from:"Shi, Tao"

Re: [R] comparing 2 long lists in R

2015-09-24 Thread Shi, Tao via R-help

Bogdan,

I would look into bioconductor for packages handling this type choromosomal 
range data.  cntools is one poped into my mind.

Tao

On Thursday, September 24, 2015 12:59 PM, Sarah Goslee  
wrote:

merge() most likely, but: are these really lists in the R sense?

The correct answer depends on what the format actually is; you need to
use dput() or some other unambiguous way of providing sample data.

Without a reproducible example that includes some sample data provided
using dput() (fake is fine), the code you used, and some clear idea of
what output you expect, it's impossible to figure out how to help you.
Here are some suggestions for creating a good reproducible example:
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example

Sarah

On Thu, Sep 24, 2015 at 3:43 PM, Bogdan Tanasa  wrote:
> Dear all,
>
> please could you advise on a computationally quick way to compare and merge
> 2 long lists in R;
> the lists are of the following type, for example :
>
> <> in list 1 :
>
> chromosome, coordinateA, coordinateB, value1
> chromosome, coordinateC, coordinateC, value2,
> etc
>
> <> in list 2 :
>
> chromosome, coordinateX, coordinateY, value6
> chromosome, coordinateZ, coordinateT, value8,
> etc
>
> In the unified list, if coordinateA=coordinateX, and
> coordinateB=coordinateY, then we write :
>
> chromosome, coordinateA, coordinateB, value1, coordinateX, coordinateY,
> value6,
>
> otherwise, we write the individual values :
>
> chromosome, coordinateA, coordinateB, value1,
> chromosome, coordinateX, coordinateY, value6,
>
> thanks,
>
> bogdan
>
> [[alternative HTML version deleted]]
>
and please don't post in HTML.

-- 
Sarah Goslee
http://www.functionaldiversity.org

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Re: [R] how to change the ff properties of a ff-related R object after the original ff output folder has been moved

2015-06-26 Thread Shi, Tao via R-help

Hi Jens,
Thanks for the example!  I can see that you can change the 'filename' attribute 
for a ff object one-by-one, but is there a way to issue one command that will 
automatically change the attribute to all the ff objects in your workspace, as 
you can imagine when I have large number of objects like this, doing one-by-one 
is cumbersome?  After all, all it needs to change is the folder path, right?
May be this is a too wishful thinking :-)
Best,
Tao
 


 On Friday, June 26, 2015 3:31 AM, Jens Oehlschlägel 
jens.oehlschlae...@truecluster.com wrote:
   

 Tao,

I do assume that the ff-files are still at some location and not deleted 
by a finalizer. The following explains how to manipulate file locations 
with ff and ffdf objects.

Kind regards
jens

library(ff)
path1 - c:/tmp
path2 - c:/tmp2
# create ffdf,
# using non-standard path sets finalizer to 'close' instead of 'delete'
fdf1 - as.ffdf(iris, col_args=list(pattern=file.path(path1,iris)))
# let's copy the old metadata (but not the files, useclone for that)
# using ffs hybrid copying semantics
fdf2 - fdf1
# note both are open
is.open(fdf1)
is.open(fdf2)
# close the files
close(fdf1)
# and note that
is.open(fdf1)
is.open(fdf2)
# the magic has kept physical metadata in synch even in the copy
# (virtual metadata is not kept in synch
# which allows different virtual views into the same files
# not unlike SQL VIEWs virtualize dastabase TABLEs)

# filename on a ffdf
filename(fdf2)
# is a shortcut for
lapply(physical(fdf2), filename)
# so filename is a physical attribute
# actually moving the files can be done with the filename- method
lapply(physical(fdf2), function(x)filename(x) - sub(path1, path2, 
filename(x)))
# check this
filename(fdf1)
filename(fdf2)

# filename on ff
filename(fdf1$Species)
# is a shortcut for
attr(attr(fdf1$Species, physical), filename)
# and if you directly manipulate this attribute
# you circummvent the filename method
# and the file itself will not be moved
attr(attr(fdf1$Species, physical), filename) - sub(path2, path1, 
filename(fdf1$Species))
# now the metadata points to a different location
filename(fdf1$Species)
# note that this physical attribute was also changed
# for the copy
filename(fdf2$Species)
# of course you can fix the erroneous metadata by
attr(attr(fdf1$Species, physical), filename) - sub(path1, path2, 
filename(fdf1$Species))
# or for all columns in a ffdf by
lapply(physical(fdf2), function(x)attr(attr(x, physical), filename) 
- sub(path2, path1, filename(x)))
# now we have your situation with broken metadata
open(fdf2)
# and can fix that by
lapply(physical(fdf2), function(x)attr(attr(x, physical), filename) 
- sub(path1, path2, filename(x)))
# check
open(fdf2)



Am 26.06.2015 um 01:04 schrieb Shi, Tao:
 Hi all,

 I'm new to ff package through the using Bioconductor package crlmm.  Here 
 is my problem:

 I've created a few R objects (e.g. an CNSet) using crlmm based on my data and 
 save them in a .RData file.  crlmm heavily uses ff package to store results 
 on a local folder.  For certain reasons, I have moved the ff output folder to 
 somewhere else.  Now when I go back to R, I can't open those CNSet, for 
 example, anymore, as the file has a property still storing the old ff output 
 folder path.

 My question is: is there a quick way to change these paths to the new one, so 
 I don't have to re-run the own analysis.

 Many thanks!

 Tao



  
[[alternative HTML version deleted]]

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Re: [R] how to change the ff properties of a ff-related R object after the original ff output folder has been moved

2015-06-26 Thread Shi, Tao via R-help

Hi David,
Normally, I would have a R code example for this, but since I'm new to this too 
and just didn't have time to do that.  Hopefully, Jen's code illustrates the 
problem.
Tao
 


 On Thursday, June 25, 2015 8:53 PM, David Winsemius 
dwinsem...@comcast.net wrote:
   

 
On Jun 25, 2015, at 4:04 PM, Shi, Tao via R-help wrote:

 Hi all,
 
 I'm new to ff package through the using Bioconductor package crlmm.  Here 
 is my problem:
 
 I've created a few R objects (e.g. an CNSet) using crlmm based on my data and 
 save them in a .RData file.  crlmm heavily uses ff package to store results 
 on a local folder.  For certain reasons, I have moved the ff output folder to 
 somewhere else.  Now when I go back to R, I can't open those CNSet, for 
 example, anymore, as the file has a property still storing the old ff output 
 folder path. 
 
 My question is: is there a quick way to change these paths to the new one, so 
 I don't have to re-run the own analysis.
 

The way to approach this is to create a small example that illustrates teh 
problem. In many case all will becove clear, but if not then you will have 
something that you can then post ... IN R CODE ... that will let us (most of 
whom are not ff-urers) see the problem.

--
David Winsemius
Alameda, CA, USA


  
[[alternative HTML version deleted]]

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[R] how to change the ff properties of a ff-related R object after the original ff output folder has been moved

2015-06-25 Thread Shi, Tao via R-help

Hi all,

I'm new to ff package through the using Bioconductor package crlmm.  Here 
is my problem:

I've created a few R objects (e.g. an CNSet) using crlmm based on my data and 
save them in a .RData file.  crlmm heavily uses ff package to store results on 
a local folder.  For certain reasons, I have moved the ff output folder to 
somewhere else.  Now when I go back to R, I can't open those CNSet, for 
example, anymore, as the file has a property still storing the old ff output 
folder path. 

My question is: is there a quick way to change these paths to the new one, so I 
don't have to re-run the own analysis.

Many thanks!

Tao

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

[R] Error in title(...) : X11 font ....

2015-05-12 Thread Shi, Tao

Hi list,

Could anybody help me to explain the following error message and fix it?  Thank 
you very much!

Tao


 sessionInfo() 
R version 3.1.2 (2014-10-31) 
Platform: x86_64-unknown-linux-gnu (64-bit) 

locale: 
[1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C 
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 
[7] LC_PAPER=en_US.UTF-8   LC_NAME=C 
[9] LC_ADDRESS=C   LC_TELEPHONE=C 
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C 

attached base packages: 
[1] stats graphics  grDevices utils datasets  methods   base 
 
 
 plot(1:10, xlab=haha) 
 plot(1:10, ylab=haha) 
 plot(1:10, main=haha) 
Error in title(...) : 
X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 2 at size 14 could 
not be loaded

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[R] Rtools 3.3 is not compatible with R 3.2.0.?

2015-04-21 Thread Shi, Tao

hi list,

Any updates on this issue?  Thank you very much!

Tao


 devtools::install_github(rstudio/packrat) 
WARNING: Rtools 3.3 found on the path at c:/Rtools is not compatible with R 
3.2.0. 

Please download and install Rtools 3.1 from 
http://cran.r-project.org/bin/windows/Rtools/, remove the incompatible version 
from your PATH, then run find_rtools(). 
Downloading github repo rstudio/packrat@master 
Installing packrat 
C:/PROGRA~1/R/R-32~1.0/bin/x64/R --vanilla CMD INSTALL  \ 
C:/Users/tshi/AppData/Local/Temp/Rtmp6VYlhX/devtools25dc273e706c/rstudio-packrat-42b76ad
 --library=C:/Program Files/R/R-3.2.0/library  \ 
--install-tests 

* installing *source* package 'packrat' ... 
** R 
** inst 
** tests 
** preparing package for lazy loading 
** help 
*** installing help indices 
** building package indices 
** testing if installed package can be loaded 
* DONE (packrat) 

 find_rtools() 
WARNING: Rtools 3.3 found on the path at c:/Rtools is not compatible with R 
3.2.0. 

Please download and install Rtools 3.1 from 
http://cran.r-project.org/bin/windows/Rtools/, remove the incompatible version 
from your PATH, then run find_rtools(). 

 sessionInfo() 
R version 3.2.0 (2015-04-16) 
Platform: x86_64-w64-mingw32/x64 (64-bit) 
Running under: Windows 7 x64 (build 7601) Service Pack 1 

locale: 
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  
  LC_MONETARY=English_United States.1252 
[4] LC_NUMERIC=C   LC_TIME=English_United States.1252 

attached base packages: 
[1] stats graphics  grDevices utils datasets  methods   base 

other attached packages: 
[1] devtools_1.7.0   packrat_0.4.3-19 

loaded via a namespace (and not attached): 
[1] httr_0.6.1 tools_3.2.0RCurl_1.95-4.5 stringr_0.6.2  bitops_1.0-6

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Re: [R] interactive labeling/highlighting on multiple xy scatter plots

2014-08-06 Thread Shi, Tao

This is new to me.  Thanks for suggesting!

Tao



On Friday, August 1, 2014 3:05 AM, Michael Lawrence lawrence.mich...@gene.com 
wrote:



You should check out the animint package.

https://github.com/tdhock/animint





On Mon, Jul 28, 2014 at 5:48 PM, Shi, Tao shida...@yahoo.com wrote:

hi list,

I'm comparing the changes of ~100 analytes in multiple treatment conditions.  
I plotted them in several different xy scattter plots.  It would be nice if I 
mouse over one point on one scatter plot, the label of the analyte on that 
scatter plot AS WELL AS on all other scatter plots will be automatically 
shown.  I know brushing in rggobi does this, but its interface is not good and 
it needs R or ggobi to run (I want send the results to the collaborators and 
let them to play with it without the need of installing R or ggobi on their 
machine).  rCharts is nice but so far it can only create one scatter plot at a 
time. 

Any good suggestions?

Many thanks!

Tao

__
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Re: [R] interactive labeling/highlighting on multiple xy scatter plots

2014-08-06 Thread Shi, Tao

Just saw this from the Rstudio webinar too.  Will explore it more.  Thanks!

Tao



On Thursday, July 31, 2014 11:11 AM, Greg Snow 538...@gmail.com wrote:



The brushing may only be available in the development version of
ggvis.  See here for the example:
https://github.com/rstudio/webinars/tree/master/2014-01


On Thu, Jul 31, 2014 at 10:17 AM, Shi, Tao shida...@yahoo.com wrote:
 I looked at ggvis briefly before, but didn't notice its brushing capability.  
 Now you explained.

 Thanks, both!

 Tao




 On Wednesday, July 30, 2014 9:50 AM, Ramnath Vaidyanathan 
 ramnath.vaidyanat...@mcgill.ca wrote:



 ggvis is an excellent option to do this kind of stuff.

 The only limitation currently is that all sorts of interactivity (tooltips, 
 brushing etc.) are done on the server side using Shiny. So you have to upload 
 your HTML to a shiny server for the interactivity to work.

 Best,
 Ramnath



 __
 Ramnath Vaidyanathan
 Assistant Professor of Operations Management
 Desautels Faculty of Management
 1001 Sherbrooke Street West
 Montreal, QC H3A 1G5
 Ph: +1 (514) 398-1457
 __


 On Wed, Jul 30, 2014 at 12:45 PM, Greg Snow 538...@gmail.com wrote:

 Another option that is in developement, but may do what you want is
ggvis (http://ggvis.rstudio.com/).  I have seen an example of brushing
created with ggvis that can then be embedded in a web page.  I am not
sure if you can send the html and support files directly to someone
without R (probably Rstudio) or if you need to upload it to a server
for others to see, but the later is still an option for collaborators
who do not have R installed.


On Tue, Jul 29, 2014 at 2:13 PM, Shi, Tao shida...@yahoo.com wrote:
 Thank you very much, Greg and Ramnath, for the pointers!  I'll explore more.




 On Tuesday, July 29, 2014 8:10 AM, Ramnath Vaidyanathan 
 ramnath.vaidyanat...@mcgill.ca wrote:



 There are plugins for rCharts that help you create custom charts.

 Here is a scatterplot matrix example

 http://mostlyconjecture.com/2014/02/09/scatterplot-matrix-with-rcharts/


 It doesn't support brushing, but I think it won't be hard adding that 
 behavior if you contact its author.

 Hope this helps.

 Best,
 Ramnath



 __
 Ramnath Vaidyanathan
 Assistant Professor of Operations Management
 Desautels Faculty of Management
 1001 Sherbrooke Street West
 Montreal, QC H3A 1G5
 Ph: +1 (514) 398-1457
 __


 On Tue, Jul 29, 2014 at 11:01 AM, Greg Snow 538...@gmail.com wrote:

 There is the TkBrush function in the TeachingDemos package that gives
brushing in a scatterplot matrix using a Tk interface rather than
ggobi.  There is also the iplots package which allows you to create
multiple scatterplots, histograms, boxplots, barcharts, etc. and
points selected in any one of the plots will then be highlighted in
all the others.  Both of those solutions require R to be installed.

I don't know of any way to get what you want without installing at
least one of ggobi or R (or some other program of similar complexity
to install).

On Mon, Jul 28, 2014 at 6:48 PM, Shi, Tao shida...@yahoo.com wrote:
 hi list,

 I'm comparing the changes of ~100 analytes in multiple treatment 
 conditions.  I plotted them in several different xy scattter plots.  It 
 would be nice if I mouse over one point on one scatter plot, the label of 
 the analyte on that scatter plot AS WELL AS on all other scatter plots 
 will be automatically shown.  I know brushing in rggobi does this, but 
 its interface is not good and it needs R or ggobi to run (I want send the 
 results to the collaborators and let them to play with it without the 
 need of installing R or ggobi on their machine).  rCharts is nice but so 
 far it can only create one scatter plot at a time.

 Any good suggestions?

 Many thanks!

 Tao

 __
 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.



--
Gregory (Greg) L. Snow Ph.D.

538...@gmail.com




--
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com




-- 
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com

__
R-help@r-project.org mailing list
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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] interactive labeling/highlighting on multiple xy scatter plots

2014-07-31 Thread Shi, Tao

I looked at ggvis briefly before, but didn't notice its brushing capability.  
Now you explained.

Thanks, both!

Tao




On Wednesday, July 30, 2014 9:50 AM, Ramnath Vaidyanathan 
ramnath.vaidyanat...@mcgill.ca wrote:



ggvis is an excellent option to do this kind of stuff.

The only limitation currently is that all sorts of interactivity (tooltips, 
brushing etc.) are done on the server side using Shiny. So you have to upload 
your HTML to a shiny server for the interactivity to work.

Best,
Ramnath



__
Ramnath Vaidyanathan
Assistant Professor of Operations Management
Desautels Faculty of Management
1001 Sherbrooke Street West
Montreal, QC H3A 1G5
Ph: +1 (514) 398-1457
__


On Wed, Jul 30, 2014 at 12:45 PM, Greg Snow 538...@gmail.com wrote:

Another option that is in developement, but may do what you want is
ggvis (http://ggvis.rstudio.com/).  I have seen an example of brushing
created with ggvis that can then be embedded in a web page.  I am not
sure if you can send the html and support files directly to someone
without R (probably Rstudio) or if you need to upload it to a server
for others to see, but the later is still an option for collaborators
who do not have R installed.


On Tue, Jul 29, 2014 at 2:13 PM, Shi, Tao shida...@yahoo.com wrote:
 Thank you very much, Greg and Ramnath, for the pointers!  I'll explore more.




 On Tuesday, July 29, 2014 8:10 AM, Ramnath Vaidyanathan 
 ramnath.vaidyanat...@mcgill.ca wrote:



 There are plugins for rCharts that help you create custom charts.

 Here is a scatterplot matrix example

 http://mostlyconjecture.com/2014/02/09/scatterplot-matrix-with-rcharts/


 It doesn't support brushing, but I think it won't be hard adding that 
 behavior if you contact its author.

 Hope this helps.

 Best,
 Ramnath



 __
 Ramnath Vaidyanathan
 Assistant Professor of Operations Management
 Desautels Faculty of Management
 1001 Sherbrooke Street West
 Montreal, QC H3A 1G5
 Ph: +1 (514) 398-1457
 __


 On Tue, Jul 29, 2014 at 11:01 AM, Greg Snow 538...@gmail.com wrote:

 There is the TkBrush function in the TeachingDemos package that gives
brushing in a scatterplot matrix using a Tk interface rather than
ggobi.  There is also the iplots package which allows you to create
multiple scatterplots, histograms, boxplots, barcharts, etc. and
points selected in any one of the plots will then be highlighted in
all the others.  Both of those solutions require R to be installed.

I don't know of any way to get what you want without installing at
least one of ggobi or R (or some other program of similar complexity
to install).

On Mon, Jul 28, 2014 at 6:48 PM, Shi, Tao shida...@yahoo.com wrote:
 hi list,

 I'm comparing the changes of ~100 analytes in multiple treatment 
 conditions.  I plotted them in several different xy scattter plots.  It 
 would be nice if I mouse over one point on one scatter plot, the label of 
 the analyte on that scatter plot AS WELL AS on all other scatter plots 
 will be automatically shown.  I know brushing in rggobi does this, but its 
 interface is not good and it needs R or ggobi to run (I want send the 
 results to the collaborators and let them to play with it without the need 
 of installing R or ggobi on their machine).  rCharts is nice but so far it 
 can only create one scatter plot at a time.

 Any good suggestions?

 Many thanks!

 Tao

 __
 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.



--
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com




--
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com


__
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.

Re: [R] interactive labeling/highlighting on multiple xy scatter plots

2014-07-29 Thread Shi, Tao

Thank you very much, Greg and Ramnath, for the pointers!  I'll explore more.




On Tuesday, July 29, 2014 8:10 AM, Ramnath Vaidyanathan 
ramnath.vaidyanat...@mcgill.ca wrote:



There are plugins for rCharts that help you create custom charts.

Here is a scatterplot matrix example

http://mostlyconjecture.com/2014/02/09/scatterplot-matrix-with-rcharts/


It doesn't support brushing, but I think it won't be hard adding that behavior 
if you contact its author.

Hope this helps.

Best,
Ramnath



__
Ramnath Vaidyanathan
Assistant Professor of Operations Management
Desautels Faculty of Management
1001 Sherbrooke Street West
Montreal, QC H3A 1G5
Ph: +1 (514) 398-1457
__


On Tue, Jul 29, 2014 at 11:01 AM, Greg Snow 538...@gmail.com wrote:

There is the TkBrush function in the TeachingDemos package that gives
brushing in a scatterplot matrix using a Tk interface rather than
ggobi.  There is also the iplots package which allows you to create
multiple scatterplots, histograms, boxplots, barcharts, etc. and
points selected in any one of the plots will then be highlighted in
all the others.  Both of those solutions require R to be installed.

I don't know of any way to get what you want without installing at
least one of ggobi or R (or some other program of similar complexity
to install).

On Mon, Jul 28, 2014 at 6:48 PM, Shi, Tao shida...@yahoo.com wrote:
 hi list,

 I'm comparing the changes of ~100 analytes in multiple treatment conditions. 
  I plotted them in several different xy scattter plots.  It would be nice if 
 I mouse over one point on one scatter plot, the label of the analyte on that 
 scatter plot AS WELL AS on all other scatter plots will be automatically 
 shown.  I know brushing in rggobi does this, but its interface is not good 
 and it needs R or ggobi to run (I want send the results to the collaborators 
 and let them to play with it without the need of installing R or ggobi on 
 their machine).  rCharts is nice but so far it can only create one scatter 
 plot at a time.

 Any good suggestions?

 Many thanks!

 Tao

 __
 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.



--
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com


__
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.

[R] interactive labeling/highlighting on multiple xy scatter plots

2014-07-28 Thread Shi, Tao

hi list,

I'm comparing the changes of ~100 analytes in multiple treatment conditions.  I 
plotted them in several different xy scattter plots.  It would be nice if I 
mouse over one point on one scatter plot, the label of the analyte on that 
scatter plot AS WELL AS on all other scatter plots will be automatically shown. 
 I know brushing in rggobi does this, but its interface is not good and it 
needs R or ggobi to run (I want send the results to the collaborators and let 
them to play with it without the need of installing R or ggobi on their 
machine).  rCharts is nice but so far it can only create one scatter plot at a 
time. 

Any good suggestions?

Many thanks!

Tao

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Re: [R] tab auto-fill and arrow keys are not working in R on a linux cluster

2014-06-04 Thread Shi, Tao


Thank you, Jeff!  I'll try that.

Tao




On Tuesday, June 3, 2014 5:22 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us 
wrote:
FAQ 7.20
---
Jeff Newmiller                        The     .       .  Go Live...
DCN:jdnew...@dcn.davis.ca.us        Basics: ##.#.       ##.#.  Live Go...
                                      Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
/Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.




On June 3, 2014 4:47:58 PM PDT, Shi, Tao shida...@yahoo.com wrote:
Hi List,

We have R 3.1.0 installed on the head node of our linux cluster, but
the tab auto-complete and the arrow keys are not working.  When I was
trying to use the up/down arrow key to scroll through the old command
history I got something like this.  Any ideas on what's going on here?

Many thanks!

Tao


 sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.iso885915   LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915    LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=en_US.iso885915   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base
 ^[[A^[[A^[[A^[[A
Error: unexpected input in 

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[R] tab auto-fill and arrow keys are not working in R on a linux cluster

2014-06-03 Thread Shi, Tao

Hi List,

We have R 3.1.0 installed on the head node of our linux cluster, but the tab 
auto-complete and the arrow keys are not working.  When I was trying to use the 
up/down arrow key to scroll through the old command history I got something 
like this.  Any ideas on what's going on here?

Many thanks!

Tao


 sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.iso885915   LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915    LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=en_US.iso885915   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base
 ^[[A^[[A^[[A^[[A
Error: unexpected input in 

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[R] code folding for both TeX sections and R code chunks in .rnw file

2013-09-13 Thread Shi, Tao


Hi list,

Sorry, this is not a question directly for R, rather for R code editor.  I'm 
posting it here to capture wider audience.

The problem I'm facing is that as sometimes my .rnw file gets bigger and 
bigger, navigating through it becomes an issue.  Scrolling back-n-forth or 
remembering the line number of the section you want to go to are just not 
efficient.  It would be nice for the text editor to show a table of content 
tree NOT ONLY for .tex section/subsection headers BUT ALSO for R code chunks.  
It's kind of like what WinEdt is doing for .tex file but also adding R code 
chunks into the tree.  (please see the first figure on   
http://www.winedt.com/snap.html ).  Rstudio does pretty good job on folding R 
code, but not the .tex section headers.  


What are your best solutions?

Thanks!

Tao


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[R] XML package installation -- an old question

2013-08-15 Thread Shi, Tao

Hi list,

I have encountered the Cannot find xml2-config problem too during XML package 
installation on my 64-bit Redhat (v. 6.4) linux machine.  After looking through 
the old posts I checked all the necessary libraries and they all seem to be 
properly installed (see below).  I don't understand why R can't see the 
xml2-confg during the installation process.  Help, please!

Many thanks!

Tao



==

[root ~]# yum install libxml2
Setting up Install Process
Package matching libxml2-2.7.6-8.el6_3.3.x86_64 already installed. Checking for 
update.
Nothing to do
[root ~]# yum install libxml2-devel
Setting up Install Process
Package matching libxml2-devel-2.7.6-8.el6_3.3.x86_64 already installed. 
Checking for update.
Nothing to do
[root ~]# xml2-config --version
2.7.6
[root ~]# curl-config --version
libcurl 7.19.7



  R session ==


 install.packages(XML)
Installing package into \u2018/usr/lib64/R/library\u2019
(as \u2018lib\u2019 is unspecified)
trying URL 'http://cran.stat.ucla.edu/src/contrib/XML_3.98-1.1.tar.gz'
Content type 'application/x-tar' length 1582216 bytes (1.5 Mb)
opened URL
==
downloaded 1.5 Mb

* installing *source* package \u2018XML\u2019 ...
** package \u2018XML\u2019 successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... rm: cannot remove 
`a.out.dSYM': Is a directory
a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package \u2018XML\u2019
* removing \u2018/usr/lib64/R/library/XML\u2019

The downloaded source packages are in
    \u2018/tmp/RtmpwnAIFH/downloaded_packages\u2019
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(XML) :
  installation of package \u2018XML\u2019 had non-zero exit status


 sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C  
 [3] LC_TIME=en_US.UTF-8    LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C LC_NAME=C 
 [9] LC_ADDRESS=C   LC_TELEPHONE=C    
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base 

other attached packages:
[1] BiocInstaller_1.10.3

loaded via a namespace (and not attached):
[1] tcltk_3.0.1 tools_3.0.1
 


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Re: [R] XML package installation -- an old question

2013-08-15 Thread Shi, Tao

Hi Duncan,

Thank you very much for your quick response!  


It turns out I was typing the shell commands in another xterm which was ssh'ed 
to another linux computer and I completely forgot about it.  After finding that 
out and checking with my own computer, the libxml2 is installed but 
libxml2-devel is missing.  Installation libxml2-devel solved the problem.  My 
mistake!  Sorry about that.



Tao




- Original Message -
From: Duncan Temple Lang dtemplel...@ucdavis.edu
To: r-help@r-project.org
Cc: 
Sent: Thursday, August 15, 2013 10:38 AM
Subject: Re: [R] XML package installation -- an old question

Hi Tao

In the same R session as you call install.packages(),
what does

  system(which xml2-config, intern = TRUE)

return?

Basically, the error message from the configuration script for the
XML package is complaining that it cannot find the executable xml2-config
in your PATH.


(You can also send _me_ the config.log file from the attempted installation.)

  D.



On 8/15/13 10:13 AM, Shi, Tao wrote:
 Hi list,
 
 I have encountered the Cannot find xml2-config problem too during XML 
 package installation on my 64-bit Redhat (v. 6.4) linux machine.  After 
 looking through the old posts I checked all the necessary libraries and they 
 all seem to be properly installed (see below).  I don't understand why R 
 can't see the xml2-confg during the installation process.  Help, please!
 
 Many thanks!
 
 Tao
 
 
 
 ==
 
 [root ~]# yum install libxml2
 Setting up Install Process
 Package matching libxml2-2.7.6-8.el6_3.3.x86_64 already installed. Checking 
 for update.
 Nothing to do
 [root ~]# yum install libxml2-devel
 Setting up Install Process
 Package matching libxml2-devel-2.7.6-8.el6_3.3.x86_64 already installed. 
 Checking for update.
 Nothing to do
 [root ~]# xml2-config --version
 2.7.6
 [root ~]# curl-config --version
 libcurl 7.19.7
 
 
 
   R session ==
 
 
 install.packages(XML)
 Installing package into \u2018/usr/lib64/R/library\u2019
 (as \u2018lib\u2019 is unspecified)
 trying URL 'http://cran.stat.ucla.edu/src/contrib/XML_3.98-1.1.tar.gz'
 Content type 'application/x-tar' length 1582216 bytes (1.5 Mb)
 opened URL
 ==
 downloaded 1.5 Mb
 
 * installing *source* package \u2018XML\u2019 ...
 ** package \u2018XML\u2019 successfully unpacked and MD5 sums checked
 checking for gcc... gcc
 checking for C compiler default output file name... rm: cannot remove 
 `a.out.dSYM': Is a directory
 a.out
 checking whether the C compiler works... yes
 checking whether we are cross compiling... no
 checking for suffix of executables... 
 checking for suffix of object files... o
 checking whether we are using the GNU C compiler... yes
 checking whether gcc accepts -g... yes
 checking for gcc option to accept ISO C89... none needed
 checking how to run the C preprocessor... gcc -E
 checking for sed... /bin/sed
 checking for pkg-config... /usr/bin/pkg-config
 checking for xml2-config... no
 Cannot find xml2-config
 ERROR: configuration failed for package \u2018XML\u2019
 * removing \u2018/usr/lib64/R/library/XML\u2019
 
 The downloaded source packages are in
     \u2018/tmp/RtmpwnAIFH/downloaded_packages\u2019
 Updating HTML index of packages in '.Library'
 Making 'packages.html' ... done
 Warning message:
 In install.packages(XML) :
   installation of package \u2018XML\u2019 had non-zero exit status
 
 
 sessionInfo()
 R version 3.0.1 (2013-05-16)
 Platform: x86_64-redhat-linux-gnu (64-bit)
 
 locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8  
  [7] LC_PAPER=C                 LC_NAME=C                
  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C      
 
 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base    
 
 other attached packages:
 [1] BiocInstaller_1.10.3
 
 loaded via a namespace (and not attached):
 [1] tcltk_3.0.1 tools_3.0.1

 
 
 __
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 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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[R] compare objects in two different workspaces

2013-02-07 Thread Shi, Tao

Hi list,

Is there a easy way to compare objects in two different workspace files (i.e. 
.RData files) in R?  I can use some generic file compare softwares (e.g. 
BeyondCompare) to binary comparison, but when it says they're different you 
can't tell where the difference are from.

Thanks!

Tao


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

Re: [R] compare objects in two different workspaces

2013-02-07 Thread Shi, Tao

In fact, they have objects with exact same names.  They were created by the 
same code at different time points.  The code is not version-controlled, so I 
only have the most recent version, but I want to know what's changed.

Tao




- Original Message -
 From: Bert Gunter gunter.ber...@gene.com
 To: R. Michael Weylandt michael.weyla...@gmail.com
 Cc: Shi, Tao shida...@yahoo.com; r-help@r-project.org 
 r-help@r-project.org
 Sent: Thursday, February 7, 2013 1:30 PM
 Subject: Re: [R] compare objects in two different workspaces
 
 ... but you need to load them into different environments in case they
 have objects with the same name, right?
 
 -- Bert
 
 On Thu, Feb 7, 2013 at 1:25 PM, R. Michael Weylandt
 michael.weyla...@gmail.com wrote:
  On Thu, Feb 7, 2013 at 5:53 PM, Shi, Tao shida...@yahoo.com wrote:
  Hi list,
 
  Is there a easy way to compare objects in two different workspace files 
 (i.e. .RData files) in R?  I can use some generic file compare softwares 
 (e.g. 
 BeyondCompare) to binary comparison, but when it says they're different you 
 can't tell where the difference are from.
 
  Load them both and compare within R?
 
  MW
 
 
  Thanks!
 
  Tao
 
 
  __
  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.
 
  __
  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.
 
 
 
 -- 
 
 Bert Gunter
 Genentech Nonclinical Biostatistics
 
 Internal Contact Info:
 Phone: 467-7374
 Website:
 http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm


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Re: [R] compare objects in two different workspaces

2013-02-07 Thread Shi, Tao

Thanks, Bert!  Never used it, but reading it now.

Tao





- Original Message -
 From: Bert Gunter gunter.ber...@gene.com
 To: Shi, Tao shida...@yahoo.com
 Cc: R. Michael Weylandt michael.weyla...@gmail.com; r-help@r-project.org 
 r-help@r-project.org
 Sent: Thursday, February 7, 2013 2:05 PM
 Subject: Re: [R] compare objects in two different workspaces
 
 Ummm...
 
 Have you actually read ?load to see how do this using the
 environment argument?
 
 -- Bert
 
 On Thu, Feb 7, 2013 at 1:58 PM, Shi, Tao shida...@yahoo.com wrote:
  In fact, they have objects with exact same names.  They were created by the 
 same code at different time points.  The code is not version-controlled, so I 
 only have the most recent version, but I want to know what's changed.
 
  Tao
 
 
 
 
  - Original Message -
  From: Bert Gunter gunter.ber...@gene.com
  To: R. Michael Weylandt michael.weyla...@gmail.com
  Cc: Shi, Tao shida...@yahoo.com; 
 r-help@r-project.org r-help@r-project.org
  Sent: Thursday, February 7, 2013 1:30 PM
  Subject: Re: [R] compare objects in two different workspaces
 
  ... but you need to load them into different environments in case they
  have objects with the same name, right?
 
  -- Bert
 
  On Thu, Feb 7, 2013 at 1:25 PM, R. Michael Weylandt
  michael.weyla...@gmail.com wrote:
   On Thu, Feb 7, 2013 at 5:53 PM, Shi, Tao 
 shida...@yahoo.com wrote:
   Hi list,
 
   Is there a easy way to compare objects in two different 
 workspace files
  (i.e. .RData files) in R?  I can use some generic file compare 
 softwares (e.g.
  BeyondCompare) to binary comparison, but when it says they're 
 different you
  can't tell where the difference are from.
 
   Load them both and compare within R?
 
   MW
 
 
   Thanks!
 
   Tao
 
 
   __
   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.
 
   __
   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.
 
 
 
  --
 
  Bert Gunter
  Genentech Nonclinical Biostatistics
 
  Internal Contact Info:
  Phone: 467-7374
  Website:
 
 http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
 
 
 
 
 -- 
 
 Bert Gunter
 Genentech Nonclinical Biostatistics
 
 Internal Contact Info:
 Phone: 467-7374
 Website:
 http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm


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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] what's this character?

2012-11-30 Thread Shi, Tao

Thank you, Jim, Peter, and John, for your help!   Turns out it is a non-break 
space.  No idea how it got there (the file is from somebody else).  Thanks to 
Excel, I guess.

Tao





 From: John j...@surewest.net
To: r-help@r-project.org 
Cc: Shi, Tao shida...@yahoo.com 
Sent: Wednesday, November 28, 2012 10:17 PM
Subject: Re: [R] what's this character?
 
On Wed, 28 Nov 2012 16:44:59 -0800 (PST)
Shi, Tao shida...@yahoo.com wrote:

 Hi list,
 
 I've encounter this problem (see below).  I know it's particularly
 R-related and it's easy to get by but it still bothers me a lot.  
 
 
 It looks the last character of N.C.  is a space to me, but it's
 clearly not.  Can someone tell me a way to figure out what character
 is in the last position.
 
 Thanks!
 
 Tao

In the sample you provide it is HEX 20 which is ASCII for space.  So
either, it really is a space, or it didn't copy in your message.  I
would suggest copying the string and pasting into a hex editor. 

Doing that with the N.C.  from your message yields:

22 4E 2E 43 2E 20 22

The 20 is the ASCII space character.  Just possibly, if you are
using a file saved in a unicode format, it could be a no-break space
- Unicode point U+00A0, or UTF-8 c2 a0.  Good luck.

JWDougherty




[[alternative HTML version deleted]]

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[R] what's this character?

2012-11-28 Thread Shi, Tao

Hi list,

I've encounter this problem (see below).  I know it's particularly R-related 
and it's easy to get by but it still bothers me a lot.  


It looks the last character of N.C.  is a space to me, but it's clearly not.  
Can someone tell me a way to figure out what character is in the last position.

Thanks!

Tao



 levels(dat$flag)[3]
[1] N.C. 
 levels(dat$flag)[3]==N.C. 
[1] FALSE
 substr(levels(dat$flag)[3],5,5)
[1]  
 substr(levels(dat$flag)[3],5,5)== 
[1] FALSE
 N.C. ==N.C.    ## NOTE: this last one can't be reproduced after 
 copy-n-paste
[1] FALSE

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[R] warning message

2012-10-15 Thread Shi, Tao

Hi list,

Can somebody explain why there are these warning messages?  I just don't get 
it.  I'm using R 2.15.1 on WinXP.

Thanks!

Tao


 x
[1] -2.143510 -1.157450 -1.315581  1.033562 -1.225440 -1.179909

  ifelse(x0, log2(x), -log2(-x))
[1] -1.099975 -0.210950 -0.395700  0.047625 -0.293300 -0.238675
Warning messages:
1: In ifelse(x  0, log2(x), -log2(-x)) : NaNs produced
2: In ifelse(x  0, log2(x), -log2(-x)) : NaNs produced


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Re: [R] warning message

2012-10-15 Thread Shi, Tao

Never mind.  I got it.  Thanks!

Tao

- Original Message -
 From: Shi, Tao shida...@yahoo.com
 To: r-help@r-project.org r-help@r-project.org
 Cc: 
 Sent: Monday, October 15, 2012 4:08 PM
 Subject: [R] warning message

 Hi list,

 Can somebody explain why there are these warning messages?  I just don't get 
 it.  I'm using R 2.15.1 on WinXP.

 Thanks!

 Tao

  x
 [1] -2.143510 -1.157450 -1.315581  1.033562 -1.225440 -1.179909

   ifelse(x0, log2(x), -log2(-x))
 [1] -1.099975 -0.210950 -0.395700  0.047625 -0.293300 -0.238675
 Warning messages:
 1: In ifelse(x  0, log2(x), -log2(-x)) : NaNs produced
 2: In ifelse(x  0, log2(x), -log2(-x)) : NaNs produced

 __
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 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] warning message

2012-10-15 Thread Shi, Tao

Thank you, Simon and Kevin!

Tao

- Original Message -
 From: Simon Knapp sleepingw...@gmail.com
 To: Shi, Tao shida...@yahoo.com
 Cc: r-help@r-project.org r-help@r-project.org
 Sent: Monday, October 15, 2012 4:25 PM
 Subject: Re: [R] warning message

T he second and third arguments to ifelse are evaluated for all
 elements of x (producing your warnings), then the appropriate elements
 of each result are combined based on the (logical) values of the first
 argument to ifelse.

 On Tue, Oct 16, 2012 at 10:08 AM, Shi, Tao shida...@yahoo.com wrote:
  Hi list,

  Can somebody explain why there are these warning messages?  I just 
 don't get it.  I'm using R 2.15.1 on WinXP.

  Thanks!

  Tao

  x
  [1] -2.143510 -1.157450 -1.315581  1.033562 -1.225440 -1.179909

   ifelse(x0, log2(x), -log2(-x))
  [1] -1.099975 -0.210950 -0.395700  0.047625 -0.293300 -0.238675
  Warning messages:
  1: In ifelse(x  0, log2(x), -log2(-x)) : NaNs produced
  2: In ifelse(x  0, log2(x), -log2(-x)) : NaNs produced

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Re: [R] Sweave encoding option

2012-09-05 Thread Shi, Tao

Hi Yihui,

Thanks for your quick reply!Â  Yes, it was a long vacation, but definitely not 
long enoughÂ  :-).


Seriously, I have not changed my R, my tex engine etc.Â  Nothing.Â  And I was 
running the command just a couple of weeks ago and everything was fine.Â  But 
now I need to specify this encoding option

Still puzzled.

Tao





 From: Yihui Xie x...@yihui.name
To: Shi, Tao shida...@yahoo.com 
Cc: r-help@r-project.org r-help@r-project.org 
Sent: Tuesday, September 4, 2012 7:40 PM
Subject: Re: [R] Sweave encoding option
 
What happened might be that your vacation took too long. The encoding
argument was introduced in R 2.13.1 (July last year). Nothing has
changed in your Rnw document, but things have always been changing in
R, so the best thing to do is to check out help(Sweave).

Regards,
Yihui
--
Yihui Xie xieyi...@gmail.com
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA


On Tue, Sep 4, 2012 at 7:02 PM, Shi, Tao shida...@yahoo.com wrote:


 Hi list,

 I was running Sweave on one of my .rnw file.Â  Everything was fine, until I 
 came back from the vacation.Â  Nothing changed (at least to my knowledge), 
 but now I have this problem:

Â  Â   Sweave(myfile.rnw)
 Error: âCOLO001final.rnwâ is not ASCII and does not declare an encoding


 After snooping around on the web, I found this solution:

 Sweave(myfile.rnw, encoding=utf8)

 Now everything works fine.

 Could somebody explain to me what happened?Â  Why I need to specify the 
 encoding now for it to work?Â  What has changed (beyond my knowledge) in 
 my computer that is causing this error?

 I'm running R 2.15.1 on WinXP.

 Thanks!

 Tao

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[R] Sweave encoding option

2012-09-04 Thread Shi, Tao



Hi list,

I was running Sweave on one of my .rnw file.  Everything was fine, until I came 
back from the vacation.  Nothing changed (at least to my knowledge), but now I 
have this problem:

 Sweave(myfile.rnw)
Error: ‘COLO001final.rnw’ is not ASCII and does not declare an encoding


After snooping around on the web, I found this solution:

 Sweave(myfile.rnw, encoding=utf8)

Now everything works fine.

Could somebody explain to me what happened?  Why I need to specify the 
encoding now for it to work?  What has changed (beyond my knowledge) in my 
computer that is causing this error?

I'm running R 2.15.1 on WinXP.

Thanks!

Tao

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Re: [R] .rda vs. .RData

2012-04-24 Thread Shi, Tao

Thank you, all!

 From: Barry Rowlingson b.rowling...@lancaster.ac.uk
To: Jeff Newmiller jdnew...@dcn.davis.ca.us 
Cc: Shi, Tao shida...@yahoo.com; Ista Zahn istaz...@gmail.com; 
r-help@r-project.org r-help@r-project.org 
Sent: Tuesday, April 24, 2012 12:36 AM
Subject: Re: [R] .rda vs. .RData

On Tue, Apr 24, 2012 at 12:51 AM, Jeff Newmiller
jdnew...@dcn.davis.ca.us wrote:
 My bad, I was thinking of rds (?saveRDS). RData and rda are mentioned under 
 ?data as alternate file extensions for the same data format. Sorry for 
 posting without checking first.

Understandable mistake. Confusingly similar file extensions are
confusingly similar.

I'd have called them .Rob for the current .rds file format (single
object), and .Ros for the current .rda file format (1 objects).

[actually I would have called them .Rob or .Robject, and .Rwk or
.Rworkspace but then I noticed that if you had a .Rob you had to have
a .Ros so as not to favour one or other of the project originators :)]

Barry

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[R] load only one object from a .RData file

2012-04-24 Thread Shi, Tao

Hi list,


Is there a way to load one specific object from a .RData file which contains 
multiple data objects?  Thanks,

...Tao


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Re: [R] load only one object from a .RData file

2012-04-24 Thread Shi, Tao

Thank you, Michael and Henrik.  I'll try what you suggested.

 From: Henrik Bengtsson h...@biostat.ucsf.edu
To: Shi, Tao shida...@yahoo.com 
Cc: r-help@r-project.org r-help@r-project.org 
Sent: Tuesday, April 24, 2012 12:37 PM
Subject: Re: [R] load only one object from a .RData file

You could do:

library(R.utils);
value - loadToEnv(MyFile.RData)[[nameOfObject]];

It still load all of the data, but it is not kept; only the object you grab.

/Henrik

On Tue, Apr 24, 2012 at 11:30 AM, Shi, Tao shida...@yahoo.com wrote:
 Hi list,

 Is there a way to load one specific object from a .RData file which contains 
 multiple data objects?  Thanks,

 ...Tao

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[R] .rda vs. .RData

2012-04-23 Thread Shi, Tao

Are they the same with .RData being the newer format?  Thanks,

...Tao


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Re: [R] barplot with both color and shading

2012-02-22 Thread Shi, Tao

Thank you both, Michael and Jim, for the answers!

- Original Message -
 From: Michael Bibo michael_b...@health.qld.gov.au
 To: r-h...@stat.math.ethz.ch
 Cc: 
 Sent: Wednesday, February 22, 2012 12:46 AM
 Subject: Re: [R] barplot with both color and shading

 Shi, Tao shidaxia at yahoo.com writes:

  Hi list,

  I want to draw a bar plot with color indicating one grouping and different
 shading on top of the color
  indicating another grouping.  How should I proceed?

  Thanks!

  ...Tao

 Does this help?

 http://finzi.psych.upenn.edu/Rhelp10/2010-September/252219.html 

 Michael Bibo
 michael_biboathealth.qld.gov.au

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[R] barplot with both color and shading

2012-02-21 Thread Shi, Tao

Hi list,

I want to draw a bar plot with color indicating one grouping and different 
shading on top of the color indicating another grouping.  How should I proceed?

Thanks!

...Tao


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Re: [R] barplot with both color and shading

2012-02-21 Thread Shi, Tao

Hi Michael,

Thanks for your reply! 

I'm not sure if I was clear.  I was really thinking about shading lines.  


I have just came up with a solution on my own:
barplot(1:10, col=rep(0:1, each=5))

barplot(1:10, angle=20, density=c(0,20), col=2, add=T)


Here is my initial failed attempt:

barplot(1:10, angle=20, density=c(0,20), col=rep(0:1, each=5))


...Tao




- Original Message -
 From: R. Michael Weylandt michael.weyla...@gmail.com
 To: Shi, Tao shida...@yahoo.com
 Cc: r-help@r-project.org r-help@r-project.org
 Sent: Tuesday, February 21, 2012 6:49 PM
 Subject: Re: [R] barplot with both color and shading
 
T his seems like a natural fit for ggplot2 graphics, but I'm not aware
 of shading as a widely implemented graphical element: this might have
 some useful information --
 http://had.co.nz/ggplot2/geom_histogram.html
 
 Can you find an example of shading in R? (perhaps in the R Graphics
 Gallery) If you look at example(barplot) there's an example of how to
 use different line patterns, but I don't find it particularly clear.
 The grouping techniques seem much clearer to me.
 
 Michael
 
 On Tue, Feb 21, 2012 at 5:24 PM, Shi, Tao shida...@yahoo.com wrote:
  Hi list,
 
  I want to draw a bar plot with color indicating one grouping and different 
 shading on top of the color indicating another grouping.  How should I 
 proceed?
 
  Thanks!
 
  ...Tao
 
 
  __
  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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Re: [R] extract worksheet names from an Excel file

2011-06-25 Thread Shi, Tao

Thanks, Gabor!  That's really helpful!

...Tao

- Original Message -
 From: Gabor Grothendieck ggrothendi...@gmail.com
 To: Shi, Tao shida...@yahoo.com
 Cc: r-help@r-project.org r-help@r-project.org
 Sent: Friday, June 24, 2011 5:02 AM
 Subject: Re: [R] extract worksheet names from an Excel file

 On Fri, Jun 24, 2011 at 12:41 AM, Shi, Tao shida...@yahoo.com wrote:
  Hi list,

  Is there a R function I can use to extract the worksheet names from an 
 Excel file?  If no, any other automatic ways (not using R) to do this?

  thanks!

 Many or all of the Excel interfaces listed here:

 http://rwiki.sciviews.org/doku.php?id=tips:data-io:ms_windowss=excel

 can do that but be careful since one or more the packages listed there
 always returns the sheet names sorted in alphabetical order which
 means that you can't tell which is the first sheet, which is the
 second, etc. (if that is important).

 gdata has a specific function to do it:

 library(gdata)
 sheetNames(myfile.xls)

 -- 
 Statistics  Software Consulting
 GKX Group, GKX Associates Inc.
 tel: 1-877-GKX-GROUP
 email: ggrothendieck at gmail.com

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[R] extract worksheet names from an Excel file

2011-06-23 Thread Shi, Tao

Hi list,

Is there a R function I can use to extract the worksheet names from an Excel 
file?  If no, any other automatic ways (not using R) to do this?

thanks!

...Tao


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Re: [R] extract worksheet names from an Excel file

2011-06-23 Thread Shi, Tao

Thank you, David and Bill!  I'll try that.

...Tao

- Original Message -
 From: David Scott d.sc...@auckland.ac.nz
 To: bill.venab...@csiro.au
 Cc: shida...@yahoo.com; r-help@r-project.org
 Sent: Thursday, June 23, 2011 10:11 PM
 Subject: Re: [R] extract worksheet names from an Excel file

   On 24/06/11 16:55, bill.venab...@csiro.au wrote:
  Package XLConnect appears to provide this kind of thing.

  -Original Message-
  From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
 Behalf Of Shi, Tao
  Sent: Friday, 24 June 2011 2:42 PM
  To: r-help@r-project.org
  Subject: [R] extract worksheet names from an Excel file

  Hi list,

  Is there a R function I can use to extract the worksheet names from an 
 Excel file?  If no, any other automatic ways (not using R) to do this?

  thanks!

  ...Tao

  __
  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
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  __
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 http://www.R-project.org/posting-guide.html
  and provide commented, minimal, self-contained, reproducible code.

 If you use RODBC to connect to an xls or xlsx file you can use sqlTables 
 to show not only the worksheet names, but the presence of any named data 
 ranges.

 Sample code from a student exercise:

 require(RODBC)
 channel - odbcConnectExcel(bikesWithDate.xls)
 sqlTables(channel)

 David

 -- 
 _
 David Scott    Department of Statistics
         The University of Auckland, PB 92019
         Auckland 1142,    NEW ZEALAND
 Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
 Email:    d.sc...@auckland.ac.nz,  Fax: +64 9 373 7018

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[R] a bug in heatmap.plus?

2011-06-08 Thread Shi, Tao

Hi Allen and list,

See the code below.  I've tried it on R2.13 and R2.8.0 using either 
heatmap.plus 1.3 or the latest.  All gave the same results.  The problem is in 
the last line: when I tried to plot two different color bars, the one 
corresponding to cm.colors(10) is not correct (it starts with one black and 
one red.  Not sure where they're from?)

Any ideas?

Thanks!

...Tao


library(heatmap.plus)
set.seed(1234)

x - matrix(rnorm(400), ncol=10)
heatmap(x, ColSideColors= cm.colors(10), Colv=NA)
heatmap.plus(x, ColSideColors=cbind(cm.colors(10), cm.colors(10)), Colv=NA)
heatmap.plus(x, ColSideColors=cbind(rep(1:2,each=5), cm.colors(10)), Colv=NA)

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Re: [R] network package in R

2011-05-28 Thread Shi, Tao

Weiwei,

I know this is not a Bioconductor-specific question, but you may also want to 
post it on BiC help list, as there may be more people there understand what you 
want to do.  I'm also curious about the answers to your question.

...Tao





- Original Message 
 From: Weiwei Shi helprh...@gmail.com
 To: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch
 Sent: Fri, May 27, 2011 2:32:23 PM
 Subject: [R] network package in R
 
 Hi there,
 
 I need a network builder and it can change the node size and  color; I am not
 sure if network package in R can do this or not. The other  functions I
 wanted have been found in that package.
 
 BTW, if there is  another package in R relating to this, please suggest  too.
 
 Thanks,
 
 Weiwei
 
 -- 
 Weiwei Shi, Ph.D
 Research  Scientist
 
 
 Did you always know?
 No, I did not. But I  believed...
 ---Matrix III
 
 [[alternative HTML  version deleted]]
 
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Re: [R] changes in coxph in survival from older version?

2011-05-20 Thread Shi, Tao

Thank you very much, Frank and Terry, again, for all your answers!

...Tao

- Original Message 
 From: Terry Therneau thern...@mayo.edu
 To: Shi, Tao shida...@yahoo.com
 Cc: Frank Harrell f.harr...@vanderbilt.edu; r-help@r-project.org
 Sent: Fri, May 20, 2011 6:36:28 AM
 Subject: Re: [R] changes in coxph in survival from older version?

 On Thu, 2011-05-19 at 17:03 -0700, Shi, Tao wrote:
  Thank you, Frank  and Terry, for all your answers!  I'll upgrade my 
survival 

   package for sure!

  It seems to me that you two are pointing to  two different issues: 1) Is 
stepwise 

  model selection a good approach  (for any data)?  2) Whether the data I 
  have 
has 

  enough information  that even worth to model?  For #1, I'm not in a good 
position 

  to  judge and need to read up on it.  For #2, I'm still a bit confused 
  about 

  Terry's last comment.  If we forget about multivariate model  building and 
just 

  look at variable one by one and select the best  predictor (let's say it's 
highly 

  significant, e.g. p0.0001), the  resulting univariate model still can be 
wrong?

  What if I use  this data as a validation set to validate an existing model? 

   Anything different?

  Many thanks!

  Stepwise regression is  a bad idea. Whether you let the machine do it or
 you have a human do it (run  all univariates, read the output, pick the
 best) it is still stepwise  selection.  It is still very unstable, even
 with very large sample  size.

   Terry T.

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Re: [R] changes in coxph in survival from older version?

2011-05-19 Thread Shi, Tao

Thank you, Frank and Terry, for all your answers! I'll upgrade my survival
package for sure!

It seems to me that you two are pointing to two different issues: 1) Is
stepwise
model selection a good approach (for any data)? 2) Whether the data I have has
enough information that even worth to model? For #1, I'm not in a good
position
to judge and need to read up on it. For #2, I'm still a bit confused about
Terry's last comment. If we forget about multivariate model building and just
look at variable one by one and select the best predictor (let's say it's
highly
significant, e.g. p0.0001), the resulting univariate model still can be wrong?

What if I use this data as a validation set to validate an existing model?
Anything different?

Many thanks!

...Tao

- Original Message
From: Frank Harrell f.harr...@vanderbilt.edu
To: r-help@r-project.org
Sent: Tue, May 17, 2011 10:51:02 AM
Subject: Re: [R] changes in coxph in survival from older version?

It's worse if the model does converge because then you don't have a warning
about the result being nonsense.
Frank

Terry Therneau-2 wrote:

-- begin included message ---
I did realize that there are way more predictors in the model. My
initial thinking was use that as an initial model for stepwise model
selection. Now I wonder if the model selection result is still valid
if the initial model didn't even converge?
--- end inclusion ---

You have 17 predictors with only 22 events. All methods of variable
selection in such a scenario will give essentially random results.
There is simply not enough information present to determine a best
predictor or best subset of predictors.

Terry Therneau

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-
Frank Harrell
Department of Biostatistics, Vanderbilt University
--
View this message in context:
http://r.789695.n4.nabble.com/changes-in-coxph-in-survival-from-older-version-tp3516101p3530024.html

Sent from the R help mailing list archive at Nabble.com.

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Re: [R] changes in coxph in survival from older version?

2011-05-16 Thread Shi, Tao

Hi Terry,

Really appreciate your help!  Sorry for my late reply.

I did realize that there are way more predictors in the model.  My initial 
thinking was use that as an initial model for stepwise model selection.  Now I 
wonder if the model selection result is still valid if the initial model didn't 
even converge?

Thanks!

...Tao




- Original Message 
 From: Terry Therneau thern...@mayo.edu
 To: Shi, Tao shida...@yahoo.com
 Cc: r-help@r-project.org
 Sent: Thu, May 12, 2011 6:42:09 AM
 Subject: Re: changes in coxph in survival from older version?
 
 
 On Wed, 2011-05-11 at 16:11 -0700, Shi, Tao wrote:
  Hi all,
  
  I found that the two different versions of survival packages, namely  
2.36-5 

  vs. 2.36-8 or later, give different results for coxph  function.  Please 
  see 

  below and the data is attached.  The  second one was done on Linux, but 
Windows 

  gave the same results.   Could you please let me know which one I should 
trust?
  
   Thanks,
 
  In your case, neither.  Your data set has 22 events and 17  predictors;
 the rule of thumb for a reliable Cox model is 10-20 events per  predictor
 which implies no more than 2 for your data set.  As a result,  the
 coefficients of your model have very wide confidence intervals, the  coef
 for Male for instance has se of 3.26, meaning the CI goes from 1/26  to
 26 times the estimate; i.e., there is no biological meaning to  the
 estimate.
 
   Nevertheless, why did coxph give a different  answer?  The later
 version 2.36-9 failed to converge (20 iterations)  with a final
 log-likelihood of -19.94, the earlier code converges in 10  iterations to
 -19.91.  In version 2.36-6 an extra check was put into the  maximizer for
 coxph in response to an exceptional data set which caused the  routine to
 fail due to overflow of the exp function; the Newton-Raphson  iteration
 algorithm had made a terrible guess in it's iteration path, which  can
 happen with all NR based search methods.  
I put a limit  on the size the linear predictor in the Cox model of
 21.  The basic  argument is that exp(linear-predictor) = relative risk
 for a subject, and  that there is not much biological meaning for risks
 to be less than exp(-21)  ~ 1/(population of the earh).  There is more to
 the reasoning,  interested parties should look at the comments in
 src/coxsafe.c, a 5 line  routine with 25 lines of discussion.  I will
 happily accept input the  best value for the constant.
 
I never expected to see a data set  with both convergence of the LL
 and linear predictors larger than +-15.   Looking at the fit (older code)
  round(fit2$linear.predictor, 2)
   [1]   2.26   0.89   4.96 -19.09 -12.10   1.392.82   3.10
  [9]  18.57 -25.25  22.94   8.75   5.52  -27.64  14.88 -23.41
 [17]  13.70 -28.45  -1.84   10.04  12.62   2.54   6.33  -8.76
 [25]   9.684.39   2.92   3.51   6.02 -17.24   5.97
 
 This says  that, if the model is to be believed, you have several near
 immortals in the  data set. (Everyone else on earth will perish first).
 
 Terry  Therneau
 
 
 


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Re: [R] changes in coxph in survival from older version?

2011-05-16 Thread Shi, Tao

Hi Frank,

I know it's kind of beyond the scope of R help, but I would appreciate it if
you
can elaborate further on this. Are you worrying about this variable selection
approach or you think that there is something wrong with the data (it's
actually
a real dataset)? If it's the first one, I believe I can always narrow down the
variables based on univarate analysis and build a multivariate model from that.

Many thanks in advance.

...Tao

- Original Message
From: Frank Harrell f.harr...@vanderbilt.edu
To: r-help@r-project.org
Sent: Mon, May 16, 2011 11:25:20 AM
Subject: Re: [R] changes in coxph in survival from older version?

Please don't be serious about doing variable selection with this dataset.
Frank

Shi, Tao wrote:

Hi Terry,

Really appreciate your help! Sorry for my late reply.

I did realize that there are way more predictors in the model. My initial
thinking was use that as an initial model for stepwise model selection.
Now I
wonder if the model selection result is still valid if the initial model
didn't
even converge?

Thanks!

...Tao

- Original Message
From: Terry Therneau lt;thern...@mayo.edugt;
To: Shi, Tao lt;shida...@yahoo.comgt;
Cc: r-help@r-project.org
Sent: Thu, May 12, 2011 6:42:09 AM
Subject: Re: changes in coxph in survival from older version?

On Wed, 2011-05-11 at 16:11 -0700, Shi, Tao wrote:
Hi all,

I found that the two different versions of survival packages, namely
2.36-5

vs. 2.36-8 or later, give different results for coxph function.
Please see

below and the data is attached. The second one was done on Linux, but
Windows

gave the same results. Could you please let me know which one I
should
trust?

Thanks,

In your case, neither. Your data set has 22 events and 17 predictors;
the rule of thumb for a reliable Cox model is 10-20 events per predictor
which implies no more than 2 for your data set. As a result, the
coefficients of your model have very wide confidence intervals, the coef
for Male for instance has se of 3.26, meaning the CI goes from 1/26 to
26 times the estimate; i.e., there is no biological meaning to the
estimate.

Nevertheless, why did coxph give a different answer? The later
version 2.36-9 failed to converge (20 iterations) with a final
log-likelihood of -19.94, the earlier code converges in 10 iterations to
-19.91. In version 2.36-6 an extra check was put into the maximizer for
coxph in response to an exceptional data set which caused the routine to
fail due to overflow of the exp function; the Newton-Raphson iteration
algorithm had made a terrible guess in it's iteration path, which can
happen with all NR based search methods.
I put a limit on the size the linear predictor in the Cox model of
21. The basic argument is that exp(linear-predictor) = relative risk
for a subject, and that there is not much biological meaning for risks
to be less than exp(-21) ~ 1/(population of the earh). There is more to
the reasoning, interested parties should look at the comments in
src/coxsafe.c, a 5 line routine with 25 lines of discussion. I will
happily accept input the best value for the constant.

I never expected to see a data set with both convergence of the LL
and linear predictors larger than +-15. Looking at the fit (older code)
round(fit2$linear.predictor, 2)
[1] 2.26 0.89 4.96 -19.09 -12.10 1.39 2.82 3.10
[9] 18.57 -25.25 22.948.75 5.52 -27.64 14.88 -23.41
[17] 13.70 -28.45 -1.84 10.04 12.62 2.54 6.33 -8.76
[25] 9.684.39 2.923.51 6.02 -17.24 5.97

This says that, if the model is to be believed, you have several near
immortals in the data set. (Everyone else on earth will perish first).

Terry Therneau

Sent from the R help mailing list archive at Nabble.com.

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Re: [R] R versions for Red Hat Linux

2011-05-11 Thread Shi, Tao

I second Marc on this.  I just installed R2.12.2 on my linux box running RHEL.  
Now I also see R2.13.0 available by typing yum info R.

...Tao




- Original Message 
 From: Marc Schwartz marc_schwa...@me.com
 To: Marta Avalos marta.ava...@isped.u-bordeaux2.fr
 Cc: r-help@r-project.org
 Sent: Wed, May 11, 2011 10:08:00 AM
 Subject: Re: [R] R versions for Red Hat Linux
 
 On May 11, 2011, at 10:12 AM, Marta Avalos wrote:
 
  Dear all,
   The latest R version available for Red Hat Linux is 2.10 (from November 
   2009), whereas the latest version available for Debian, Suse or Ubuntu 
  Linux 

  is 2.13 (from May 2011). 
  Has someone some information about  the development/release of new R 
  versions 

  for Red Hat?
  
   Thank you in advance,
  Marta 
 
 
 R for RHEL based Linux  distributions has been available for some time via 
 the 
EPEL:
 
http://fedoraproject.org/wiki/EPEL
 
 You can review the instructions there  for configuring your system to use the 
EPEL and then use 'yum' to install  R:
 
   sudo yum install R
 
 If by Red Hat, you are actually  referring to Fedora, R is available via the 
regular Fedora repos. Just use the  same command line incantation as above.
 
 Also, just an FYI that there is a  R-SIG-Fedora list, which focused on RH and 
Fedora specific issues. More info  at:
 
   https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
 
 HTH,
 
 Marc  Schwartz
 
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[R] changes in coxph in survival from older version?

2011-05-11 Thread Shi, Tao

Hi all,

I found that the two different versions of survival packages, namely 2.36-5 
vs. 2.36-8 or later, give different results for coxph function.  Please see 
below and the data is attached.  The second one was done on Linux, but Windows 
gave the same results.  Could you please let me know which one I should trust?

Thanks,

...Tao





# R2.13.0, survival 2.36-9 
=
 dat=read.csv(tmp1.csv, header=T)
 fit2 - coxph(Surv(tt, cens) ~., data=dat)
Warning message:
In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Ran out of iterations and did not converge
 summary(fit2)
## the estimates are different
.
 sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United 
States.1252LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C   LC_TIME=English_United States.1252   
 


attached base packages:
[1] grDevices datasets  splines   graphics  stats tcltk utils 
methods   base 


other attached packages:
[1] svSocket_0.9-51 TinnR_1.0.3 R2HTML_2.2  Hmisc_3.8-3 
survival_2.36-9

loaded via a namespace (and not attached):
[1] cluster_1.13.3  grid_2.13.0 lattice_0.19-23 svMisc_0.9-61   
tools_2.13.0  

# 
=


# R2.12.2, survival 2.36-5 
=
 dat=read.csv(tmp1.csv, header=T)
 fit2 - coxph(Surv(tt, cens) ~., data=dat)
 summary(fit2)
## the estimates are different
.
 
 sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C  
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C  LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C 
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] splines   stats graphics  grDevices utils datasets  methods  
[8] base 

other attached packages:
[1] survival_2.36-5
# 
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Re: [R] a bug in write.csv?

2011-04-08 Thread Shi, Tao

As pointed out by Ista, please read the help file.

write.csv and write.csv2 provide convenience wrappers for writing CSV files.  
They set sep, dec and qmethod, and col.names to NA if row.names = TRUE and 
TRUE otherwise. 




From: John Kane jrkrid...@yahoo.ca
To: r-help r-help@r-project.org; Santosh santosh2...@gmail.com
Sent: Fri, April 8, 2011 3:23:40 PM
Subject: Re: [R] a bug in write.csv?

I believe write.csv had been revamped and some options are no longer available.

--- On Fri, 4/8/11, Santosh santosh2...@gmail.com wrote:

 From: Santosh santosh2...@gmail.com
 Subject: [R] a bug in write.csv?
 To: r-help r-help@r-project.org
 Received: Friday, April 8, 2011, 4:18 PM
 Dear Rxperts!
 
 A simple example where write.csv does not seem to accept
 user specified
 arguments.. Why?
 
 write.csv(t(1:10),./te1.csv,quo=F,col.names=F)
 Warning message:
 In write.csv(t(1:10), ./te1.csv, quo = F, col.names = F)
 :
   attempt to set 'col.names' ignored
 
 
 However, write.table does fine..
 write.table(t(1:10),./te1.csv,quo=F,col.names=F,sep=,)
 
 
 Would really appreciate your thoughts/suggestions..
 
 [[alternative HTML version deleted]]
 
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 mailing list
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 reproducible code.


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[R] read password-protected files

2011-03-31 Thread Shi, Tao

Hi list,

I have a bunch of .csv files that are password-protected.  I wonder if there is 
a way to read them in in R without manually removing the password protection 
for 
each file?

Thank you very much!


...Tao
[[alternative HTML version deleted]]

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Re: [R] How to update R?

2011-03-31 Thread Shi, Tao

This question has been asked by many people already.  The easiest way is:

1) install the new version
2) copy all or the libraries that you installed later from the library folder 
of older version to the new version
3) uninstall the old version
4) do a library update in the new version

Done!

...Tao






From: Li, Yunfei yunfei...@wsu.edu
To: r-help@r-project.org
Sent: Thu, March 31, 2011 10:16:23 AM
Subject: [R] How to update R?

Hi,

My R version is old, and I would like to update it. How can I update R and keep 
all the libraries? Thanks

Best,

Yunfei Li
--

Research Assistant
Department of Statistics 
School of Molecular Biosciences
Biotechnology Life Sciences Building 427
Washington State University
Pullman, WA 99164-7520
Phone: 509-339-5096
http://www.wsu.edu/~ye_lab/people.html


[[alternative HTML version deleted]]

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[[alternative HTML version deleted]]

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Re: [R] How to update R?

2011-03-31 Thread Shi, Tao

Forgot to mention that my way of updating is for Windows only.

...Tao






From: Joshua Wiley jwiley.ps...@gmail.com
To: Li, Yunfei yunfei...@wsu.edu
Cc: r-help@r-project.org
Sent: Thu, March 31, 2011 11:05:29 AM
Subject: Re: [R] How to update R?

Hi Yunfei,

It really depends to some extent on the version of R (and your OS) you
were using.  Here is a link to a blog post that discusses some
potential strategies:
http://www.r-statistics.com/2010/04/changing-your-r-upgrading-strategy-and-the-r-code-to-do-it-on-windows/


There are also a number of messages if you search the R-help archive.
However, old version of libraries may not be portable to the most
recent R, so you may need to update R and update all your libraries
too.

Cheers,

Josh

On Thu, Mar 31, 2011 at 10:16 AM, Li, Yunfei yunfei...@wsu.edu wrote:
 Hi,

 My R version is old, and I would like to update it. How can I update R and 
 keep 
all the libraries? Thanks

 Best,

 Yunfei Li
--
-
 Research Assistant
 Department of Statistics 
 School of Molecular Biosciences
 Biotechnology Life Sciences Building 427
 Washington State University
 Pullman, WA 99164-7520
 Phone: 509-339-5096
 http://www.wsu.edu/~ye_lab/people.html


[[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.




-- 
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/

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Re: [R] read password-protected files

2011-03-31 Thread Shi, Tao

Hi Josh and Prof. Ripley,

Thanks for the quick replies!

Sorry about the HTML email.  It's the default for my yahoo account and forgot 
to 
switch.

The question was asked by a colleague of mine.  After double-checking, yes, 
they 
are actually Excel files.  Any idea on how to approach this?

Thanks!

...Tao




From: Prof Brian Ripley rip...@stats.ox.ac.uk

Cc: r-help@r-project.org
Sent: Thu, March 31, 2011 11:15:35 AM
Subject: Re: [R] read password-protected files

On Thu, 31 Mar 2011, Shi, Tao wrote:

 Hi list,

 I have a bunch of .csv files that are password-protected.  I wonder if there 
is

There is nothing in the CSV standard about password protection.  I 
very much doubt that these actually CSV files.  So please follow the 
posting guide [*]

 a way to read them in in R without manually removing the password protection 
for
 each file?

[[elided Yahoo spam]]


 ...Tao
 [[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.

[*] as above: and as you sent HTML you are either full of contempt for 
the helpeRs or failed to do your homework.


-- 
Brian D. Ripley,  rip...@stats.ox.ac.uk
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

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Re: [R] read password-protected files

2011-03-31 Thread Shi, Tao

Thanks, Josh.  I use xlsReadWrite routinely.  It would be nice if it has a 
password option.

...Tao




- Original Message 
 From: Joshua Wiley jwiley.ps...@gmail.com
 To: Shi, Tao shida...@yahoo.com
 Cc: r-help@r-project.org
 Sent: Thu, March 31, 2011 11:50:27 AM
 Subject: Re: [R] read password-protected files
 
 Hi Tao,
 
 There are a number of R packages to work with reading/writing  Excel
 files (e.g., xlsReadWrite).  If Excel is on the system in  question, as
 long as you have opened the file in Excel, you should be able to  use
 RODBC with  RDCOMClient or rcom, but I am not sure those will work  if
 it is password protected unless it is currently unlocked in  Excel.
 
 HTH,
 
 Josh
 
 On Thu, Mar 31, 2011 at 11:33 AM, Shi, Tao  shida...@yahoo.com wrote:
  Hi  Josh and Prof. Ripley,
 
  Thanks for the quick  replies!
 
  Sorry about the HTML email.  It's the default for my  yahoo account and 
forgot to
  switch.
 
  The question was  asked by a colleague of mine.  After double-checking, 
  yes, 
they
  are  actually Excel files.  Any idea on how to approach this?
 
   Thanks!
 
  ...Tao
 
 
 
   
  From: Prof Brian Ripley rip...@stats.ox.ac.uk
  To:  Shi, Tao shida...@yahoo.com
  Cc: r-help@r-project.org
  Sent: Thu,  March 31, 2011 11:15:35 AM
  Subject: Re: [R] read password-protected  files
 
  On Thu, 31 Mar 2011, Shi, Tao wrote:
 
   Hi list,
 
  I have a bunch of .csv files that are  password-protected.  I wonder if 
there
  is
 
  There is  nothing in the CSV standard about password protection.  I
  very much  doubt that these actually CSV files.  So please follow the
  posting guide  [*]
 
  a way to read them in in R without manually removing the  password 
protection
 for
  each  file?
 
  Thank you very  much!
 
 
  ...Tao
  [[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.
 
  [*] as above: and as  you sent HTML you are either full of contempt for
  the helpeRs or failed  to do your homework.
 
 
  --
  Brian D. Ripley,   rip...@stats.ox.ac.uk
  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, UK Fax:  +44 1865 272595


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Re: [R] read password-protected files

2011-03-31 Thread Shi, Tao

Thanks, Henrique!  I'll try that.

...Tao

- Original Message 
 From: Henrique Dallazuanna www...@gmail.com
 To: Shi, Tao shida...@yahoo.com
 Cc: Prof Brian Ripley rip...@stats.ox.ac.uk; r-help@r-project.org
 Sent: Thu, March 31, 2011 12:00:45 PM
 Subject: Re: [R] read password-protected files

 Using RDCOMCliente:

 library(RDCOMClient)
 eApp -  COMCreate(Excel.Application)
 wk -  eApp$Workbooks()$Open(Filename=your_file,Password=your_password)
 tf -  tempfile()
 wk$Sheets(1)$SaveAs(tf, 3)

 DF -  read.table(sprintf(%s.txt, tf), header = TRUE, sep = \t)

 On Thu, Mar  31, 2011 at 3:33 PM, Shi, Tao shida...@yahoo.com wrote:
  Hi  Josh and Prof. Ripley,

  Thanks for the quick  replies!

  Sorry about the HTML email.  It's the default for my  yahoo account and 
forgot to
  switch.

  The question was  asked by a colleague of mine.  After double-checking, 
  yes, 
they
  are  actually Excel files.  Any idea on how to approach this?

   Thanks!

  ...Tao

  From: Prof Brian Ripley rip...@stats.ox.ac.uk

   Cc: r-help@r-project.org
  Sent: Thu,  March 31, 2011 11:15:35 AM
  Subject: Re: [R] read password-protected  files

  On Thu, 31 Mar 2011, Shi, Tao wrote:

   Hi list,

  I have a bunch of .csv files that are  password-protected.  I wonder if 
there
  is

  There is  nothing in the CSV standard about password protection.  I
  very much  doubt that these actually CSV files.  So please follow the
  posting guide  [*]

  a way to read them in in R without manually removing the  password 
protection
 for
  each file?

   [[elided Yahoo spam]]

  ...Tao
   [[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.

  [*] as above: and as  you sent HTML you are either full of contempt for
  the helpeRs or failed  to do your homework.

  --
  Brian D. Ripley,   rip...@stats.ox.ac.uk
  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, UK Fax:  +44 1865 272595

   __
  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.

 -- 
 Henrique  Dallazuanna
 Curitiba-Paraná-Brasil
 25° 25' 40 S 49° 16' 22 O

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[R] confusion matrix

2011-03-08 Thread Shi, Tao

Hi list,

Is there already a function somewhere to output the confusion matrix from two 
input vectors?  table always automatically delete rows or columns with all 
0's.  For example, I would like the columns for 10 and 30 added back.

Thanks!

...Tao



  20 40 50 60 70 80 90 100
  10   0  0  1  0  0  0  1   0
  20   1  2  0  4  0  0  0   1
  30   0  0  0  0  0  0  1   1
  40   0  0  1  1  2  0  0   0
  50   0  1  0  0  0  1  0   0
  60   0  0  0  0  0  0  1   1
  70   0  0  1  1  1  1  1   1
  80   0  1  0  0  0  0  0   1
  90   0  0  0  0  0  0  0   3
  100  0  0  0  0  1  0  0   3

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Re: [R] confusion matrix

2011-03-08 Thread Shi, Tao

Thanks, Richard, for your speedy reply!

From: Richard M. Heiberger r...@temple.edu
To: Shi, Tao shida...@yahoo.com
Cc: r-help@r-project.org
Sent: Tue, March 8, 2011 12:28:05 PM
Subject: Re: [R] confusion matrix

You need to make your variables into factors and specify the levels.

 x - c(1,3,4,5)
 table(x)
x
1 3 4 5 
1 1 1 1 
 factor(x)
[1] 1 3 4 5
Levels: 1 3 4 5
 table(factor(x))
1 3 4 5 
1 1 1 1 
 table(factor(x, levels=1:5))
1 2 3 4 5 
1 0 1 1 1 

Rich

On Tue, Mar 8, 2011 at 3:22 PM, Shi, Tao shida...@yahoo.com wrote:

Hi list,

Is there already a function somewhere to output the confusion matrix from two
input vectors?  table always automatically delete rows or columns with all
0's.  For example, I would like the columns for 10 and 30 added back.

Thanks!

...Tao

 20 40 50 60 70 80 90 100
 10   0  0  1  0  0  0  1   0
 20   1  2  0  4  0  0  0   1
 30   0  0  0  0  0  0  1   1
 40   0  0  1  1  2  0  0   0
 50   0  1  0  0  0  1  0   0
 60   0  0  0  0  0  0  1   1
 70   0  0  1  1  1  1  1   1
 80   0  1  0  0  0  0  0   1
 90   0  0  0  0  0  0  0   3
 100  0  0  0  0  1  0  0   3

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Re: [R] which functions are being debugged?

2011-02-17 Thread Shi, Tao

Hi Henrique,

Thanks for the reply!

I posted the question in a hurry yesterday.  After a bit research today, I 
found 
that back in 2009, Andrew actually asked the same question and there was a good 
discussion about it:

http://r.789695.n4.nabble.com/how-do-you-know-which-functions-are-being-debugged-td906109.html


Steve's approach of keeping a record of the debugged functions yourself is more 
proper, but your function works well for me for now.  


Thanks!

...Tao






From: Henrique Dallazuanna www...@gmail.com

Cc: r-help@r-project.org
Sent: Wed, February 16, 2011 4:56:01 PM
Subject: Re: [R] which functions are being debugged?

Try this:

isDebug - lapply(sapply(search(), lapply, ls), function(f)sapply(f, 
function(.f)tryCatch(isdebugged(.f), error = function(...)FALSE)))
which(unlist(isDebug))




Hi list,

Is there a function that can let me know which functions are being debugged?  I
know I'm probably not doing a very good job of keeping track of things, but it
does get messier when you dig into different layers of a function.  I know
there
is isdebugged, but it only works on one function at a time.

Thanks!

...Tao




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-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O



  
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[R] which functions are being debugged?

2011-02-16 Thread Shi, Tao

Hi list,

Is there a function that can let me know which functions are being debugged?  I 
know I'm probably not doing a very good job of keeping track of things, but it 
does get messier when you dig into different layers of a function.  I know 
there 
is isdebugged, but it only works on one function at a time.

Thanks!

...Tao



  
[[alternative HTML version deleted]]

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Re: [R] UniCox in R

2010-12-17 Thread Shi, Tao

Hi Samuel,

The help file explains which is which:

A list with components 
devcvm Average drop in CV deviance for each lambda value 
ncallcvm=ncallcvm Average  number of features with non-zero wts in the CV, for 
each lambda value 

se.devcvm Standard error of average drop in CV deviance for each lambda value 
devcv Drop in CV deviance for each lambda value 
ncallcv Number of features with non-zero wts in the CV, for each lambda value 
folds Indices for CV folds 
call Call to this function 
So the following code will do:

 plot(aa[[2]], aa[[1]], type=b, ylim=c(0,25))
 segments(aa[[2]], aa[[1]]-aa[[3]], aa[[2]], aa[[1]]+aa[[3]])

Can't figure out how he made the horizontal bars at the ends of each error bar 
vary in length.

How do you like uniCox?  Have seen my previous post regarding the error message?

https://stat.ethz.ch/pipermail/r-help/2010-November/260857.html

...Tao







To: jim holtman jholt...@gmail.com
Cc: r-help@r-project.org
Sent: Wed, December 8, 2010 5:59:40 AM
Subject: Re: [R] UniCox in R

Thank you for your reply. My question was how to create Fig. 2? I am using 
UniCox; the aa=uniCoxCV gives list of  aa$ devcvm  aa$ncallcvm aa$se.devcvm, 
aa$devcv, aa$ ncallcv and aa$ folds, which data I should plot here to create 
the 
graph in Fig. 2?

Many thanks,
Sam


--- On Wed, 8/12/10, jim holtman jholt...@gmail.com wrote:

From: jim holtman jholt...@gmail.com
Subject: Re: [R] UniCox in R

Cc: r-help@r-project.org
Date: Wednesday, 8 December, 2010, 5:25

Do a little reading on how to use the graphics commands.  I would look at

plot
lines
segments

a combination of those will let you easily create the output.  It
would seem you need some data object that has the dimensions of the
bar lengths you want to create, but given that, it is not much of a
problem to solve.






 Hello,

 I am interested in Figure 2 in

 http://www-stat.stanford.edu/~tibs/ftp/cus.pdf

 Can anyone tell please how to create this plot?

 Many thanks
 Samuel






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-- 
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What is the problem that you are trying to solve?



  
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[R] given a sensitivity calculate specificity based on a ROC curve

2010-11-29 Thread Shi, Tao

Hi list,

I know this is not hard to implement based on the returned objects from ROC, 
ROCR or a couple of other roc-related packages.  I'm just wondering if there is 
already such a function exist.

Thanks!

...Tao

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[R] question on uniCox

2010-11-22 Thread Shi, Tao

Hi list,

I’m testing out uniCox R package (version 1.0, on R2.12.0, WinXP). 

When I ran uniCox on my data, there are always some NA’s in the beta matrix,  
which in turn causes problems in uniCoxCV call.  I don’t see anything  wrong 
with the corresponding data (e.g. no NAs) and if I fit a  univariate Cox model, 
the features that give NA beta estimates are  actually pretty significant.  
Could you please let me know what  happened and how to avoid this?

I’ve attached the outputs of the function calls below.

Thank you very much!


...Tao


 a - uniCox(x=t(dat.ave.train.base), y=sampleinfo.ave.train.base$tm2dthr, 
status=sampleinfo.ave.train.base$censrdth)
lambda value  1 out of  20
lambda value  2 out of  20
lambda value  3 out of  20
lambda value  4 out of  20
lambda value  5 out of  20
lambda value  6 out of  20
lambda value  7 out of  20
lambda value  8 out of  20
lambda value  9 out of  20
lambda value  10 out of  20
lambda value  11 out of  20
lambda value  12 out of  20
lambda value  13 out of  20
lambda value  14 out of  20
lambda value  15 out of  20
lambda value  16 out of  20
lambda value  17 out of  20
lambda value  18 out of  20
lambda value  19 out of  20
lambda value  20 out of  20
5  betas missing

  aa - uniCoxCV(a, x=t(dat.ave.train.base),  
y=sampleinfo.ave.train.base$tm2dthr,  
status=sampleinfo.ave.train.base$censrdth)
FOLD= 1
lambda value  1 out of  20
lambda value  2 out of  20
lambda value  3 out of  20
lambda value  4 out of  20
lambda value  5 out of  20
lambda value  6 out of  20
lambda value  7 out of  20
lambda value  8 out of  20
lambda value  9 out of  20
lambda value  10 out of  20
lambda value  11 out of  20
lambda value  12 out of  20
lambda value  13 out of  20
lambda value  14 out of  20
lambda value  15 out of  20
lambda value  16 out of  20
lambda value  17 out of  20
lambda value  18 out of  20
lambda value  19 out of  20
lambda value  20 out of  20
3  betas missing
1
Error in coxph(Surv(y[ii], status[ii]) ~ eta.new) :
  No (non-missing) observations

 a[[2]][(rowSums(is.na(a[[2]])))0,]
 [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,]  92.6641  NaN  NaN  NaN00000 0 0 0 0   
 

0 0 0 0 0 0 0
[2,]  NaN00000000 0 0 0 0   
 

0 0 0 0 0 0 0
[3,] 567.3650  NaN0000000 0 0 0 0   
 

0 0 0 0 0 0 0




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Re: [R] calculating martingale residual on new data using predict.coxph

2010-11-22 Thread Shi, Tao

Thank you, Terry!

- Original Message 
 From: Terry Therneau thern...@mayo.edu
 To: Shi, Tao shida...@yahoo.com
 Cc: r-help@r-project.org; dieter.me...@menne-biomed.de; r_ting...@hotmail.com
 Sent: Mon, November 22, 2010 6:11:15 AM
 Subject: Re:  calculating martingale residual on new data using 
predict.coxph

 This feature has been added in survival 2.36-1, which is now on CRAN.
 (2.36-2  should appear in another day or so)
  Terry  T.

 -begin included message 
 I was trying to use  predict.coxph to calculate martingale residuals on
 a test 
 data,  however, as pointed out  before

 http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html

 predict(mycox1,  newdata, type=expected) is not implemented yet.  

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Re: [R] calculating martingale residual on new data using

2010-11-22 Thread Shi, Tao

Thank you for the advice, Frank!

...Tao

- Original Message 
 From: Frank Harrell f.harr...@vanderbilt.edu
 To: r-help@r-project.org
 Sent: Sun, November 21, 2010 5:49:36 AM
 Subject: Re: [R] calculating martingale residual on new data using

 The tendency is to use residual-like diagnostics on the entire dataset  that
 was available for model development.  For test data we typically  run
 predictive accuracy analyses.  For example, one of the strongest  validations
 is to show, in a high-resolution calibration plot, that absolute  predictions
 (e.g., probability of survival at 2 years) are  accurate.

 Frank

 -
 Frank Harrell
 Department of  Biostatistics, Vanderbilt University
 -- 
 View this message in context:  
http://r.789695.n4.nabble.com/calculating-martingale-residual-on-new-data-using-predict-coxph-tp3050712p3052377.html

 Sent  from the R help mailing list archive at Nabble.com.

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Re: [R] calculating martingale residual on new data using predict.coxph

2010-11-22 Thread Shi, Tao

Thank you, David!  You've been always helpful!

...Tao

- Original Message 
 From: David Winsemius dwinsem...@comcast.net
 To: Shi, Tao shida...@yahoo.com
 Cc: r-help@r-project.org; dieter.me...@menne-biomed.de; r_ting...@hotmail.com
 Sent: Sun, November 21, 2010 5:50:31 AM
 Subject: Re: [R] calculating martingale residual on new data using 
predict.coxph

 On Nov 21, 2010, at 3:42 AM, Shi, Tao wrote:

  Hi David,

  Thanks, but I don't quite follow your examples below.

 I wasn't  really sure they did anything useful anyway.

  The residuals  you
  calculated are still based on the training data from which your cox  model 
was
  generated.  I'm interested in the testing  data.

   The survest function in rms and the survfit function in  survival will 
calculate survival probabilities given a model and newdata, and  depending on 
your definition of residual you could take the difference between  the 
calculation and validation data. That must be what happens (at least at a  
gross 
level of description) when Harrell runs his validate function on his cph  
models 
in the rms/Design package, although I don't know if something that you  would 
recognize as a martingale residual is an identifiable  intermediate.

   If you are using survfit, it would appear from my  reading that you would 
need to set the individual parameter to TRUE. I'm  assuming you planned to 
calculate these (1- expected) at the event times of the  validation cohort 
(which it appears the default method fixes via the censor  argument)?

 --David

  Best,

   ...Tao

  - Original  Message 
  From: David Winsemius dwinsem...@comcast.net
   To: David Winsemius dwinsem...@comcast.net
   Cc: Shi, Tao shida...@yahoo.com; r-help@r-project.org;
  dieter.me...@menne-biomed.de; r_ting...@hotmail.com
  Sent:  Fri, November 19, 2010 10:53:26 AM
  Subject: Re: [R] calculating  martingale residual on new data using
  predict.coxph

  On Nov 19, 2010, at 12:50 PM, David Winsemius  wrote:

  On  Nov 19, 2010, at  12:32 PM, Shi, Tao wrote:

  Hi   list,

  I was trying to use  predict.coxph to calculate  martingale residuals 
  on 
a
   test
  data, however, as pointed out   before

  What about resid(fit) ?  It's my  reading of  Therneau  Gramsch [and of
  help(coxph.object) ]  that they consider those  martingale residuals.

   The manner in which I _thought_ this would work was  to insert some dummy 

cases
  into the original data and then to get residuals by   weighting the cases
  appropriately. That doesn't seem to be as  successful as I  imagined:

  test1 -  list(time=c(4,3,1,1,2,2,3,3),  weights=c(rep(1,7), 0),
  +  status=c(1,1,1,0,1,1,0,1),
  + x=c(0,2,1,1,1,0,0,1),
  + sex=c(0,0,0,0,1,1,1,1))
   coxph(Surv(time, status) ~ x , test1,  weights=weights)$weights
   Error in fitter(X, Y, strats, offset, init, control,  weights =  weights, 

:
   Invalid weights, must be 0
  #  OK then  make it a small number
  test1 -  list(time=c(4,3,1,1,2,2,3,3),  weights=c(rep(1,7), 0.01),
   + status=c(1,1,1,0,1,1,0,1),
  + x=c(0,2,1,1,1,0,0,1),
  + sex=c(0,0,0,0,1,1,1,1))
   print(resid( coxph(Surv(time, status) ~ x ,  test1,weights=weights)  )
  ,digits=3)
   1 2   3   4 5   6   7 8
  -0.6410 -0.5889  0.8456 -0.1544  0.4862   0.6931  -0.6410  0.0509
  Now take out constructed case and  weights

  test1 -  list(time=c(4,3,1,1,2,2,3),
  + status=c(1,1,1,0,1,1,0),
  + x=c(0,2,1,1,1,0,0),
  +  sex=c(0,0,0,0,1,1,1))
  print(resid( coxph(Surv(time, status) ~  x  , test1) ) ,digits=3)
  1   2   3  4  5   6   7
  -0.632 -0.589  0.846  -0.154  0.486  0.676  -0.632

  Expecting  approximately the same residuals for first 7 cases but  not  
really
  getting it. There must be something about weights in coxph  that I  don't
  understand, unless a one-hundreth of a case gets  up indexed inside the
  machinery of coxph?

   Still think that inserting a single constructed case  into a real dataset 

of
  sufficient size ought to be able to yield some sort of   estimate, and 
  only 
be a
  minor perturbation,  although I must  admit I'm  having trouble figuring 
  out 
...
  why are we  attempting such a maneuver? The  notion of residuals around
   constructed cases makes me statistically  suspicious, although I suppose  
that is
  just some sort of cumulative  excess/deficit death  fraction.

   http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html

  predict(mycox1, newdata, type=expected) is not  implemented  yet.  
Dieter
  suggested to use 'cph'  and 'predict.Design', but  from my reading so 
far,
  I'm  not
  sure they can do that.

  Do you other ways to calculate martingale residuals on a  new  data?

  Thank you very  much!

  ...Tao

   --David

Re: [R] calculating martingale residual on new data using predict.coxph

2010-11-21 Thread Shi, Tao

Hi David,

Thanks, but I don't quite follow your examples below.  The residuals you 
calculated are still based on the training data from which your cox model was 
generated.  I'm interested in the testing data.


Best,

...Tao





- Original Message 
 From: David Winsemius dwinsem...@comcast.net
 To: David Winsemius dwinsem...@comcast.net
 Cc: Shi, Tao shida...@yahoo.com; r-help@r-project.org; 
dieter.me...@menne-biomed.de; r_ting...@hotmail.com
 Sent: Fri, November 19, 2010 10:53:26 AM
 Subject: Re: [R] calculating martingale residual on new data using 
predict.coxph
 
 
 On Nov 19, 2010, at 12:50 PM, David Winsemius wrote:
 
  
  On  Nov 19, 2010, at 12:32 PM, Shi, Tao wrote:
  
  Hi  list,
  
  I was trying to use predict.coxph to calculate  martingale residuals on 
  a 
test
  data, however, as pointed out  before
  
  What about resid(fit) ?  It's my reading of  Therneau  Gramsch [and of 
help(coxph.object) ] that they consider those  martingale residuals.
 
 The manner in which I _thought_ this would work was  to insert some dummy 
 cases 
into the original data and then to get residuals by  weighting the cases 
appropriately. That doesn't seem to be as successful as I  imagined:
 
  test1 - list(time=c(4,3,1,1,2,2,3,3),  weights=c(rep(1,7), 0),
 +status=c(1,1,1,0,1,1,0,1),
 +x=c(0,2,1,1,1,0,0,1),
 +sex=c(0,0,0,0,1,1,1,1))
  coxph(Surv(time, status) ~ x , test1,  weights=weights)$weights
 Error in fitter(X, Y, strats, offset, init, control,  weights = weights,  :
   Invalid weights, must be 0
 # OK then  make it a small number
  test1 - list(time=c(4,3,1,1,2,2,3,3),  weights=c(rep(1,7), 0.01),
 +status=c(1,1,1,0,1,1,0,1),
 +x=c(0,2,1,1,1,0,0,1),
 +sex=c(0,0,0,0,1,1,1,1))
  print(resid( coxph(Surv(time, status) ~ x ,  test1,weights=weights) ) 
,digits=3)
   12   3   45   6   78
 -0.6410 -0.5889  0.8456 -0.1544  0.4862  0.6931  -0.6410  0.0509
 Now take out constructed case and weights
 
   test1 - list(time=c(4,3,1,1,2,2,3),
 +status=c(1,1,1,0,1,1,0),
 +x=c(0,2,1,1,1,0,0),
 +sex=c(0,0,0,0,1,1,1))
  print(resid( coxph(Surv(time, status) ~ x  , test1) ) ,digits=3)
  1  2   3  4  5  6   7
 -0.632 -0.589  0.846 -0.154  0.486  0.676  -0.632
 
 Expecting approximately the same residuals for first 7 cases but  not really 
getting it. There must be something about weights in coxph that I  don't 
understand, unless a one-hundreth of a case gets up indexed inside the  
machinery of coxph?
 
 Still think that inserting a single constructed case  into a real dataset of 
sufficient size ought to be able to yield some sort of  estimate, and only be 
a 
minor perturbation,  although I must admit I'm  having trouble figuring out 
... 
why are we attempting such a maneuver? The  notion of residuals around 
constructed cases makes me statistically  suspicious, although I suppose that 
is 
just some sort of cumulative  excess/deficit death fraction.
 
   http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html
  
  predict(mycox1, newdata, type=expected) is not implemented  yet.  Dieter
  suggested to use 'cph' and 'predict.Design', but  from my reading so far, 
I'm not
  sure they can do that.
  
  Do you other ways to calculate martingale residuals on a new  data?
  
  Thank you very much!
  
   ...Tao
 
 --David Winsemius, MD
 West Hartford, CT
 


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[R] calculating martingale residual on new data using predict.coxph

2010-11-19 Thread Shi, Tao

Hi list,

I was trying to use predict.coxph to calculate martingale residuals on a test 
data, however, as pointed out before

http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html

predict(mycox1, newdata, type=expected) is not implemented yet.  Dieter 
suggested to use 'cph' and 'predict.Design', but from my reading so far, I'm 
not 
sure they can do that.

Do you other ways to calculate martingale residuals on a new data?

Thank you very much!

...Tao

__
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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] calculating martingale residual on new data using predict.coxph

2010-11-19 Thread Shi, Tao

Hi David,

Thank you for the quick reply!   

resid(fit) only gives the residuals on the training data not on test data.

...Tao




- Original Message 
 From: David Winsemius dwinsem...@comcast.net
 To: Shi, Tao shida...@yahoo.com
 Cc: r-help@r-project.org; dieter.me...@menne-biomed.de; r_ting...@hotmail.com
 Sent: Fri, November 19, 2010 9:50:06 AM
 Subject: Re: [R] calculating martingale residual on new data using 
predict.coxph
 
 
 On Nov 19, 2010, at 12:32 PM, Shi, Tao wrote:
 
  Hi list,
  
  I was trying to use predict.coxph to calculate martingale residuals  on a 
test
  data, however, as pointed out before
 
 What about  resid(fit) ?  It's my reading of Therneau  Gramsch [and of  
help(coxph.object) ] that they consider those martingale residuals.
 
  
  http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html
  
  predict(mycox1, newdata, type=expected) is not implemented yet.   Dieter
  suggested to use 'cph' and 'predict.Design', but from my reading  so far, 
  I'm 
not
  sure they can do that.
  
  Do you other  ways to calculate martingale residuals on a new data?
  
  Thank you  very much!
  
  ...Tao
 
 
 David Winsemius, MD
 West  Hartford, CT
 


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Re: [R] date calculation

2010-10-30 Thread Shi, Tao

Hi Phil,

Thanks for the reply, but I don't think you have 
explained where the decimal part is coming from

...Tao



- Original Message -
 From:Phil Spector spec...@stat.berkeley.edu
 To:Shi, Tao shida...@yahoo.com
 Cc:r-h...@stat.math.ethz.ch
 Sent:Friday, October 29, 2010 5:04:23 PM
 Subject:Re: [R] date calculation
 
 
 Tao -
The documentation for the difftime function 
 says:

Function ‘difftime’ calculates a difference of two 
 date/time
  objects and returns an object of class 
 ‘difftime’ with an
  attribute indicating the 
 units.

So that answers your question.

If you want it to be an 
 integer, you're certainly free to make it one:

 
 as.integer(difftime(strptime(24NOV2004, format=%d%b%Y), 
+
 
 strptime(13MAY2004,format=%d%b%Y), units=days))
[1] 195


 
 - Phil Spector

  Statistical Computing 
 Facility

  Department of Statistics

 
  UC Berkeley

 
 ymailto=mailto:spec...@stat.berkeley.edu; 
 href=mailto:spec...@stat.berkeley.edu;spec...@stat.berkeley.edu



On 
 Fri, 29 Oct 2010, Shi, Tao wrote:

 Hi list,

 Could 
 someone explain to me why the following result is not a 
 integer?


 difftime(strptime(24NOV2004, 
 format=%d%b%Y), strptime(13MAY2004,
 format=%d%b%Y), 
 units=days)
 Time difference of 195.0417 days

 I'm using 
 R2.12.0 on WinXP.

 Thanks!

 ...Tao

 
 __
 
 ymailto=mailto:R-help@r-project.org; 
 href=mailto:R-help@r-project.org;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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Re: [R] date calculation

2010-10-30 Thread Shi, Tao

Hi Ben,

That must be the case!  In fact if I do:

 difftime(strptime(24NOV2004, format=%d%b%Y), 
 strptime(13MAY2004,format=%d%b%Y), units=days, tz=GMT)
Time difference of 195 days


which supports your claim.

Can someone from the R development team confirm this?

Thanks!

...Tao





- Original Message -
 From:Ben Bolker bbol...@gmail.com
 To:r-h...@stat.math.ethz.ch
 Cc:
 Sent:Friday, October 29, 2010 7:54:53 PM
 Subject:Re: [R] date calculation
 
 
 Shi, Tao shidaxia at 
 href=http://yahoo.com;yahoo.com writes:

 Could someone 
 explain to me why the following result is not a integer?
 
  
 difftime(strptime(24NOV2004, format=%d%b%Y), strptime(13MAY2004, 
 
 format=%d%b%Y), units=days)
 Time difference of 195.0417 
 days

  Presumably because this goes across a daylight-savings 
 time
adjustment?  0.0417=1/24 days is 1 hour ...

  Ben 
 Bolker

__

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 href=mailto:R-help@r-project.org;R-help@r-project.org mailing list

 href=https://stat.ethz.ch/mailman/listinfo/r-help; target=_blank 
 https://stat.ethz.ch/mailman/listinfo/r-help
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 guide http://www.R-project.org/posting-guide.html
and provide commented, 
 minimal, self-contained, reproducible code.

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Re: [R] date calculation

2010-10-30 Thread Shi, Tao

Hi Ben and Josh,

No, I don't think that there is a bug.  It's just due to my lack of knowledge 
on Date class, I was simply amazed that it has the daylight saving time built 
in at first.  But on the second thought, it really should.

Thank you all for the explanations!

...Tao




From: Ben Bolker bbol...@gmail.com
To: Shi, Tao shida...@yahoo.com
Cc: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch
Sent: Saturday, October 30, 2010 7:22:04 AM
Subject: Re: [R] date calculation

On 10-10-30 02:02 AM, Shi, Tao wrote:
 Hi Ben,
 
 That must be the case!  In fact if I do:
 
 difftime(strptime(24NOV2004, format=%d%b%Y), 
 strptime(13MAY2004,format=%d%b%Y), units=days, tz=GMT)
 Time difference of 195 days
 
 
 which supports your claim.
 
 Can someone from the R development team confirm this?
 
 Thanks!
 
 ...Tao
 
 

   It sounds like you think this is a bug.  It's not (although it's
arguably not what you want).  The general advice when using dates and
time in R is to use the *least* specific date format that will do what
you want, i.e. don't use a format that incorporates time zone
information (daylight savings time) information if you don't want to
deal with these complexities.

I would suggest the chron package:

library(chron)
diff(chron(dates.=c(24/11/2004,13/05/2004),format=d/m/y))

 
 
 
 - Original Message -
 From:Ben Bolker bbol...@gmail.com
 To:r-h...@stat.math.ethz.ch
 Cc:
 Sent:Friday, October 29, 2010 7:54:53 PM
 Subject:Re: [R] date calculation


 Shi, Tao shidaxia at 
 href=http://yahoo.com;yahoo.com writes:
 
 Could someone 
 explain to me why the following result is not a integer?


 difftime(strptime(24NOV2004, format=%d%b%Y), strptime(13MAY2004, 

 format=%d%b%Y), units=days)
 Time difference of 195.0417 
 days
 
   Presumably because this goes across a daylight-savings 
 time
 adjustment?  0.0417=1/24 days is 1 hour ...
 
   Ben 
 Bolker
 
 __
 
 ymailto=mailto:R-help@r-project.org; 
 href=mailto:R-help@r-project.org;R-help@r-project.org mailing list
 
 href=https://stat.ethz.ch/mailman/listinfo/r-help; target=_blank 
 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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Re: [R] date calculation

2010-10-30 Thread Shi, Tao

I think this demonstrate on of the differences between Class 'Date' and 
'POSIXlt'.  Thanks, Marc!

...Tao

From: Marc Schwartz marc_schwa...@me.com
To: Ben Bolker bbol...@gmail.com
Cc: Shi, Tao shida...@yahoo.com; r-h...@stat.math.ethz.ch 
r-h...@stat.math.ethz.ch
Sent: Saturday, October 30, 2010 7:48:05 AM
Subject: Re: [R] date calculation

On Oct 30, 2010, at 9:22 AM, Ben Bolker wrote:

 On 10-10-30 02:02 AM, Shi, Tao wrote:
 Hi Ben,

 That must be the case!  In fact if I do:

 difftime(strptime(24NOV2004, format=%d%b%Y), 
 strptime(13MAY2004,format=%d%b%Y), units=days, tz=GMT)
 Time difference of 195 days

 which supports your claim.

 Can someone from the R development team confirm this?

 Thanks!

 ...Tao

   It sounds like you think this is a bug.  It's not (although it's
 arguably not what you want).  The general advice when using dates and
 time in R is to use the *least* specific date format that will do what
 you want, i.e. don't use a format that incorporates time zone
 information (daylight savings time) information if you don't want to
 deal with these complexities.

 I would suggest the chron package:

 library(chron)
 diff(chron(dates.=c(24/11/2004,13/05/2004),format=d/m/y))

Ben,

If time and time zone are not relevant, any reason not to use:

 diff(as.Date(c(13/05/2004, 24/11/2004), format = %d/%m/%Y))
Time difference of 195 days

or perhaps conceptually easier:

Date2 - as.Date(24/11/2004, format = %d/%m/%Y)
Date1 - as.Date(13/05/2004, format = %d/%m/%Y)

 Date2 - Date1
Time difference of 195 days

R has built in arithmetic operations for such dates, without the need to use 
another package, since they are effectively numerics with a Date class:

 str(Date1)
Class 'Date'  num 12551

 str(Date2)
Class 'Date'  num 12746

?

HTH,

Marc Schwartz

 - Original Message -
 From:Ben Bolker bbol...@gmail.com
 To:r-h...@stat.math.ethz.ch
 Cc:
 Sent:Friday, October 29, 2010 7:54:53 PM
 Subject:Re: [R] date calculation

 Shi, Tao shidaxia at 
 href=http://yahoo.com;yahoo.com writes:

 Could someone 
 explain to me why the following result is not a integer?

 difftime(strptime(24NOV2004, format=%d%b%Y), strptime(13MAY2004, 

 format=%d%b%Y), units=days)
 Time difference of 195.0417 
 days

  Presumably because this goes across a daylight-savings 
 time
 adjustment?  0.0417=1/24 days is 1 hour ...

  Ben 
 Bolker

[[alternative HTML version deleted]]

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[R] date calculation

2010-10-29 Thread Shi, Tao

Hi list,

Could someone explain to me why the following result is not a integer?


 difftime(strptime(24NOV2004, format=%d%b%Y), strptime(13MAY2004, 
format=%d%b%Y), units=days)
Time difference of 195.0417 days

I'm using R2.12.0 on WinXP.

Thanks!

...Tao

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Re: [R] pairs with same xlim and ylim scale

2010-09-02 Thread Shi, Tao

Hi Dejian,

You're right on this!  Do you know how to pass those two argument into 
lower.panel?  Thanks!

...Tao



From: Dejian Zhao zha...@ioz.ac.cn
To: r-help@r-project.org
Sent: Tue, August 31, 2010 6:10:16 PM
Subject: Re: [R] pairs with same xlim and ylim scale

I think you have successfully passed the xlim and ylim into the 
function pairs1. Compare the two graphs produced by the codes you 
provided, you can find the xlim and ylim in the second graph have been 
reset to the assigned value. It seems that the program halted in 
producing the second plot after adding xlim and ylim. According to the 
error message, the two added parameters were not used in lower.panel, or 
the customized function f.xy.

On 2010-9-1 2:26, Shi, Tao wrote:
 Hi list,

 I have a function which basically is a wrapper of pairs with some useful panel
 functions.  However, I'm having trouble to pass the xlim and ylim into the
 function so the x and y axes are in the same scale and 45 degree lines are
 exactly diagonal.   I've looked at some old posts, they didn't help much.  I
[[elided Yahoo spam]]

 Thanks!

 ...Tao


 pairs1- function(x, ...) {
  f.xy- function(x, y, ...) {
  points(x, y, ...)
  abline(0, 1, col = 2)
  }

  panel.cor- function(x, y, digits=2, prefix=, cex.cor) {
   usr- par(usr); on.exit(par(usr))
   par(usr = c(0, 1, 0, 1))
   r- abs(cor(x, y, method=p, use=pairwise.complete.obs))
   txt- format(c(r, 0.123456789), digits=digits)[1]
   txt- paste(prefix, txt, sep=)
   if(missing(cex.cor)) cex- 0.8/strwidth(txt)
   text(0.5, 0.5, txt, cex = cex * r)
   }

   panel.hist- function(x, ...) {
   usr- par(usr); on.exit(par(usr))
   par(usr = c(usr[1:2], 0, 1.5) )
   h- hist(x, plot = FALSE)
   breaks- h$breaks; nB- length(breaks)
   y- h$counts; y- y/max(y)
   rect(breaks[-nB], 0, breaks[-1], y, col=cyan, ...)
   }

  pairs(x, lower.panel=f.xy, upper.panel=panel.cor, diag.panel=panel.hist,
 ...)
 }


 x- rnorm(100, sd=0.2)
 x- cbind(x=x-0.1, y=x+0.1)
 pairs1(x)
 pairs1(x, xlim=c(-1,1), ylim=c(-1,1))
  
 Error in lower.panel(...) :
unused argument(s) (xlim = c(-1, 1), ylim = c(-1, 1))



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[R] pairs with same xlim and ylim scale

2010-08-31 Thread Shi, Tao

Hi list,

I have a function which basically is a wrapper of pairs with some useful panel 
functions.  However, I'm having trouble to pass the xlim and ylim into the 
function so the x and y axes are in the same scale and 45 degree lines are 
exactly diagonal.   I've looked at some old posts, they didn't help much.  I 
think this is b/c I have multiple panel functions.  Help!

Thanks!

...Tao


pairs1 - function(x, ...) {
f.xy - function(x, y, ...) {
points(x, y, ...)
abline(0, 1, col = 2)
}

panel.cor - function(x, y, digits=2, prefix=, cex.cor) {
 usr - par(usr); on.exit(par(usr))
 par(usr = c(0, 1, 0, 1))
 r - abs(cor(x, y, method=p, use=pairwise.complete.obs))
 txt - format(c(r, 0.123456789), digits=digits)[1]
 txt - paste(prefix, txt, sep=)
 if(missing(cex.cor)) cex - 0.8/strwidth(txt)
 text(0.5, 0.5, txt, cex = cex * r)
 }

 panel.hist - function(x, ...) {
 usr - par(usr); on.exit(par(usr))
 par(usr = c(usr[1:2], 0, 1.5) )
 h - hist(x, plot = FALSE)
 breaks - h$breaks; nB - length(breaks)
 y - h$counts; y - y/max(y)
 rect(breaks[-nB], 0, breaks[-1], y, col=cyan, ...)
 }

pairs(x, lower.panel=f.xy, upper.panel=panel.cor, diag.panel=panel.hist, 
...)
}

 x - rnorm(100, sd=0.2)
 x - cbind(x=x-0.1, y=x+0.1) 
 pairs1(x)
 pairs1(x, xlim=c(-1,1), ylim=c(-1,1))
Error in lower.panel(...) : 
  unused argument(s) (xlim = c(-1, 1), ylim = c(-1, 1))


  
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Re: [R] R eat my data

2010-05-25 Thread Shi, Tao

Changbin,

It looks you're trying to read in a gene annotation file and usually it has 
many strange characters, e.g. #, ,   (as other people also suggest).   
I encounter this all the time.  So try to be very thorough about your search 
(the first place I'll look for is the line where R stop reading.  See if any 
thing strange there.)  

Also, changing read.table to read.delim often works.

...Tao





- Original Message 
 From: Changbin Du changb...@gmail.com
 To: David Winsemius dwinsem...@comcast.net
 Cc: r-help@r-project.org
 Sent: Tue, May 25, 2010 9:12:58 AM
 Subject: Re: [R] R eat my data
 
 644727344ABC-2 type transporterABC-2 type 
 transporter
644727345conserved hypothetical protein  
   conserved hypothetical
protein

Here is the last two lines of 
 the file id_name_gh5.txt.



On Tue, May 25, 2010 at 8:57 AM, David 
 Winsemius 
 href=mailto:dwinsem...@comcast.net;dwinsem...@comcast.netwrote:


 
 On May 25, 2010, at 11:42 AM, Changbin Du wrote:

  HI, Dear 
 R community,

 My original file has 1932 lines, but when I 
 read into R, it changed to
 1068
 lines, how 
 comes?


 We are being asked to investigate this quest, 
 how?

 Have you looked at the last line to see if it looks like 
 gene_name?

 Isn't this isomorphic to genetics questions? What 
 sort of mutation is it?
 Deletion? Abnormal stop codon? Figure out where 
 the transcription process
 went wrong.  This sort of analysis would 
 appear to be right up the alley of
 someone doing 
 genetics.




 c...@nuuk:~/operon$ wc 
 -l id_name_gh5.txt
 1932 
 id_name_gh5.txt


  
 gene_name-read.table(/home/cdu/operon/id_name_gh5.txt, 
 sep=\t,

 skip=0, header=F, 
 fill=T)

 dim(gene_name)

 
 [1] 10683


 
 --



 David Winsemius, MD
 West 
 Hartford, CT




-- 
 
Sincerely,
Changbin
--

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 version deleted]]

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Re: [R] doubt about samr siggenes.table$genes.up

2010-05-25 Thread Shi, Tao

Leo,

This question is more suited for the BioC help list.  Please post your question 
over there.

Also, offer more info about how you arrived this siggenes.table, what version 
of R and siggenes package you're using would be helpful.  Please read the 
posting guide!

...Tao



- Original Message 
 From: Peter Ehlers ehl...@ucalgary.ca
 To: Leonardo K shik...@gmail.com
 Cc: r-help@r-project.org
 Sent: Tue, May 25, 2010 1:41:36 PM
 Subject: Re: [R] doubt about samr siggenes.table$genes.up
 
 On 2010-05-25 10:54, Leonardo K wrote:

 Hi, here's my 
 siggenes.table$genes.up snippet.

 Two class unpaired SAMR 
 analysis.

 Row Gene ID Gene Name Score(d) Numerator(r) 
 Denominator(s+s0)
 Fold Change q-value(%)
 1 25 
 RPL15P22 RPL15P22 -1.44115338424578 -18 12.4899959967968
 
 1.27368448239355 0
 2 47 CHAF1A CHAF1A -1.44115338424578 
 -18 12.4899959967968
 1.30356683838951 0
 3 48 PARP2 
 PARP2 -1.44115338424578 -18 12.4899959967968
 1.09780831177589 
 0
 4 52 HMGXB4 HMGXB4 -1.44115338424578 -18 
 12.4899959967968
 1.22596090318945 0

 Why do I get 
 one column more in the data block (9) than the header (8)?

 Looks 
 like the second column (25,47,48,etc) does not make 
 sense.


Presumably you are getting this from an application of 
 write.table?
If so, use the argument 'row.names = FALSE' to remove the 
 *first*
column. See the first sentence in the 'CSV files' section 
 of
?write.table.

Your second column is part of the data you're saving 
 (probably
rownames from a larger dataframe or matrix).

  -Peter 
 Ehlers

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 href=mailto:R-help@r-project.org;R-help@r-project.org mailing list

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 https://stat.ethz.ch/mailman/listinfo/r-help
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Re: [R] Fast Matrix Computation

2010-05-22 Thread Shi, Tao

One way to do it:

apply(B, 1, function(x) t(apply(A, 1, function(y) abs(y-x) )) )





- Original Message 
 From: David Neu da...@davidneu.com
 To: r-help@r-project.org
 Sent: Sat, May 22, 2010 10:35:32 AM
 Subject: [R] Fast Matrix Computation
 
 Hi,

I have two (large) matrices A and B of dimensions (m,n) and (p,n) 
 respectively.

I'd like to see if the is a fast way to compute a new 
 matrix C with
dimension (m*p,n) in which each row in C is found by applying 
 some
function f to each pair of rows (x,y) where x is a row in A and y is 
 a
row in B.

For example, if

A - matrix(c(1, 2, 3, 4, 5, 6), 
 byrow=TRUE, ncol=3)
B - matrix(c(7, 8, 9), byrow=TRUE, ncol=3)

and 
 f - function(x,y) abs(y-x)

then

C - matrix(c(6, 6, 6, 3, 
 3, 3), byrow=TRUE, ncol=3)

Many 
 thanks!

Cheers,
David

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 href=mailto:R-help@r-project.org;R-help@r-project.org mailing list

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 https://stat.ethz.ch/mailman/listinfo/r-help
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Re: [R] Concatenation

2010-05-21 Thread Shi, Tao

Well, it seems a simple c will do.

e.g. 

df - matrix(rnorm(100), ncol=4)
c(t(df[1:10,]))  # concatenate rows

c(df)  # concatenate columns







From: santana sarma aimanusa...@gmail.com
To: Shi, Tao shida...@yahoo.com; r-help@r-project.org
Sent: Thu, May 20, 2010 11:45:25 PM
Subject: Re: Concatenation


Ok -let's forget about the dataframe. 


Say, I have this (huge) spreadsheet that has some rows and columns, with 
unique rownames and column names. 

Using R, I wish to FINALLY have a spreadsheet where the values of the first 10 
rows remain in a single row. And, the values of the next 10 rows remain in the 
next row  and so on.


Example: 


row1 = 2, 3.4, 5, 6
row2 = 3, 4.3, 0, 2
...
row 10 = 1,3, 4, 5


new_row_should_be_like = 2, 3.4, 5, 6, 3, 4.3, 0, 2, .. 1, 3, 4, 5  




Similarly, 

Similarly, for columns, the new spreadsheet should FINALLY contain : the 
values of the columns coming one below the other (i.e., resulting in a single 
column, without the identifiers). 


col1   col2   col3. col10 
2   3 45
1   2 50
...
...


new_column_should_be_like = 
2 
1 
...
3 
2 

4 
5
... 
5
0  
.
..






Cheers,




= = = === = = = = =


On Fri, May 21, 2010 at 5:51 PM, Shi, Tao shida...@yahoo.com wrote:

Still not clear.  Follow the posting guide and some examples always help.

Not sure how you concatenate numbers?

You can try, for example,

apply(df[1:10,], 2, paste, collapse= )

but this will turn everything into strings.  Is this what you want?

..Tao





- Original Message 
 From: santana sarma aimanusa...@gmail.com
 To: David Winsemius dwinsem...@comcast.net
 Cc: r-help@r-project.org
 Sent: Thu, May 20, 2010 9:21:33 PM
 Subject: Re: [R] Concatenation

 Hi David,

SORRY - I am trying to be more clearer this time.

Let's
 say the dataframe has some rows and columns, with unique rownames and
column
 names. The rest of the data in the dataframe are just numbers.

I wish to
 concatenate those rows. That means : I wish to concatenate first
10 rows'
 values in one row, then next 20 rows's values in the next row 
and so
 on.

Similarly, for columns : The first 10 column's values will be one
 below the
other ... and so on.

Cheers,


= = = = = = = =
 =  = =


On Fri, May 21, 2010 at 3:53 PM, David Winsemius 
 ymailto=mailto:dwinsem...@comcast.net;
 href=mailto:dwinsem...@comcast.net;dwinsem...@comcast.netwrote:




 On May 20, 2010, at 11:05 PM, santana sarma wrote:


 Hi,

 I have a dataframe with some 800 rows and 14
 columns.

 Could you please advise how I can concatenate
 the rows - one after
 another.
 Similarly for columns, one
 below the other.


 Not sure exactly what you are
 after:

 unlist might accomplish the second task.


 Whether c(apply(df, 1, I)) would be satisfactory for the first task
 might
 depend on whether the columns in the dataframe were all of the
 same type.
 Now that I think of it, both soolutions would force the types
 to be that
 same.

 ?c
 ?I

 ?apply

 df[1:nrow(df), ]   ...  would essentially give
 you the first request, but
 it would not be any different than just
 typing df. So  what do intend
 this process to
 accomplish?

 --

 David Winsemius, MD
 West
 Hartford, CT




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Re: [R] p-values 2.2e-16 not reported

2010-05-20 Thread Shi, Tao

Will,

 I'm wondering if you have any 
insights after looking at the cor.test source code.  It seems to be fine to me, 
as the p value is either calculated by your first method or a 
.C code.

...Tao



- Original Message 
 From: Will Eagle will.ea...@gmx.net
 To: r-help@r-project.org
 Sent: Wed, May 19, 2010 3:31:26 PM
 Subject: Re: [R] p-values  2.2e-16 not reported
 
 Dear all,

thanks for your feedback so far. With the help of a colleague I 
 think I found the solution to my problem:

 
 pt(10,100,lower=FALSE)
[1] 4.950844e-17

IS *NOT* EQUAL TO

 
 1-pt(10,100,lower=TRUE)
[1] 0

This means that R is capable of 
 providing p-values  2.2e-16, however, if the value is used in a substraction 
 or addition then the default value of the machine epsilon .Machine$double.eps 
 =  2.220446e-16 is applied. This causes that all p-values smaller than this 
 threshold are set to zero. This problem applies also to other distribution 
 functions like pnorm() and others. For your information I would also like to 
 quote the relevant part of the R manual on .Machine$double.eps:
the smallest 
 positive floating-point number x such that 1 + x != 1. It equals 
 base^ulp.digits 
 if either base is 2 or rounding is 0; otherwise, it is (base^ulp.digits)/ 
 2.  Normally 2.220446e-16.

Although different opinions were 
 expressed on whether it makes sense to differentiate p-values below the 
 machine 
 epsilon, in my opinion different effect sizes should correspond with 
 different 
 p-values when reporting statistical results. Additionally, in certain 
 scientific 
 fields, eg genetics, where usually many tests are performed and simple 
 methods, 
 eg Bonferroni method, are used to adjust for multiple testing, it is 
 important 
 to know the exact size of the p-value.

Therefore, I would like to suggest 
 that operations of the 2nd variant (ie 1-pt(10,100,lower=TRUE)) should be 
 deprecated to calculate p-values and operations of the 1st variant (ie 
 pt(10,100,lower=FALSE)) should be used  instead. Since I have seen the 2nd 
 variant being frequently used (also by very experienced R users) and I assume 
 that it is hidden in many statistical test functions, eg cor.test(), this 
 issue 
 seems to me quite important.

Best 
 regards,

Will

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Re: [R] About the breakpoint when making heatmap with lots of variables

2010-05-20 Thread Shi, Tao

The breakpoint you mentioned is irrelevant here.  Clustering 15672 
genes (I assume this is a microarray data) requires lots of memory.  I 
suggest you either filter your gene list down to thousands or just plot 
the column dendrogram without showing the heatmap.

plot(hclust(dist(x)))

...Tao




- Original Message 
 From: Meng Wu mengwu1...@gmail.com
 To: r-help@r-project.org
 Sent: Wed, May 19, 2010 7:31:29 PM
 Subject: [R] About the breakpoint when making heatmap with lots of variables
 
 HI,All

I am trying to create a heatmap with 24 samples with 15672 
 varibles, I read
in the table in R, and then made it as a matrix, then try to 
 create the
heatmap using heatmap(x,...)

However, I received the error 
 message as:
 heatmap(t(x))
Error: cannot allocate vector of size 936.8 
 Mb
R(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error 
 code=12)
*** error: can't allocate region
*** set a breakpoint in 
 malloc_error_break to debug
R(2925,0xa0b16500) malloc: *** 
 mmap(size=982261760) failed (error code=12)
*** error: can't allocate 
 region
*** set a breakpoint in malloc_error_break to 
 debug
R(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error 
 code=12)
*** error: can't allocate region
*** set a breakpoint in 
 malloc_error_break to debug
R(2925,0xa0b16500) malloc: *** 
 mmap(size=982261760) failed (error code=12)
*** error: can't allocate 
 region
*** set a breakpoint in malloc_error_break to 
 debug
R(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error 
 code=12)
*** error: can't allocate region
*** set a breakpoint in 
 malloc_error_break to debug
R(2925,0xa0b16500) malloc: *** 
 mmap(size=982261760) failed (error code=12)
*** error: can't allocate 
 region
*** set a breakpoint in malloc_error_break to 
 debug
R(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error 
 code=12)
*** error: can't allocate region
*** set a breakpoint in 
 malloc_error_break to debug


It seems like I do not have enough 
 memory, how can I set a breakpoint 
 as
suggested?

Thanks,

Meng


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Re: [R] colored venn diagram

2010-05-20 Thread Shi, Tao

Thank you for the suggestions, Peter and David!

- Original Message 
 From: Peter Ehlers ehl...@ucalgary.ca
 To: David Winsemius dwinsem...@comcast.net
 Cc: Shi, Tao shida...@yahoo.com; r-help@r-project.org
 Sent: Wed, May 19, 2010 8:45:24 PM
 Subject: Re: [R] colored venn diagram

 Tao,

You might also have a look at the venneuler package.

 -Peter Ehlers

On 2010-05-19 21:37, David Winsemius wrote:

 On May 19, 2010, at 7:15 PM, Shi, Tao wrote:

 Hi 
 list,

 This is probably too much to ask, but I'm 
 wondering if there is a
 ready-to-use function somewhere that allows 
 me to color one area of a
 venn diagram (e.g. the intersection of two 
 sets)?

 There is an intersectDiagrapm in plotrix that 
 accepts color arguments,
 although it is not really a Venn 
 diagram.

 The venn function in gplots does not accept color. It 
 is a wrapper to
 getVennCounts and drawVennDiagram, and if you hack the 
 second function
 you can get colors. For the example in the help page for 
 Venn, you need
 to find the section that handles the correct number of 
 sets and add a
 color argument to the polygon call. If you want 
 intersections you will
 need transparency. I do not know how to address 
 specific subsets:

 require(gplots)
 require(seqinr) # for 
 col2alpha for transparency

 getAnywhere(drawVennDiagram) # add an 
 assignment operator and trim out
 this stuff
 A single object 
 matching ‘drawVennDiagram’ was found
 It was found in the following 
 places
 namespace:gplots
 with value
 --end 
 trimming--
 function (data, small = 0.7, showSetLogicLabel = 
 FALSE, simplify = FALSE)
 {
 numCircles - NA
 .

 .
 # make mod to n==4 section
 + polygon(relocate_elp(elps, 45, 
 130, 170), col=col2alpha(red, 0.5) )
 + polygon(relocate_elp(elps, 45, 
 200, 200), col=col2alpha(blue, 0.5) )
 + polygon(relocate_elp(elps, 
 135, 200, 200))
 + polygon(relocate_elp(elps, 135, 270, 170))

 .
 .
 ... And then pass the result from venn to 
 drawVennDiagram:

 gv - venn(input)

 drawVennDiagram(data = gv, small = 0.7, showSetLogicLabel = FALSE,

 simplify = FALSE)

 Set #1 in pink set2 in blue and the 
 intersection is purple.

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Re: [R] Concatenation

2010-05-20 Thread Shi, Tao

Still not clear.  Follow the posting guide and some examples always help.   

Not sure how you concatenate numbers?

You can try, for example,

apply(df[1:10,], 2, paste, collapse= )

but this will turn everything into strings.  Is this what you want?

..Tao




- Original Message 
 From: santana sarma aimanusa...@gmail.com
 To: David Winsemius dwinsem...@comcast.net
 Cc: r-help@r-project.org
 Sent: Thu, May 20, 2010 9:21:33 PM
 Subject: Re: [R] Concatenation
 
 Hi David,

SORRY - I am trying to be more clearer this time.

Let's 
 say the dataframe has some rows and columns, with unique rownames and
column 
 names. The rest of the data in the dataframe are just numbers.

I wish to 
 concatenate those rows. That means : I wish to concatenate first
10 rows' 
 values in one row, then next 20 rows's values in the next row 
and so 
 on.

Similarly, for columns : The first 10 column's values will be one 
 below the
other ... and so on.

Cheers,


= = = = = = = = 
 =  = =


On Fri, May 21, 2010 at 3:53 PM, David Winsemius 
 ymailto=mailto:dwinsem...@comcast.net; 
 href=mailto:dwinsem...@comcast.net;dwinsem...@comcast.netwrote:


 
 On May 20, 2010, at 11:05 PM, santana sarma wrote:

  
 Hi,

 I have a dataframe with some 800 rows and 14 
 columns.

 Could you please advise how I can concatenate 
 the rows - one after
 another.
 Similarly for columns, one 
 below the other.


 Not sure exactly what you are 
 after:

 unlist might accomplish the second task.

 
 Whether c(apply(df, 1, I)) would be satisfactory for the first task 
 might
 depend on whether the columns in the dataframe were all of the 
 same type.
 Now that I think of it, both soolutions would force the types 
 to be that
 same.

 ?c
 ?I
 
 ?apply

 df[1:nrow(df), ]   ...  would essentially give 
 you the first request, but
 it would not be any different than just 
 typing df. So  what do intend
 this process to 
 accomplish?

 --

 David Winsemius, MD
 West 
 Hartford, CT



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 version deleted]]

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 href=https://stat.ethz.ch/mailman/listinfo/r-help; target=_blank 
 https://stat.ethz.ch/mailman/listinfo/r-help
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 guide http://www.R-project.org/posting-guide.html
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 minimal, self-contained, reproducible code.

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Re: [R] save in for loop

2010-05-19 Thread Shi, Tao

Ivan,

Try this:

eval(parse(text=paste(save(file, i, , file=\file, i, .RData\), sep=)))

...Tao




- Original Message 
 From: Ivan Calandra ivan.calan...@uni-hamburg.de
 To: r-help@r-project.org
 Sent: Wed, May 19, 2010 7:56:44 AM
 Subject: [R] save in for loop
 
 Dear users,

My problem concerns save() within a for loop.
Here is my 
 code:

for (i in 1:4) {
temp - data.frame(a=(i+1):(i+10), 
 b=LETTERS[(i+1):(i+10)])
filename - paste(file, i, sep=)

 assign(filename, temp)
save(filename, file=paste(filename, .rda, 
 sep=))
}

As you can see, save() doesn't work as I would like: (1) 
 the object saved is called filename (instead of file1, file2, etc), and 
 (2) it of course contains only the name (as character) instead of the 
 data.frame

How can I fix it?

I usually use lists for such cases, 
 but (1) in the real thing, it gets complicated with the names and structure 
 (because I want to save lists with 3 dimensions instead of simple 
 data.frames, 
 as in this example) and (2) I prefer saving each list separately (and I 
 cannot 
 save only one element of an object either).

I'm not sure I'm really clear 
 because it's difficult for me to explain it, but I hope you'll understand 
 (and 
 let me know what you would help you to understand)

Thank you in 
 advance
Ivan

-- Ivan CALANDRA
PhD Student
University of 
 Hamburg
Biozentrum Grindel und Zoologisches Museum
Abt. 
 Säugetiere
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 
 42838 6231

 href=mailto:ivan.calan...@uni-hamburg.de;ivan.calan...@uni-hamburg.de

**
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php

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[R] colored venn diagram

2010-05-19 Thread Shi, Tao

Hi list,

This is probably too much to ask, but I'm wondering if there is a ready-to-use 
function somewhere that allows me to color one area of a venn diagram (e.g. the 
intersection of two sets)?

Thanks!

...Tao

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Re: [R] automate curve drawing on nls() object

2010-05-18 Thread Shi, Tao

I can't directly answer your question regarding 'expression', but can you just 
replace b, c,d, and e with coef(obj)[1], coef(obj)[2], ... etc.   You still can 
automate the whole process this way, right?





- Original Message 
 From: array chip arrayprof...@yahoo.com
 To: r-help@r-project.org
 Sent: Tue, May 18, 2010 4:13:33 PM
 Subject: [R] automate curve drawing on nls() object
 
 Hi, I would like to use the curve() function to draw the predicted curve from 
 an 
 nls() object. for 
 example:

dd-read.table(dd.txt,sep='\t',header=T,row.names=1)
obj-nls(y~c+(d-c)/(1+(x/e)^b),data=dd,start=list(b=-1, 
 c=0, d=100, e=150))
coef(obj)
  b  
  c   d
e 
-1.1416422   0.6987028 102.8613176 
 135.9373131
curve(0.699+(102.86-0.699)/(1+(x/135.94)^(-1.1416)),1,2)

Now 
 I am going to have a lot of datasets to do this, so certainly I would like to 
 automate this. Suppose that I can create a character string for the formula, 
 but 
 I am not sure how to pass that character string into the curve() to make it 
 work. The help page of curve() says the first argument is an expression 
 written 
 as a function of x, or alternatively the name of a function which will be 
 plotted. I tried the following, for example:

substitute(expression(c + 
 (d - c)/(1 + (x/e)^b)),as.list(coef(obj)))
will 
 return:
expression(0.698704171233635 + (102.861317499063 - 
 0.698704171233635)/(1 + (x/135.937317917920)^-1.14164217993857))

so I 
 tried:
curve(substitute(expression(c + (d - c)/(1 + (x/e)^b)), 
 as.list(coef(obj))), 1,2)

but it returns an error:
Error in 
 xy.coords(x, y, xlabel, ylabel, log) : 
  'x' and 'y' lengths 
 differ

Any suggestions?


A related question:

If I do 
 this:
substitute(expression(c + (d - c)/(1 + 
 (x/e)^b)),as.list(coef(obj)))

I will get: 
 
expression(0.698704171233635 + (102.861317499063 - 0.698704171233635)/(1 + 
 (x/135.937317917920)^-1.14164217993857))

But if I 
 do:
substitute(parse(text=as.character(obj$call$formula[3]),srcfile=NULL),as.list(coef(obj)))

I 
 only get:
parse(text = as.character(obj$call$formula[3]), srcfile = NULL) 
 as a result, not have b,c,d,e replaced by coefficient 
 values.

where

 
parse(text=as.character(obj$call$formula[3]),srcfile=NULL)
returns the 
 wanted expression:
expression(c + (d - c)/(1 + (x/e)^b))

Why is 
 that?

Thanks

John

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 https://stat.ethz.ch/mailman/listinfo/r-help
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 guide http://www.R-project.org/posting-guide.html
and provide commented, 
 minimal, self-contained, reproducible code.

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Re: [R] automate curve drawing on nls() object

2010-05-18 Thread Shi, Tao

In this case, Ben's approach is the way to go.  

I'm curious how you fit nls without knowing the model formula beforehand?

...Tao





- Original Message 
 From: array chip arrayprof...@yahoo.com
 To: r-help@r-project.org; TaoShi shida...@yahoo.com
 Sent: Tue, May 18, 2010 5:22:47 PM
 Subject: Re: [R] automate curve drawing on nls() object
 
 well, this is not going automate enough because you have to know how the 
 model 
 (formula) looks like, and how many parameters there are in the model 
 beforehand 
 to do what you are suggesting.

Thanks


--- On Tue, 5/18/10, 
 Shi, Tao 
 href=mailto:shida...@yahoo.com;shida...@yahoo.com wrote:

 
 From: Shi, Tao 
 href=mailto:shida...@yahoo.com;shida...@yahoo.com
 Subject: Re: 
 [R] automate curve drawing on nls() object
 To: array chip 
 ymailto=mailto:arrayprof...@yahoo.com; 
 href=mailto:arrayprof...@yahoo.com;arrayprof...@yahoo.com, 
 ymailto=mailto:r-help@r-project.org; 
 href=mailto:r-help@r-project.org;r-help@r-project.org
 Date: 
 Tuesday, May 18, 2010, 7:42 PM
 I can't directly answer your 
 question
 regarding 'expression', but can you just replace b, c,d, 
 and
 e with coef(obj)[1], coef(obj)[2], ...
 etc.   You still can 
 automate the whole
 process this way, right?
 
 
 
 
 
 
 - Original Message 
  From: array 
 chip 
 href=mailto:arrayprof...@yahoo.com;arrayprof...@yahoo.com
  
 To: 
 href=mailto:r-help@r-project.org;r-help@r-project.org
  Sent: 
 Tue, May 18, 2010 4:13:33 PM
  Subject: [R] automate curve drawing on 
 nls() object
  
  Hi, I would like to use the curve() 
 function to draw
 the predicted curve from an 
  nls() object. 
 for 
  example:
 
 
 dd-read.table(dd.txt,sep='\t',header=T,row.names=1)
 
 obj-nls(y~c+(d-c)/(1+(x/e)^b),data=dd,start=list(b=-1,
 
  
 c=0, d=100, e=150))
 coef(obj)
   b  
 
   c   
d
 e 
 
 -1.1416422   0.6987028 102.8613176 
  135.9373131
 
 curve(0.699+(102.86-0.699)/(1+(x/135.94)^(-1.1416)),1,2)
 
 
 Now 
  I am going to have a lot of datasets to do this, so
 
 certainly I would like to 
  automate this. Suppose that I can create 
 a character
 string for the formula, but 
  I am not sure how 
 to pass that character string into
 the curve() to make it 
  
 work. The help page of curve() says the first argument
 is an expression 
 written 
  as a function of x, or alternatively the name of a
 
 function which will be 
  plotted. I tried the following, for 
 example:
 
 substitute(expression(c + 
  (d - c)/(1 + 
 (x/e)^b)),as.list(coef(obj)))
 will 
  return:
 
 expression(0.698704171233635 + (102.861317499063 - 
  
 0.698704171233635)/(1 +
 
 (x/135.937317917920)^-1.14164217993857))
 
 so I 
  
 tried:
 curve(substitute(expression(c + (d - c)/(1 + (x/e)^b)), 
 
  as.list(coef(obj))), 1,2)
 
 but it returns an 
 error:
 Error in 
  xy.coords(x, y, xlabel, ylabel, log) : 
 
   'x' and 'y' lengths 
  differ
 
 Any 
 suggestions?
 
 
 A related question:
 
 If I 
 do 
  this:
 substitute(expression(c + (d - c)/(1 + 
 
  (x/e)^b)),as.list(coef(obj)))
 
 I will get: 
  
 
 expression(0.698704171233635 + (102.861317499063 -
 
 0.698704171233635)/(1 + 
  
 (x/135.937317917920)^-1.14164217993857))
 
 But if I 
 
  do:
 
 substitute(parse(text=as.character(obj$call$formula[3]),srcfile=NULL),as.list(coef(obj)))
 
 
 I 
  only get:
 parse(text = 
 as.character(obj$call$formula[3]), srcfile =
 NULL) 
  as a 
 result, not have b,c,d,e replaced by coefficient
 
  
 values.
 
 where
 
  
 
 parse(text=as.character(obj$call$formula[3]),srcfile=NULL)
 returns the 
 
  wanted expression:
 expression(c + (d - c)/(1 + 
 (x/e)^b))
 
 Why is 
  that?
 
 
 Thanks
 
 John
 
 
 __
 
  
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 href=mailto:R-help@r-project.org;R-help@r-project.org
 
 
  href=mailto:
 href=mailto:R-help@r-project.org;R-help@r-project.org
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 target=_blank https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE 
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 http://www.R-project.org/posting-guide.html
 and provide commented, 
 
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Re: [R] SAS for R-users

2010-05-14 Thread Shi, Tao

Thomas,

If you're thinking to leverage your R programming skill in learning SAS, you'll 
be disappointed, as the two have quite different grammar.  The book Erik 
mentioned is a good start.  After that, just reading the SAS help file, which 
is pretty comprehensive, will keep you busy. 

...Tao




- Original Message 
 From: Erik Iverson er...@ccbr.umn.edu
 To: Thomas Levine thomas.lev...@gmail.com
 Cc: r-help@r-project.org
 Sent: Fri, May 14, 2010 6:18:04 AM
 Subject: Re: [R] SAS for R-users
 
 Thomas Levine wrote:
 There are loads of resources for users of any 
 other
 statistics package who are learning R. For example
 
 
 http://www.google.com/search?q=r+for+sas-users;
 
 The 
 reverse isn't the case
 
 
 href=http://www.google.com/search?q=; target=_blank 
 http://www.google.com/search?q=sas+for+r-users;

snip

 
 I can't wait that long. Until then and until I can
 convince colleagues 
 and teachers to use better
 software, how do you suggest that I learn 
 SAS?
 I suspect that it'll be a book on R for SAS-users,
 so I'm 
 expecting recommendations of books like
 those that are best for R-users 
 learning SAS.
 
 This question would be more appropriate for 
 a
 SAS mailing list, I couldn't find any except for
 those of a 
 few regional groups.

I don't think there is any shortage of SAS books, 
 since it's been around so long.  I think they even have their own 
 Press.  The books don't need to assume you do or don't know R.  If you 
 know nothing of SAS, I personally recommend The Little SAS Book: A Primer.  
 It's short, basic, and useful for 
 beginners.

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[R] rpart: how to use each variable only once?

2010-05-14 Thread Shi, Tao

Hi list,

Is there a way in rpart to force the variables only used once when doing the 
splits?

This is how the question came about.  Often time, the tree constructed uses the 
same variable (say X1) for the first and second splits, for example.  However, 
due to practical reason, the researcher doesn't like this.  The prefer to see 
the second split using other variables (say X2).  Therefore the question.  I 
understand the performance will suffer.  However if there is a performance 
improvement for the tree with X1 as 1st split and X2 as 2nd split comparing the 
tree with one single split using X1, I guess it's still a reasonable thing to 
do, right? 

Many thanks!

...Tao

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Re: [R] Multiple plots; single x(y) labels

2010-05-14 Thread Shi, Tao

Gurmeet,

I think Xin is more interested in the common axes, rather than just one single 
xlab or ylab.

Jim's solution is much more fancier than mine :-)

...Tao




- Original Message 
 From: Gurmeet r.emailing.l...@gmail.com
 To: Jim Lemon j...@bitwrit.com.au
 Cc: r-help@r-project.org
 Sent: Fri, May 14, 2010 10:00:03 AM
 Subject: Re: [R] Multiple plots; single x(y) labels
 
 Hi Xin,

Or, just try adding oma and mtext 
 commands:

?par
?mtext

# 
 Code
par(mfcol=c(2,2))
par(oma=c(2,2,0,0))
plot(x - sort(rnorm(7)), 
 type = s, main = , ylab=, xlab=)
plot(x - sort(rnorm(27)), type = 
 s, main = , ylab=, xlab=)
plot(x - sort(rnorm(47)), type = s, 
 main = , ylab=, xlab=)
plot(x - sort(rnorm(67)), type = s, main = 
 , ylab=, xlab=)
mtext(One x-label, side = 1, 
 outer=TRUE)
mtext(One y-label, side = 2, 
 outer=TRUE)

~Gurmeet


On Fri, May 14, 2010 at 4:14 AM, Jim 
 Lemon 
 href=mailto:j...@bitwrit.com.au;j...@bitwrit.com.au wrote:

 
 On 05/14/2010 02:04 AM, Xin Ge wrote:

 Hi 
 All,

 Can anyone please help me with getting a single x 
 and y-axis label while
 plotting muliple plots. Here is the 
 code:

 par(mfcol=c(2,2))
 plot(x- 
 sort(rnorm(7)), type = s, main = , ylab=, xlab=)
 plot(x- 
 sort(rnorm(27)), type = s, main = , ylab=, xlab=)
 
 plot(x- sort(rnorm(47)), type = s, main = , ylab=, 
 xlab=)
 plot(x- sort(rnorm(67)), type = s, main = , 
 ylab=, xlab=)

 also, how can remove x-tick lables 
 using plot()?

  Hi Xin,
 Fortunately, this 
 wheel is pretty easy to reinvent:

 
 require(plotrix)

 x1-rnorm(7)
 
 x2-rnorm(27)
 x3-rnorm(47)
 x4-rnorm(67)
 
 allxlim-c(1,67)
 allylim-range(c(x1,x2,x3,x4))
 
 panes(matrix(1:4,nrow=2,byrow=TRUE),widths=c(1.1,1),
  
 heights=c(1,1.1))
 par(mar=c(0,4,2,0))
 
 plot(sort(x1),xlim=allxlim,ylim=allylim,type=s,
  
 main=,ylab=,xlab=,xaxt=n)
 tab.title(Plot of 
 x1,tab.col=orange)
 par(mar=c(0,0,2,1))
 
 plot(sort(x2),xlim=allxlim,ylim=allylim,type=s,
  
 main=,ylab=,xlab=,xaxt=n,yaxt=n)
 tab.title(Plot of 
 x2,tab.col=orange)
 par(mar=c(4,4,2,0))
 
 plot(sort(x3),xlim=allxlim,ylim=allylim,type=s,
  
 main=,ylab=,xlab=)
 tab.title(Plot of 
 x3,tab.col=orange)
 par(mar=c(4,0,2,1))
 
 plot(sort(x4),xlim=allxlim,ylim=allylim,type=s,
  
 main=,ylab=,xlab=,yaxt=n)
 tab.title(Plot of 
 x4,tab.col=orange)

 Jim


 
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 href=mailto:R-help@r-project.org;R-help@r-project.org mailing list
 
 
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 posting guide
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 code.


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Re: [R] Putting 6 graphs on one page

2010-05-14 Thread Shi, Tao

Without the actual data, it's hard to see what's going on here, but It seems 
you have to restructure your data object to a long table, then it should be 
easy to use 'dotplot' to generate your plots.

...Tao




- Original Message 
 From: Dimitri Liakhovitski dimitri.liakhovit...@gmail.com
 To: r-help@r-project.org
 Sent: Fri, May 14, 2010 10:19:38 AM
 Subject: [R] Putting 6 graphs on one page
 
 Apologies, if it's a very simple question, but I am really not very
good with 
 trellis.
I have a piece of a code (below) that works just fine and builds 
 6
graphs - in a loop. I loop through 6 conditions and build one graph
for 
 each.
What would be the most efficient way of creating one page with 
 6
graphs instead? (2 rows and 3 columns)?
Thanks a 
 lot!
Dimitri

conditions-c(a,b,c,d,e,f)
conditions.long-c(It's 
 a,It's b,It's c,It's d,It's e,It's f)

for(i in 1:6) 
 {

 IV-conditions[i]
filename2=paste(DependentVariable 
 ,IV ,IV,.emf,sep=)

 win.metafile(file=filename2)


 out-as.data.frame(tapply(data$DependentVariable.j,data[[IV]],mean))

 out$IV-as.factor(as.numeric(row.names(out)))

 names(out)[1]-j

 out2-as.data.frame(tapply(data$DependentVariable,data[[IV]],mean))

 out-cbind(out,out2)

 names(out)[3]-rf


 par.settings=trellis.par.set(superpose.line 
 =
list(col=c(PrimaryColors[4],SecondaryColors[4]),lwd = 
 2,lty=c(1,3)),
  superpose.symbol = 
 list(cex = 1.5, pch = 
 c(1,3),
lty=c(1,3),col=c(PrimaryColors[4],SecondaryColors[4])),
  
   reference.line = list(col = 
 gray, lty =dotted))


 plot-dotplot(c(out$j,out$rf)~rep(out$IV,2),
  
 groups=rep(c(Method1,Method1), each=nrow(out)),
  
 type=b,

 scales=list(x=list(cex=1.3),y=list(cex=1.3)),
auto.key = 
 list(space = top, points = TRUE, lines = TRUE,cex=1.3),

 ylim=c(0,5),
  
 xlab=list(conditions.long[i],cex=1.2,font=2),

 ylab=list(Dependent Variable,cex=1.2,font=2),

 cex.lab=1.5,
  panel = 
 function(y,x,...) {
   
 panel.grid(h = -1, v = -1)
  
 panel.xyplot(x, y, ...)
  
   ltext(x, y, labels=round(y,2), 
 cex=1.3,col=black,font=1,pos=3)
  
 })
print(plot)

 dev.off()
}

-- 
Dimitri Liakhovitski
Ninah Consulting

 target=_blank 
 href=http://www.ninah.com;www.ninah.com

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Re: [R] Multiple plots; single x(y) labels

2010-05-14 Thread Shi, Tao

ha, I was focusing on the wrong thing!

Sorry, Gurmeet.  Good job!

From: Xin Ge xingemaill...@gmail.com
To: Shi, Tao shida...@yahoo.com
Cc: Gurmeet r.emailing.l...@gmail.com; Jim Lemon j...@bitwrit.com.au; 
r-help@r-project.org
Sent: Fri, May 14, 2010 10:51:26 AM
Subject: Re: [R] Multiple plots; single x(y) labels

Thank you all for your replies. 

@Tao: Actually Gurmeet's solution is the one I was looking for, below is a 
chunk from my last email:

*
Like for example, the following plot has a *combine* x-label (Height) and 
one y-label (Weight)

http://support.sas.com/documentation/cdl/en/grstateditug/61951/HTML/default/images/multi-panel-data.gif

*

In the process I learnt so many other stuff,
~Xin

On Fri, May 14, 2010 at 1:29 PM, Shi, Tao shida...@yahoo.com wrote:

Gurmeet,

I think Xin is more interested in the common axes, rather than just one 
single xlab or ylab.

Jim's solution is much more fancier than mine :-)

...Tao

- Original Message 
 From: Gurmeet r.emailing.l...@gmail.com
 To: Jim Lemon j...@bitwrit.com.au
 Cc: r-help@r-project.org

 Sent: Fri, May 14, 2010 10:00:03 AM
 Subject: Re: [R] Multiple plots; single x(y) labels

 Hi Xin,

Or, just try adding oma and mtext
 commands:

?par
?mtext

#
 Code
par(mfcol=c(2,2))
par(oma=c(2,2,0,0))
plot(x - sort(rnorm(7)),
 type = s, main = , ylab=, xlab=)
plot(x - sort(rnorm(27)), type =
 s, main = , ylab=, xlab=)
plot(x - sort(rnorm(47)), type = s,
 main = , ylab=, xlab=)
plot(x - sort(rnorm(67)), type = s, main =
 , ylab=, xlab=)
mtext(One x-label, side = 1,
 outer=TRUE)
mtext(One y-label, side = 2,
 outer=TRUE)

~Gurmeet

On Fri, May 14, 2010 at 4:14 AM, Jim
 Lemon 

 href=mailto:j...@bitwrit.com.au;j...@bitwrit.com.au wrote:

 On 05/14/2010 02:04 AM, Xin Ge wrote:

 Hi
 All,

 Can anyone please help me with getting a single x
 and y-axis label while
 plotting muliple plots. Here is the
 code:

 par(mfcol=c(2,2))
 plot(x-
 sort(rnorm(7)), type = s, main = , ylab=, xlab=)
 plot(x-
 sort(rnorm(27)), type = s, main = , ylab=, xlab=)

 plot(x- sort(rnorm(47)), type = s, main = , ylab=,
 xlab=)
 plot(x- sort(rnorm(67)), type = s, main = ,
 ylab=, xlab=)

 also, how can remove x-tick lables
 using plot()?

  Hi Xin,
 Fortunately, this
 wheel is pretty easy to reinvent:

 require(plotrix)

 x1-rnorm(7)

 x2-rnorm(27)
 x3-rnorm(47)
 x4-rnorm(67)

 allxlim-c(1,67)
 allylim-range(c(x1,x2,x3,x4))

 panes(matrix(1:4,nrow=2,byrow=TRUE),widths=c(1.1,1),

 heights=c(1,1.1))
 par(mar=c(0,4,2,0))

 plot(sort(x1),xlim=allxlim,ylim=allylim,type=s,

 main=,ylab=,xlab=,xaxt=n)
 tab.title(Plot of
 x1,tab.col=orange)
 par(mar=c(0,0,2,1))

 plot(sort(x2),xlim=allxlim,ylim=allylim,type=s,

 main=,ylab=,xlab=,xaxt=n,yaxt=n)
 tab.title(Plot of
 x2,tab.col=orange)
 par(mar=c(4,4,2,0))

 plot(sort(x3),xlim=allxlim,ylim=allylim,type=s,

 main=,ylab=,xlab=)
 tab.title(Plot of
 x3,tab.col=orange)
 par(mar=c(4,0,2,1))

 plot(sort(x4),xlim=allxlim,ylim=allylim,type=s,

 main=,ylab=,xlab=,yaxt=n)
 tab.title(Plot of
 x4,tab.col=orange)

 Jim

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Re: [R] rpart: how to use each variable only once?

2010-05-14 Thread Shi, Tao

This is just one single decision tree, not forest.  If you're asking what 
package I use to construct one single tree, it's 'rpart'. 

From: Changbin Du changb...@gmail.com
To: Shi, Tao shida...@yahoo.com
Cc: r-help@r-project.org
Sent: Fri, May 14, 2010 12:35:20 PM
Subject: Re: [R] rpart: how to use each variable only once?

is this random decision tree, I dont know is there any package can run it.  
If you know, please let me know.

On Fri, May 14, 2010 at 10:23 AM, Shi, Tao shida...@yahoo.com wrote:

Hi list,

Is there a way in rpart to force the variables only used once when doing 
the splits?

This is how the question came about.  Often time, the tree constructed uses 
the same variable (say X1) for the first and second splits, for example.  
However, due to practical reason, the researcher doesn't like this.  The 
prefer to see the second split using other variables (say X2).  Therefore 
the question.  I understand the performance will suffer.  However if there 
is a performance improvement for the tree with X1 as 1st split and X2 as 
2nd split comparing the tree with one single split using X1, I guess it's 
still a reasonable thing to do, right?

Many thanks!

...Tao

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-- 
Sincerely,
Changbin 
--

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Re: [R] Whiskers on the default boxplot {graphics}

2010-05-13 Thread Shi, Tao

Hi Robert,

Your points are well taken.  However, I reserve mine, b/c I think without this 
detailed discussion, an average R user would simply confused the interquartile 
range said in boxplot help file with the results of IQR.  Changing it to 
length of box makes it more exact and consistent, as I stated earlier.  With 
all these being said, this is up to the R core team to decide.

...Tao





- Original Message 
 From: Robert Baer rb...@atsu.edu
 To: Shi, Tao shida...@yahoo.com; Peter Ehlers ehl...@ucalgary.ca
 Cc: R Project Help R-help@r-project.org
 Sent: Thu, May 13, 2010 7:25:09 AM
 Subject: Re: [R] Whiskers on the default boxplot {graphics}
 
  Hi Peter,
 
 You're absolutely correct!  The description 
 for 'range' in 'boxplot' help file is a little bit confusing by using the 
 words 
 interquartile range. I think it should be changed to the length of the 
 box 
 to be exact and consistent with those in the help file for 
 boxplot.stats.

The issue is probably that there are multiple ways (9 to 
 be exact) of defining quantiles in R.  See 'type= ' arguement for 
 ?quantile.  The quantile function uses type=7 by default which matches the 
 quantile definition used by S-Plus(?), but differs from that used by SPSS.  
 Doesn't fivenum essentially use the equivalent of a different type=  
 arguement 
 (maybe 2 or 5) in constructing the hinges?

It seems perfectly reasonable 
 to talk about 'length of box' (or 'box height' depending how you display the 
 boxplot), but aren't the hinges simply Q1 and Q3 defined by one of the 
 possible 
 quartile definitions (as Peter points out the one used by fivenum)?  The 
 box height does not necesarily match the distance produced by IQR() which 
 also 
 seems to use the equivalent of quantile(..., type=7), but it is still an IQR, 
 is 
 it not?

Quantiles apparantly can be defined in more than one acceptable 
 way (sort of like dealing with ties in rank statistics).  The OP seemed to 
 want an exact explanation of the wiskers, and I think Peter has pointed us 
 at 
 the definition of quartiles used by fivenum, as opposed to the default  
 used with quantile(..., type=7).

All that said, I'm not convinced that 
 it is wrong to speak of interquartile range in 'boxplot' 
 help.

Rob

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Re: [R] a question about latex in Hmisc

2010-05-13 Thread Shi, Tao

Hi Duncan,

I have no problems running latex or pdflatex.  I re-ran my code and it seems 
the problem is that R (or MiKTex ?) put the .tex file (the one wrapping 
everything in a document format for displaying purpose) in a R tmp folder, but 
the corresponding .log, .aux, and .dvi in my working directory.  So when YAP 
was called, it was looking for the .dvi file in the R temp folder.  Therefore, 
the error window.  

http://i41.tinypic.com/15qz387.jpg

I wonder how to fix that?

Thanks!

...Tao





- Original Message 
 From: Duncan Murdoch murdoch.dun...@gmail.com
 To: Shi, Tao shida...@yahoo.com
 Cc: Ista Zahn istaz...@gmail.com; r-help@r-project.org
 Sent: Wed, May 12, 2010 1:40:50 PM
 Subject: Re: [R] a question about latex in Hmisc
 
 On 12/05/2010 4:33 PM, Shi, Tao wrote:
 Hi Ista,
 
 Thanks 
 for the reply!
 
 You actually misunderstood me.  I never 
 objected the tmp - latex(x) method (in fact, that's what I'm doing now in 
 my .Rnw file).  As I stated in my original post, I'm simply curious about 
 what causes the error window and wanted to get to the bottom of 
 it.
  
latex(x) returns an object of class latex.  When 
 you don't assign it, it prints.  The print method for latex objects tries 
 to run latex and then display the resulting .dvi file.  (Or maybe it runs 
 pdflatex and displays the .pdf file).

If you can't run latex, you can't 
 print those objects.  That's why you're getting an error.

Duncan 
 Murdoch

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Re: [R] a question about latex in Hmisc

2010-05-13 Thread Shi, Tao

Hi Prof. Harrell,

Originally, I was thinking that by putting tables (especially those long 
tables) into separate .tex files would make my 'big' .tex file more organized 
(i.e. rather than having an one giant .tex file).  But now I'm having a second 
thought, b/c I don't really have to worry how my 'big' .tex file looks, as it's 
just a intermediate and I'll do all my editing in the .Rnw file.  So, I think 
I'll use the latex(x, file=) method more.  This also will make my working 
directory cleaner.

Thank you very much!

...Tao





- Original Message 
 From: Frank E Harrell Jr f.harr...@vanderbilt.edu
 To: r-help@r-project.org
 Sent: Wed, May 12, 2010 4:28:20 PM
 Subject: Re: [R] a question about latex in Hmisc
 
 On 05/12/2010 03:33 PM, Shi, Tao wrote:
 Hi Ista,

 Thanks 
 for the reply!

 You actually misunderstood me.  I never 
 objected the tmp- latex(x) method (in fact, that's what I'm doing now in 
 my .Rnw file).  As I stated in my original post, I'm simply curious about 
 what causes the error window and wanted to get to the bottom of 
 it.

 ...Tao

Not clear why the earlier suggestion someone 
 made to use latex(object, 
file='') is not the method of choice with 
 Sweave.

Frank



 
 =

 If you would rather have 
 a
 separate file for your table you can continue to
 use your 
 original method,
 e.g.,
 =
 tmp- 
 latex(x,
 file=x.tex)
 @
 
 \include{x.tex}

 (not sure what your objection to
 
 this was in the first place).

 -Ista



-- 
 
Frank E Harrell Jr   Professor and Chairman
 School of Medicine

   Department of Biostatistics   Vanderbilt 
 University

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

Re: [R] Path to R script

2010-05-13 Thread Shi, Tao

In this case, deploy them as a R package is the way to go.

- Original Message 
 From: Johannes W. Dietrich j.w.dietr...@medizinische-kybernetik.de
 To: Shi, Tao shida...@yahoo.com; johannes.dietr...@rub.de
 Cc: r-help@r-project.org
 Sent: Thu, May 13, 2010 9:14:24 AM
 Subject: Re: [R] Path to R script

 At 13:19 Uhr -0700 12.05.2010, Shi, Tao wrote:
 Don't quite understand 
 your question, but it looks like a more IT issue to me.  I guess you store 
 your R scripts in a central location (e.g. a server) and everybody call them 
 from their own workstation, right?

Thank you, but this would be an easy 
 solution. The problem is that the R script and data tables are stored on the 
 individual computers (and therefore on different places depending of the 
 users' 
 preferences and of course the operating system).

If it were possible to 
 locate the files relative to the script we could write modular scripts that 
 would run on any machine without modifications.

Thanks again,

J. 
 W. D.
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 
 -- --
-- Dr. Johannes W. Dietrich, M.D.
-- Laboratory XU 44, Endocrine 
 Research
-- Medical Hospital I, Bergmannsheil University Hospitals
-- Ruhr 
 University of Bochum
-- Buerkle-de-la-Camp-Platz 1, D-44789 Bochum, NRW, 
 Germany
-- Phone: +49:234:302-6400, Fax: +49:234:302-6403
-- eMail: 
 ymailto=mailto:j.w.dietr...@medical-cybernetics.de; 
 href=mailto:j.w.dietr...@medical-cybernetics.de;j.w.dietr...@medical-cybernetics.de
-- 
 WWW: http://medical-cybernetics.de
-- WWW: http://www.bergmannsheil.de
-- 
 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --

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Re: [R] Multiple plots; single x(y) labels

2010-05-13 Thread Shi, Tao

Not sure why you want to do that b/c this can be done with one function call of 
xyplot in lattice.

Anyway, you can always set axes=F and then replot each axis using 'axis' for 
each plot.  Make sure before you do that, set your xlim and ylim, so all four 
plots have the same xlim and ylim.  Like David said, you're re-inventing the 
wheels .

...Tao




- Original Message 
 From: Xin Ge xingemaill...@gmail.com
 To: David Winsemius dwinsem...@comcast.net
 Cc: r-help@r-project.org
 Sent: Thu, May 13, 2010 10:24:56 AM
 Subject: Re: [R] Multiple plots; single x(y) labels
 
 Hi David (and Others),

I think I messed it up. Lets start afresh, I do 
 not want to use lattice for
this. I'm using multiple plot commands and then 
 eventually would like to
get a *combine* x-label and y-label for this 
 plot.

Like for example, the following plot has a combine x-label 
 (Height) and
one y-label 
 (Weight)

http://support.sas.com/documentation/cdl/en/grstateditug/61951/HTML/default/images/multi-panel-data.gif

Is 
 it possible to get a graph similar to above one using base R only ?

# R 
 code (this is just a sample data and not actual data I'm 
 using)

par(mfcol=c(2,2))
plot(1:3, 4:6, type = s, main = , 
 ylab=, xlab=)
plot(2:5, 5:8, type = s, main = , ylab=, 
 xlab=)
plot(3:6, 6:9, type = s, main = , ylab=, xlab=)
plot(4:7, 
 6:9, type = s, main = , ylab=, xlab=)

Thanks in 
 advance,
Xin

On Thu, May 13, 2010 at 1:10 PM, David Winsemius 
 ymailto=mailto:dwinsem...@comcast.net; 
 href=mailto:dwinsem...@comcast.net;dwinsem...@comcast.netwrote:


 
 On May 13, 2010, at 12:59 PM, Xin Ge wrote:

  Hi 
 David,

 Thanks for your reply. By single x and y-labels I 
 meant something like
 this:

 
 http://zoonek.free.fr/blosxom//R/2006-08-10_lattice_xyplot_quakes.png

 
 which lattice gives by default. The code you sent doesn't seem to 
 solve
 the problem, I'm sorry if I havent' explained it clearly 
 before.

 Any comments?


 Yes. 
 If you want lattice output, then don't use base graphics 
 functions

 --
 
 David.



 Thanks,
 
 Xin

 On Thu, May 13, 2010 at 12:51 PM, David Winsemius 
 
 href=mailto:dwinsem...@comcast.net;dwinsem...@comcast.net
 
 wrote:

 On May 13, 2010, at 12:35 PM, David Winsemius 
 wrote:


 ?plot  # 
 ylim

 and you need to have the data in a form (before 
 plotting) where you can
 determine the shared max and min for the y 
 limits

 On May 13, 2010, at 12:04 PM, Xin Ge 
 wrote:

 Hi All,

 Can anyone please 
 help me with getting a single x and y-axis label while
 plotting 
 muliple plots.

 I'm still not sure what a single x-label 
 might mean for such disparate
 series.

 Here 
 is the code:

 par(mfcol=c(2,2))
 plot(x - 
 sort(rnorm(7)), type = s, main = , ylab=, xlab=)
 plot(x 
 - sort(rnorm(27)), type = s, main = , ylab=, xlab=)
 
 plot(x - sort(rnorm(47)), type = s, main = , ylab=, 
 xlab=)
 plot(x - sort(rnorm(67)), type = s, main = , 
 ylab=, xlab=)


 randlist - list(); 
 randlist[[1]] - sort(rnorm(7))
 randlist[[2]] - 
 sort(rnorm(27))
 randlist[[3]] - sort(rnorm(47))
 
 randlist[[4]] - sort(rnorm(67))
 lapply(randlist, plot, 
 ylim=c(min(rapply(randlist, min)),
 
 max(rapply(randlist,max))),

  type = s, xaxt=n, main = , ylab=, 
 xlab=);
 par(opar)

 A minor 
 refinement:


 opar - 
 par(mfcol=c(2,2))
 lapply(randlist, plot, ylim=c(Reduce(min, 
 randlist), Reduce(max,
 randlist)),

  
type = s, 
 xaxt=n, main = , ylab=, xlab=)
 
 par(opar)


 also, how can remove x-tick lables 
 using plot()?

 ?par  # 
 xaxt=n


 Thanks,
 
 Xin

   [[alternative HTML version 
 deleted]]

 
 __
 
 ymailto=mailto:R-help@r-project.org; 
 href=mailto:R-help@r-project.org;R-help@r-project.org mailing 
 list
 
 target=_blank 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.

 David 
 Winsemius, MD
 West Hartford, CT

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

 
 David Winsemius, MD
 West Hartford, 
 CT



 David Winsemius, MD
 West 
 Hartford, CT



[[alternative HTML 
 version deleted]]

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 ymailto=mailto:R-help@r-project.org; 
 href=mailto:R-help@r-project.org;R-help@r-project.org mailing list

 href=https://stat.ethz.ch/mailman/listinfo/r-help; target=_blank 
 https://stat.ethz.ch/mailman/listinfo/r-help
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 guide 
 http://www.R-project.org/posting-guide.html
and provide commented, 
 minimal,

Re: [R] read table for Fisher Exact

2010-05-13 Thread Shi, Tao

Hi Prof. Harrell,

Could you please elaborate on why chi-square test is more appropriate in this 
case?  Thank you very much!

...Tao





- Original Message 
 From: Frank E Harrell Jr f.harr...@vanderbilt.edu
 To: r-help@r-project.org
 Sent: Thu, May 13, 2010 5:35:07 AM
 Subject: Re: [R] read table for Fisher Exact
 
 On 05/12/2010 03:31 PM, visser wrote:

 i have 2 groups i want to 
 compare: group A and group B
 each group contains let's say 20 
 patients
 i want to perform a Fisher Exact test on genotype 
 distribution
 so, see if there is a sign diff in genotpe 
 frequency/distribution (#AA, #AB,
 #BB) between group A and B
 not 
 for 1, but for 1000 different genes

 my question: how should i 
 build my table so i can do:

 test- 
 read.table(table1.txt)
 fisher.test(test)

 i know a lot 
 is still missing in the syntax, but i do not know what. any
 help would 
 be soo much appreciated!!

Note that in this case, Fisher's exact test has 
 a good chance of being 
less accurate than an approximate Pearson chi-square 
 test.

-- 
Frank E Harrell Jr   Professor and Chairman  
   School of Medicine
  
 Department of Biostatistics  
 Vanderbilt 
 University

__

 ymailto=mailto:R-help@r-project.org; 
 href=mailto:R-help@r-project.org;R-help@r-project.org mailing list

 href=https://stat.ethz.ch/mailman/listinfo/r-help; target=_blank 
 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@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.

Re: [R] read table for Fisher Exact

2010-05-13 Thread Shi, Tao

Thanks, David!

- Original Message 
 From: David Winsemius dwinsem...@comcast.net
 To: Frank E Harrell Jr f.harr...@vanderbilt.edu
 Cc: Shi, Tao shida...@yahoo.com; r-help@r-project.org
 Sent: Thu, May 13, 2010 8:29:31 PM
 Subject: Re: [R] read table for Fisher Exact

On May 13, 2010, at 9:24 PM, Frank E Harrell Jr wrote:

 On 
 05/13/2010 08:16 PM, Shi, Tao wrote:
 Hi Prof. Harrell,

 Could you please elaborate on why chi-square test is more 
 appropriate in this case?  Thank you very much!

 ...Tao

 Exact tests tend to not be very accurate.  
 Typically their P-values are too large.  See

 @Article{cra08how,
  author = 
 {Crans, Gerald G. and Shuster, Jonathan J.},
  title = 
  {How conservative is {Fisher's} exact 
 test? {A} quantitative evaluation of the two-sample comparative binomial 
 trial},
  journal =  Statistics in 
 Medicine,
  year = 
 2008,
  volume =  27,
  pages = 
  {3598-3611},
  annote = 
 {Fisher's exact test; $2\times 2$ contingency table;size of test; comparative 
 binomial experiment;first paper to truly quantify the conservativeness of 
 Fisher's test;``the test size of FET was less than 0.035 for nearly all 
 sample 
 sizes before 50 and did not approach 0.05 even for sample sizes over 
 100.'';conservativeness of ``exact'' methods;see \emph{Stat in Med} 
 \textbf{28}:173-179, 2009 for a criticism which was unanswered}

 }

Lest you be concerned that Frank is selectively citing the 
 literature, here are a few more citations demonstrating problems with exact 
 methods, starting with the citation in the prop.test help 
 page:

http://www.stats.org.uk/statistical-inference/Newcombe1998.pdf

And 
 a few 
 others:

http://www.jstor.org/pss/2685469
http://www.ine.pt/revstat/pdf/rs080204.pdf
http://goliath.ecnext.com/coms2/gi_0199-4388181/Evaluation-criteria-for-discrete-confidence.html
http://www.math.ist.utl.pt/~apires/PDFs/AP_COMPSTAT02.pdf

Some 
 R 
 methods:

http://finzi.psych.upenn.edu/R/library/PropCIs/html/add4ci.html
http://finzi.psych.upenn.edu/R/library/pairwiseCI/html/pairwiseCImethodsProp.html
http://finzi.psych.upenn.edu/R/library/Epi/html/ci.pd.html
http://finzi.psych.upenn.edu/R/library/binMto/html/binMtoMethods.html
http://finzi.psych.upenn.edu/R/library/pairwiseCI/html/pairwiseCI.html

 - Original 
 Message 
 From: Frank E Harrell Jr
 ymailto=mailto:f.harr...@vanderbilt.edu; 
 href=mailto:f.harr...@vanderbilt.edu;f.harr...@vanderbilt.edu

 To: 
 href=mailto:r-help@r-project.org;r-help@r-project.org

 Sent: Thu, May 13, 2010 5:35:07 AM
 Subject: Re: [R] read table 
 for Fisher Exact

 On 05/12/2010 03:31 PM, visser 
 wrote:

 i have 2 groups i want 
 to
 compare: group A and group B
 each group 
 contains let's say 20
 patients
 i want to perform 
 a Fisher Exact test on genotype
 distribution
 so, 
 see if there is a sign diff in genotpe
 frequency/distribution 
 (#AA, #AB,
 #BB) between group A and B

 not
 for 1, but for 1000 different genes

 my question: how should i
 build my table so i 
 can do:

 test-

 read.table(table1.txt)
 fisher.test(test)

 i know a lot
 is still missing in the syntax, 
 but i do not know what. any
 help would
 be soo 
 much appreciated!!

 Note that in this case, Fisher's 
 exact test has
 a good chance of being
 less accurate 
 than an approximate Pearson chi-square
 test.

 --Frank E Harrell Jr   Professor and 
 ChairmanSchool of Medicine

  Department of 
 Biostatistics   Vanderbilt University

 __

 ymailto=mailto:R-help@r-project.org; 
 href=mailto:R-help@r-project.org;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.

David Winsemius, 
 MD
West Hartford, CT

__
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.

[R] a question about latex in Hmisc

2010-05-12 Thread Shi, Tao


Hi list,

Excuse me b/c this is probably a more TeX then R 
question.

I've been using latex function in my .Rnw file to 
generate tables, but I've always been using it without assigning the 
result to a object, i.e.

x - matrix(1:6, nrow=2, 
dimnames=list(c('a','b'),c('c','d','this that')))
latex(x)

so, I always get the error window (attached) poped out.  But since I can 
just click OK and everything seems fine except in my working directory I get a 
bunch of junk files (.log, .dvi, etc...), I've been ignoring 
it.

Now I know by doing e.g. tmp - latex(x) will suppress 
this error message, but I'm still curious on how to get rid of the error window 
when I just use latex(x).   I read the Example section of 
latex help file and I tried to include the following into my PATH:

C:\Program Files\MiKTeX 2.7\tex\latex

but that didn't work.

I'm 
using R.2.11.0, Hmisc 3.7, and MiKtex 2.7 on WinXP.

Thanks!

...Tao


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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Whiskers on the default boxplot {graphics}

2010-05-12 Thread Shi, Tao

Jason, 

All these are clearly defined in the help file for 'boxplot' under 'range'.  
Don't understand how you missed that.

...Tao




- Original Message 
 From: Jason Rupert jasonkrup...@yahoo.com
 To: Dennis Murphy djmu...@gmail.com
 Cc: R Project Help R-help@r-project.org
 Sent: Wed, May 12, 2010 3:40:12 AM
 Subject: Re: [R] Whiskers on the default boxplot {graphics}
 
 Fantastic! 

It would be great if the description could be modified to 
 include the mysterious bit about the upper and lower bound whisker 
 positions:

upper whisker = min(max(x), Q_3 + 1.5 * IQR)
lower whisker 
 = max(min(x), Q_1 - 1.5 * IQR)

Maybe that is clearly written in the 
 description of boxplot.stats {grDevices}, but evidently I missed it numerous 
 times and also did not pick up on this intent from the original description 
 of 
 boxplot {graphics}.  

Your type of descriptive answer and 
 helpfulness is much appreciated and one of the reasons I continue to endorse 
 the 
 R tool over numerous others.  

More like you and the tool may be 
 headed for domination in the market. 

Thanks 
 again!







From: 
 Dennis Murphy 
 href=mailto:djmu...@gmail.com;djmu...@gmail.com

Cc: R Project 
 Help 
 href=mailto:R-help@r-project.org;R-help@r-project.org
Sent: Wed, 
 May 12, 2010 2:50:19 AM
Subject: Re: [R] Whiskers on the default boxplot 
 {graphics}

Hi:

Let's do some math 
 :)



e:

Okay...Let me see if I've got 
 it...

I'm just trying to use the default boxplot {graphics} 
 capability in R...

So I call something like the 
 following:
 boxplot(mpg~cyl,data=mtcars, main=Car Milage Data, 
 xlab=Number of Cylinders, ylab=Miles Per Gallon) \

That 
 produces something as shown in the 
 following:
http://www.statmethods.net/graphs/images/boxplot1.jpg

When 
 that default boxplot is called, i.e. boxplot {graphics}, as shown in the line 
 of 
 code above, it is actually calling into boxplot.stats {grDevices}.  When 
 boxplot.stats {grDevices} is called it has a default value for coef of 1.5, 
 i.e. coef = 1.5.

If I understand the purpose of coef 
 correctly, it means that the ‘whiskers’ should extend out 1.5 times the 
 length 
 of the box away from the box.   Is that correct?


If by 
 'length of the box' you mean the interquartile range (IQR = Q_3 - Q_1 where Q 
 refers to quartile), then assuming that
x is the numeric vector of interest 
 for a boxplot,

upper whisker = min(max(x), Q_3 + 1.5 * IQR)
lower 
 whisker = max(min(x), Q_1 - 1.5 * IQR)

So the upper whisker is located at 
 the *smaller* of the maximum x value and Q_3 + 1.5 IQR,
whereas the lower 
 whisker is located at the *larger* of the smallest x value and Q_1 - 1.5 
 IQR.

In your terms, the whiskers should extend out a *maximum* of 1.5 
 times the length of the box
away from the box. 

Visually, this means 
 that individual points more extreme in value than Q3 + 1.5 IQR are 
 plotted
separately at the high end, and those below Q1 - 1.5 IQR are plotted 
 separately on the low
end. Depending on the source, the separately plotted 
 points are called 'outside values'. On
the other hand, if the maximum or 
 minimum values of x are closer than 1.5 IQR in distance from
its nearest 
 quartile, then that is where the whisker is positioned.

Does that make 
 sense?

HTH,
Dennis


Now I look back at the plot, and 
 I'm not sure how 1.5 times the length of the box corresponds with the whisker 
 lengths shown in the image:

 href=http://www.statmethods.net/graphs/images/boxplot1.jpg; target=_blank 
 http://www.statmethods.net/graphs/images/boxplot1.jpg

Is 
 it that the whisker length is a total of 1.5 the length of the box and 
 centered 
 about the median (2nd Quartile)?

Just trying to get a handle 
 on this, so thanks again for all the help in deciphering 
 this.








From: 
 RJ Cunningham 
 href=mailto:ro...@iinet.net.au;ro...@iinet.net.au


 target=_blank href=http://ast.net;ast.net
Cc: R Project 
 Help 
 href=mailto:R-help@r-project.org;R-help@r-project.org
Sent: 
 Tue, May 11, 2010 9:57:48 PM

Subject: Re: [R] Whiskers on the 
 default boxplot {graphics}


I think not. Isn't the 
 secret here?


Arguments:

x: a 
 numeric vector for which the boxplot will be constructed
('NA's and 
 'NaN's are allowed and omitted).

coef: this determines how 
 far the plot 'whiskers' extend out
from the box.  If 'coef' is 
 positive, the whiskers extend
to the most extreme data point which is 
 no more than
'coef' times the length of the box away from the box. 
 A
value of zero causes the whiskers to extend to the 
 data
extremes (and no outliers be 
 returned).

do.conf,do.out: logicals; if 'FALSE', the 'conf' 
 or 'out'
component respectively will be empty in the 
 result.

Details:

The two 'hinges' are 
 versions of the first and third quartile,...


On Wed 
 May 12 10:35 , Jason Rupert  sent:


HummMaybe 
 I need to look some place else than boxplot.stats {grDevices} for a 
 definition 
 of how the

Re: [R] a question about latex in Hmisc

2010-05-12 Thread Shi, Tao

Hi Erik,

Thanks for the quick reply!

My attachment was in .png which should be supported by the list   I'm 
resending it.

Yes, I knew by assigning it to an object, I can avoid this.  But, I'm curious 
to know what if I choose to do e.g. just latex(x), how can I get rid of the 
error window.  It actually worked for me once (i.e. I got Yap poped out to 
preview the table I'm generating), but I had no idea what I did differently.

...Tao




- Original Message 
 From: Erik Iverson er...@ccbr.umn.edu
 To: Shi, Tao shida...@yahoo.com
 Cc: r-help@r-project.org
 Sent: Wed, May 12, 2010 12:27:32 PM
 Subject: Re: [R] a question about latex in Hmisc
 
 

Shi, Tao wrote:
 Hi list,
 
 Excuse me b/c this is 
 probably a more TeX then R question.
 
 I've been using 
 latex function in my .Rnw file to generate tables, but I've always been 
 using 
 it without assigning the result to a object, i.e.
 
 x - 
 matrix(1:6, nrow=2, dimnames=list(c('a','b'),c('c','d','this that')))
 
 latex(x)
 
 so, I always get the error window (attached) poped 
 out.  But since I can just click OK and everything seems fine except in my 
 working directory I get a bunch of junk files (.log, .dvi, etc...), I've 
 been 
 ignoring it.

Your attachment did not come through, most likely because it 
 is not a type that is supported by the list.

 
 Now I know by 
 doing e.g. tmp - latex(x) will suppress this error message, but I'm still 
 curious on how to get rid of the error window when I just use latex(x).   I 
 read the Example section of latex help file and I tried to include the 
 following into my PATH:
 
 C:\Program Files\MiKTeX 
 2.7\tex\latex

Well I can't directly help you with your issue, since I 
 don't know what error you're receiving, the reason this is happening is that 
 when you don't assign the result of your latex call, the function 
 'print.latex' 
 is getting called, which if I understand tries to compile the LaTeX output 
 and 
 display the result in a suitable viewer.  By assigning the results of the 
 latex call in R, you stop this printing from happening.

As for what your 
 issue is, I don't know since your attachment did not come through.


  __
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.

Re: [R] a question about latex in Hmisc

2010-05-12 Thread Shi, Tao

Hi Richard,

Obviously, the list doesn't like my attachment.  Here it is:

http://i41.tinypic.com/15qz387.jpg

I set the path using Windows control panel.  And didn't work means I'm still 
getting the same error window shown above.

...Tao




- Original Message 
 From: Richard M. Heiberger r...@temple.edu
 To: Shi, Tao shida...@yahoo.com
 Cc: r-help@r-project.org
 Sent: Wed, May 12, 2010 12:34:13 PM
 Subject: Re: [R] a question about latex in Hmisc
 
 Shi, Tao wrote:
 so, I always get the error window (attached) poped out. 
 
The image was stripped by the mailer.  Please type the text of the 
 error into the body of the email.

  I tried to include the 
 following into my PATH:
 
 C:\Program Files\MiKTeX 
 2.7\tex\latex
  
Where?  In the Windows environment on the 
 Control Panel?  Through R?
What does R think the the path 
 is?

   Sys.getenv(PATH)

Does it have two backslash 
 characters everywhere you only one backslash character?
My R 
 shows
C:\\Program Files\\MiKTeX 2.7\\miktex\\bin;

 but that didn't 
 work.
  
Please define didn't work.  Include the full 
 message that you received.

Rich

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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