Intercept)  c:(Intercept)  d:(Intercept)  e:(Intercept) 
  -1.6958 0.5089 6.9764  2629.7526 


attr(,logScale)
[1] TRUE
attr(,modelType)
[1] 4pl
attr(,method)
[1] drc
attr(,class)
[1] multFit





Uwe Ligges lig...@statistik.tu-dortmund.de 
09/11/2010 16:21

To
Robert Kinley kinley_rob...@lilly.com
cc
r-help@r-project.org
Subject
Re: [R] code ok in unix  R2.6 , fails in windows  R 2.12






We cannot help since we do not have the data.

Uwe


On 09.11.2010 16:40, Robert Kinley wrote:
 hello ...

 Can anyone help me with this :


 In R.exe 2.6 , Unix , :-

 plot.data-model[[i]]$data$conc
 newdata-seq(min(plot.data),max(plot.data),by=1)
 
model.pred-predict(model[[i]],data.frame(newdata),interval=prediction)
 matpoints(newdata,model.pred[,c(Lower,Upper)],l,col=blue,lty=1)

 works OK ...


 in Rgui  2.12 , Windows XP , same code

 plot.data-model[[i]]$data$conc
 newdata-seq(min(plot.data),max(plot.data),by=1)

 
model.pred-predict(model[[i]],data.frame(newdata),interval=prediction)
 Error in `[.data.frame`(newdata, , 2) : undefined columns selected



Robert Kinley  ( 'baffled' of Berkshire )



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and provide commented, minimal, self-contained, reproducible code.


[R] updating a local package

2010-10-28 Thread Robert Kinley
Hi folks

I have inherited a package which was created before release 2.10 and I 
need to have it working in release 2.12

There is a folder containing the Man, Data and R subfolders, and the 
description 
file, and there is also the corresponding zip file.

I can install the package from the zip file, but when I try to load it  I 
get the message :-
Error: package   was built before R 2.10.0: please re-install it

If I try to rebuild the zip file using 
C:\Program Files\R\R-2.12.0\bin\R.exe CMD build my.library.folder  

I get pages and pages of warnings and error messages, many of which seem 
to  refer
to the Man folder.

Having never built a formal package before, I'm a bit  stuck for what to 
do next ...

Presumably the expected structure of the folders has changed but the 
documentation
on packages looks scary - can anyone suggest the best way forward - even 
if
its only RTFM !
 
thanks  Bob Kinley 


 
 

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and provide commented, minimal, self-contained, reproducible code.


Re: [R] updating a local package

2010-10-28 Thread Robert Kinley
your advice to useR CMD INSTALL source.library did the trick

 and I now understand  packages a little better.

many thanks
 
 Bob Kinley 



 
 




Uwe Ligges lig...@statistik.tu-dortmund.de 
28/10/2010 10:30

To
Robert Kinley kinley_rob...@lilly.com
cc
r-help@r-project.org
Subject
Re: [R] updating a local package






Essential infrastructure work has been done in the meantime, both ion 
the documentation system and on the location of binaries.
That means you really need to reinstall the package and hence you need 
to start with a source package.
Details for installing from source are given in the manual R 
Installation and Administartion.

Uwe Ligges


On 28.10.2010 11:23, Robert Kinley wrote:
 Hi folks

 I have inherited a package which was created before release 2.10 and I
 need to have it working in release 2.12

 There is a folder containing the Man, Data and R subfolders, and the
 description
 file, and there is also the corresponding zip file.

 I can install the package from the zip file, but when I try to load it I
 get the message :-
  Error: package   was built before R 2.10.0: please re-install 
it

 If I try to rebuild the zip file using
  C:\Program Files\R\R-2.12.0\bin\R.exe CMD build 
my.library.folder

 I get pages and pages of warnings and error messages, many of which seem
 to  refer
 to the Man folder.

 Having never built a formal package before, I'm a bit  stuck for what to
 do next ...

 Presumably the expected structure of the folders has changed but the
 documentation
 on packages looks scary - can anyone suggest the best way forward - even
 if
 its only RTFM !

  thanks  Bob Kinley





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 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


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and provide commented, minimal, self-contained, reproducible code.


Re: [R] updating a local package

2010-10-28 Thread Robert Kinley
I stand corrected   :0) 
 
  Robert Kinley 
 

 
 




Uwe Ligges lig...@statistik.tu-dortmund.de 
28/10/2010 11:54

To
Robert Kinley kinley_rob...@lilly.com
cc
r-help@r-project.org
Subject
Re: [R] updating a local package








On 28.10.2010 12:26, Robert Kinley wrote:
 your advice to useR CMD INSTALL source.library

It's a *package*, not a library.

Uwe


 did the trick

   and I now understand  packages a little better.

  many thanks

   Bob Kinley









 Uwe Liggeslig...@statistik.tu-dortmund.de
 28/10/2010 10:30

 To
 Robert Kinleykinley_rob...@lilly.com
 cc
 r-help@r-project.org
 Subject
 Re: [R] updating a local package






 Essential infrastructure work has been done in the meantime, both ion
 the documentation system and on the location of binaries.
 That means you really need to reinstall the package and hence you need
 to start with a source package.
 Details for installing from source are given in the manual R
 Installation and Administartion.

 Uwe Ligges


 On 28.10.2010 11:23, Robert Kinley wrote:
 Hi folks

 I have inherited a package which was created before release 2.10 and I
 need to have it working in release 2.12

 There is a folder containing the Man, Data and R subfolders, and the
 description
 file, and there is also the corresponding zip file.

 I can install the package from the zip file, but when I try to load it 
I
 get the message :-
   Error: package   was built before R 2.10.0: please re-install
 it

 If I try to rebuild the zip file using
   C:\Program Files\R\R-2.12.0\bin\R.exe CMD build
 my.library.folder

 I get pages and pages of warnings and error messages, many of which 
seem
 to  refer
 to the Man folder.

 Having never built a formal package before, I'm a bit  stuck for what 
to
 do next ...

 Presumably the expected structure of the folders has changed but the
 documentation
 on packages looks scary - can anyone suggest the best way forward - 
even
 if
 its only RTFM !

   thanks  Bob Kinley





 [[alternative HTML version deleted]]

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.




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and provide commented, minimal, self-contained, reproducible code.


Re: [R] running R from Notepad++ in Windows 7

2010-03-05 Thread Robert Kinley
hi Andrew

Many thanks for the suggestion.

I gave it a try , but still get the same issue - 
a fresh Rgui window (just one)  opens, with an empty .RData, when
I submit a script ( Ctrl  F8 ).

I also tried running things as administrator, but it made no difference.

Apparently windows 7 is selling like hot buns, so there should be 
enough market pressure before too long , to encourage the providers
of Notepad++ NpptoR to fix it ...

Thanks againBob

   Robert Kinley 
  b...@lilly.com
 
 




Andrew Redd ar...@stat.tamu.edu 
Sent by: amr...@gmail.com
04/03/2010 14:17

To
Robert Kinley kinley_rob...@lilly.com
cc

Subject
Re: [R] running R from Notepad++ in Windows 7






I had a conversation with someone the other day about problems on Windows 
7.  It was caused by the compatibility mode that they were running R in.  
That might be the issue here if you are using compatibility mode.  Run 
NppToR and R both in compatibility mode and that should fix it, if that is 
the problem.  Just to make sure though, does it open a new session for 
every line of code or does it launch once then continue in that window? 
For fixing the problem it will help me to know.  Thanks,
Andrew

On Thu, Mar 4, 2010 at 3:42 AM, Robert Kinley kinley_rob...@lilly.com 
wrote:
gReetings

Running R 2.10.1 with Notepad++ and NpptoR.exe, when I submit a script to
run :-

1. On my work XP machine , it runs fine in an already-open Rgui window

2. On my home Windows 7 machine, it ignores the existing Rgui window and
fires up
a fresh one, which doesn't use the same .RData, so it fails.

Anyone else hit this and, ideally, solved it ... ?

   cheers  Bob

  Robert Kinley
 b...@lilly.com
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and provide commented, minimal, self-contained, reproducible code.


[R] running R from Notepad++ in Windows 7

2010-03-04 Thread Robert Kinley
gReetings

Running R 2.10.1 with Notepad++ and NpptoR.exe, when I submit a script to 
run :-

1. On my work XP machine , it runs fine in an already-open Rgui window

2. On my home Windows 7 machine, it ignores the existing Rgui window and 
fires up 
a fresh one, which doesn't use the same .RData, so it fails.

Anyone else hit this and, ideally, solved it ... ?

cheers  Bob

   Robert Kinley 
  b...@lilly.com
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and provide commented, minimal, self-contained, reproducible code.


[R] JMP - R ?

2009-11-26 Thread Robert Kinley
A wild thought ... 

   ...  anyone out there know if it's possible to call R code from JMP ?

Bob Kinley - Eli Lilly  co, UK
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and provide commented, minimal, self-contained, reproducible code.


Re: [R] How do I do simple string concatenation in R?

2009-09-30 Thread Robert Kinley
see ?paste


 A -klm
 B - jjj
 C-paste(A,B,sep='')
 if(C==klmjjj) print(C) 
[1] klmjjj

cheers  Bob




Dr. Arie Ben David hol_aben...@bezeqint.net 
Sent by: r-help-boun...@r-project.org
30/09/2009 09:22

To
r-help@r-project.org
cc

Subject
[R] How do I do simple string concatenation in R?





Dear R gurus
How do I do simple string concatenation in R?
For example:
A = klm
B = jjj
How can I assign a value to C such that C == klmjjj is True?
Thank you
Arie

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Re: [R] I might be dumb : a simple question about foreach

2009-07-20 Thread Robert Kinley
Your code runs fine on my windows hp machine ( XP - sp2, R.2.9.1 )

 x - foreach(i = 1:3) %do% sqrt(i)
 x
[[1]]
[1] 1

[[2]]
[1] 1.414214

[[3]]
[1] 1.732051


Are you on Vista , maybe ? 

 
Robert  Kinley

 



Michael Knudsen micknud...@gmail.com 
Sent by: r-help-boun...@r-project.org
20/07/2009 14:23

To
Olivier ETERRADOSSI olivier.eterrado...@ema.fr
cc
r-help@r-project.org
Subject
Re: [R] I might be dumb : a simple question about foreach






On Mon, Jul 20, 2009 at 3:14 PM, Olivier
ETERRADOSSIolivier.eterrado...@ema.fr wrote:

 Do you suggest some Windows related behaviour ?

I haven't used Windows for more than ten years, so unfortunately I
have no clue whatsoever. Maybe there are some Windows experts here who
can help you. America is slowly waking up now, so cross your fingers
:-)

-- 
Michael Knudsen
micknud...@gmail.com
http://lifeofknudsen.blogspot.com/

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[R] replacing zeros by NAs

2009-06-12 Thread Robert Kinley
something like ...
 
 x-c(1,2,3,0,5,6,0)
 is.na(x[x==0])-T
 x
[1]  1  2  3 NA  5  6 NA


Robert  Kinley




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[R] moving from Windows to Linux - needed help

2009-06-01 Thread Robert Kinley
Many thanks to everyone who responded to my request for help with
installing the up-to-date R binary on my Asus eee (details below).


The bulk of opinion was that one should replace Xandros with, for 
example, Ubuntu; however, for the benefit of other family members, I 
needed to keep the Xandros 'easy' version available.

Particular thanks, then, to Millo Giovanni, whose email led me to this 
site:
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/128565.html
which helped me understand where I was going wrong.

R2.9 is now installed on my eee, I can load  run packages, and the 
eee 'easy' option is still available  ... so thanks again , R list.

Bob Kinley

-
hi

I've used R for many years on windows machines, but
have now acquired an Asus eee 1000 linux machine.

In order to get the best out of the machine, I used the 
'pimpmyeee.sh' script, to get the full KDE desktop.

The version of Linux is Xandros, which I believe is
a close relative of Debian, but sadly I have only a 
nodding acquaintance with Linux at present.

Naturally I want to have the current version of R on it,
and I understand (or possibly misunderstand) that the 
binary for the Debian flavour of Linux should do the trick.

I have tried - 

1. using synaptic to add the appropriate (I think) CRAN 
repository  ... but every combination I have tried
gives a 404 error

2. downloading from CRAN what I think is a zipped-up version of 
r-base software, and thewn using the eee's file-manager 
'install DEB package' option ... but this returns 'cannot load ... '.


I'm a bit stuck ... can anyone help please ?


thanks  Bob Kinley
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[R] moving from Windows to Linux - need help

2009-05-26 Thread Robert Kinley
hi

I've used R for many years on windows machines, but
have now acquired an Asus eee 1000 linux machine.

In order to get the best out of the machine, I used the 
'pimpmyeee.sh' script, to get the full KDE desktop.

The version of Linux is Xandros, which I believe is
a close relative of Debian, but sadly I have only a 
nodding acquaintance with Linux at present.

Naturally I want to have the current version of R on it,
and I understand (or possibly misunderstand) that the 
binary for the Debian flavour of Linux should do the trick.

I have tried - 

1. using synaptic to add the appropriate (I think) CRAN 
repository  ... but every combination I have tried
gives a 404 error

2. downloading from CRAN what I think is a zipped-up version of 
r-base software, and thewn using the eee's file-manager 
'install DEB package' option ... but this returns 'cannot load ... '.


I'm a bit stuck ... can anyone help please ?


thanks  Bob Kinley
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and provide commented, minimal, self-contained, reproducible code.