[R] Question about autocomplete Keyboard Shortcut in R Markdown Latex

2020-02-05 Thread Tao Z
Hi, In R, we know how to autocomplete a function name or some arguments in the function. I usually use “Tab” to achieve this. But when I was preparing my math homework using R Markdown, I want to achieve similar results: for example, I want to autocomplete $\frac{}{}$ when I only typed $\fr$

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

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
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 wrote: Tao, I do assume that the ff-files are still at som

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 wrote: On Jun 25, 2015, at 4:

[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
hs to the new one, so I don't have to re-run the own analysis. Many thanks! Tao __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-pr

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

2015-05-11 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.UT

[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/Rt

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/we

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 wrote: You should check out the animint package. https://github.com/tdhock/animint On Mon, Jul 28, 2014 at 5:48 PM, Shi, Tao wrote: hi list, > >I'm comparing the chan

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 wrote: ggvis is an excellent option to do this kind of stuff. The only limitation currently is that all sor

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

2014-07-29 Thread Shi, Tao
h 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 wrote: >> hi list, >&

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

2014-07-28 Thread Shi, Tao
t 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 pr

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 wrote: FAQ 7.20 --- Jeff Newmiller                        The    .      .  Go Live... DCN:        B

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

2014-06-03 Thread Shi, Tao
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.iso88

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

2013-09-13 Thread Shi, Tao
le 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 __ R-h

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

2013-08-15 Thread Shi, Tao
bxml2-devel is missing.  Installation libxml2-devel solved the problem.  My mistake!  Sorry about that. Tao - Original Message - From: Duncan Temple Lang To: r-help@r-project.org Cc: Sent: Thursday, August 15, 2013 10:38 AM Subject: Re: [R] XML package installation -- an old que

[R] XML package installation -- an old question

2013-08-15 Thread Shi, Tao
.  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 ins

[R] help with R CMD check --as-cran

2013-02-22 Thread Tao Wang
und no clue to solve this problem. Can someone tell me what could be wrong with my package? Thanks a lot! Tao UT Southwestern Medical Center The future of medicine, today. [[alternative HTML version deleted]] ___

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 > To: "Shi, Tao" > Cc: R. Michael Weylandt ; "r-help@r-project.org" > > Sent: Thursday, February 7, 2013 2:05 PM > Subject: Re: [R] compare objects

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

[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. Th

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 >To: r-help@r-project.org >Cc: "S

[R] what's this character?

2012-11-28 Thread Shi, Tao
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.

Re: [R] warning message

2012-10-15 Thread Shi, Tao
Thank you, Simon and Kevin! Tao - Original Message - > From: Simon Knapp > To: "Shi, Tao" > Cc: "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 ife

Re: [R] warning message

2012-10-15 Thread Shi, Tao
Never mind.  I got it.  Thanks! Tao - Original Message - > From: "Shi, Tao" > To: "r-help@r-project.org" > Cc: > Sent: Monday, October 15, 2012 4:08 PM > Subject: [R] warning message > > Hi list, > > Can somebody explain why ther

[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(x>0, log2(x), -log2(-x)) [1] -1.099975 -0.210950 -0.395700 

Re: [R] Sweave encoding option

2012-09-04 Thread Shi, Tao
encoding option Still puzzled. Tao > > From: Yihui Xie >To: "Shi, Tao" >Cc: "r-help@r-project.org" >Sent: Tuesday, September 4, 2012 7:40 PM >Subject: Re: [R] Sweave encoding option > >What happened mi

[R] Sweave encoding option

2012-09-04 Thread Shi, Tao
my knowledge) in my computer that is causing this error? I'm running R 2.15.1 on WinXP. 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/post

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 >To: "Shi, Tao" >Cc: "r-help@r-project.org" >Sent: Tuesday, April 24, 2012 12:37 PM >Subject: Re: [R] load only one

[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 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] .rda vs. .RData

2012-04-24 Thread Shi, Tao
Thank you, all! > > From: Barry Rowlingson >To: Jeff Newmiller >Cc: "Shi, Tao" ; Ista Zahn ; >"r-help@r-project.org" >Sent: Tuesday, April 24, 2012 12:36 AM >Subject: Re: [R] .rda vs. .RData > >On Tue, A

[R] .rda vs. .RData

2012-04-23 Thread Shi, Tao
Are they the same with .RData being the newer format?  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

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 > 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 yahoo.com> wr

Re: [R] barplot with both color and shading

2012-02-21 Thread Shi, Tao
tempt: barplot(1:10, angle=20, density=c(0,20), col=rep(0:1, each=5)) ...Tao - Original Message - > From: R. Michael Weylandt > To: "Shi, Tao" > Cc: "r-help@r-project.org" > Sent: Tuesday, February 21, 2012 6:49 PM > Subject: Re: [R] barplot with both

[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 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman

[R] best subset selection on random effects model

2012-02-12 Thread Tao Zhang
Hi, I know leaps() computes the best subset selection for linear model, and the bestglm() computes the best subset selection for generalized linear model. Is there any package for best subset selection on random effects model, or mixed effects model? Thank you so much. Tao

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

2011-06-24 Thread Shi, Tao
Thanks, Gabor!  That's really helpful! ...Tao - Original Message - > From: Gabor Grothendieck > To: "Shi, Tao" > Cc: "r-help@r-project.org" > Sent: Friday, June 24, 2011 5:02 AM > Subject: Re: [R] extract worksheet names from an Excel file &g

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 > 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

[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 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help

[R] a bug in heatmap.plus?

2011-06-08 Thread Shi, Tao
rect (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),

Re: [R] network package in R

2011-05-27 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: We

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 > To: "Shi, Tao" > Cc: Frank Harrell ; r-help@r-project.org > Sent: Fri, May 20, 2011 6:36:28 AM > Subject: Re: [R] changes in coxph in &quo

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

2011-05-19 Thread Shi, Tao
x27;s say it's highly significant, e.g. p<0.0001), 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 > To:

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

2011-05-16 Thread Shi, Tao
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 > To: r-help@r-project.org > Sent: Mon, May 16, 2011 11:25:20 AM &g

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

2011-05-16 Thread Shi, Tao
didn't even converge? Thanks! ...Tao - Original Message > From: Terry Therneau > To: "Shi, Tao" > 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? > > >

[R] changes in coxph in "survival" from older version?

2011-05-11 Thread Shi, Tao
et 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, o

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 > To: Marta Avalos > Cc: r-help@r-project.org > Sent: Wed, May 11, 2011

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 To: r-help ; San

Re: [R] read password-protected files

2011-03-31 Thread Shi, Tao
Thanks, Henrique! I'll try that. ...Tao - Original Message > From: Henrique Dallazuanna > To: "Shi, Tao" > Cc: Prof Brian Ripley ; r-help@r-project.org > Sent: Thu, March 31, 2011 12:00:45 PM > Subject: Re: [R] read password-protected files > &

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 > To: "Shi, Tao" > Cc: r-help@r-project.org > Sent: Thu, March 31, 2011 11:50:27 AM > Subject: Re: [R] read passwor

Re: [R] read password-protected files

2011-03-31 Thread Shi, Tao
this? Thanks! ...Tao From: Prof Brian Ripley 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

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 To: "Li, Yunfei" 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 ext

Re: [R] How to update R?

2011-03-31 Thread Shi, Tao
sion Done! ...Tao From: "Li, Yunfei" 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? Than

[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

Re: [R] confusion matrix

2011-03-08 Thread Shi, Tao
Thanks, Richard, for your speedy reply! > >From: Richard M. Heiberger >To: "Shi, Tao" >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 lev

[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

Re: [R] which functions are being debugged?

2011-02-17 Thread Shi, Tao
-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 Cc: r-help@r-project.org Sent: Wed, February 16, 2

[R] which functions are being debugged?

2011-02-16 Thread Shi, Tao
ly works on one function at a time. Thanks! ...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

Re: [R] UniCox in R

2010-12-17 Thread Shi, Tao
; 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-Novembe

[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 __ R-help@r-project.org mailing

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 > To: "Shi, Tao" > 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

2010-11-22 Thread Shi, Tao
Thank you for the advice, Frank! ...Tao - Original Message > From: Frank Harrell > 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-li

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 > To: "Shi, Tao" > 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 d

[R] question on "uniCox"

2010-11-22 Thread Shi, Tao
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.ba

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

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 > To: "Shi, Tao" > Cc: r-help@r-project.org; dieter.me...@menne-biomed.de; r_ting...@hotm

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

2010-11-19 Thread Shi, Tao
ted 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 __ R-help@r-project.org mailing list

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 To: Ben Bolker Cc: "Shi, Tao" ; "r-h...@stat.math.ethz.ch" Sent: Saturday, October 30, 2010 7:48:05 AM Subject: Re: [R] dat

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

Re: [R] date calculation

2010-10-29 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

Re: [R] date calculation

2010-10-29 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 > To:"Shi, Tao" > Cc:r-h...@stat.math.ethz.ch > Sent:Friday, October 29, 2010 5:04:23 PM > Su

[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

Re: [R] Package build and install under Windows

2010-09-15 Thread Tao
Thanks. It seems that both Rtools210.exe and Rtools211.exe support R 1.10.x, which one is better for R 2.10.1. -- View this message in context: http://r.789695.n4.nabble.com/Package-build-and-install-under-Windows-tp2539509p2540713.html Sent from the R help mailing list archive at Nabble.com.

[R] Package build and install under Windows

2010-09-14 Thread Tao
Any other method besides using RTOOLS? I am using R 2.10.1, which version of Rtools should I use? It seems that there are two versions on the website. The commands like R CMD build should be used in the CMD window, right? Thanks. -- View this message in context: http://r.789695.n4.nabble.com/Pac

[R] R cannot be started

2010-09-07 Thread Tao
I used Rtools for installing a package under Windows XP. I used commands like R CMD INSTALL (build, check) in the CMD window. It worked well until I found that my revised package can be updated with R CMD INSTALL. After I restarted my computer, R cannot be started any more. I double click the R ic

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

2010-09-02 Thread Shi, Tao
Hi Dejian, Thanks for the reply! I finally found the problem. It is actually in the "panel.cor" function. Adding "..." in the function and "text" call fixed everything. Best, ...Tao - Original Message > From: Dejian Zhao > To: r-help@r-

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 To: r-help@r-project.org Sent: Tue, August 31, 2010 6:10:16 PM Subject: Re: [R] "pairs" with same xlim and ylim sca

[R] "pairs" with same xlim and ylim scale

2010-08-31 Thread Shi, Tao
27;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 <-

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 - Ori

Re: [R] R eat my data

2010-05-25 Thread Shi, Tao
27;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 > To: David Winsemius > Cc: r-help@r-project.org > S

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 > 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

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 >To: "Shi, Tao" ; r-help@r-project.org >Sent: Thu, May 20, 2010 11:45:25 PM >Sub

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 --

Re: [R] colored venn diagram

2010-05-20 Thread Shi, Tao
Thank you for the suggestions, Peter and David! - Original Message > From: Peter Ehlers > To: David Winsemius > Cc: "Shi, Tao" ; r-help@r-project.org > Sent: Wed, May 19, 2010 8:45:24 PM > Subject: Re: [R] colored venn diagram > > Tao, You might al

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)

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

2010-05-19 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 > To: r-help@r-project

[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 __ R-help@r-project.org mailing

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 > To: r-help@r-project.org > Sent: Wed, May 19, 2010 7:56:44 AM > Subje

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 > To: r-help@r-project.org; TaoShi > Sent: Tue, May 18, 2010 5:22:47 PM > Subject:

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 > To: r-help@r-project.org > Sent: Tue, M

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 >To: "Shi, Tao" >Cc: r-help@r-project.org >Sent: Fri, May 14, 2010 12:35:20 PM >Subject

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 >To: "Shi, Tao" >Cc: Gurmeet ; Jim Lemon ; >r-help@r-project.org >Sent: Fri, May 14, 2010 10:51:26 AM >Subject: Re: [R] Multiple plots; single x(y) labels > > >Th

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: Dim

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 > To: Jim Lemon > Cc: r-help@r-project.org > Sent: Fri, May 14,

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

2010-05-14 Thread Shi, Tao
with one single split using X1, I guess it's still a reasonable thing to do, right? 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/po

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

Re: [R] read table for Fisher Exact

2010-05-13 Thread Shi, Tao
Thanks, David! - Original Message > From: David Winsemius > To: Frank E Harrell Jr > Cc: "Shi, Tao" ; 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 H

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 > To: r-help@r-project.org > Sent: Thu, May 13, 2010 5:35:07 AM > Subject: Re: [R] re

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

2010-05-13 Thread Shi, Tao
e same xlim and ylim. Like David said, you're re-inventing the wheels . ...Tao - Original Message > From: Xin Ge > To: David Winsemius > Cc: r-help@r-project.org > Sent: Thu, May 13, 2010 10:24:56 AM > Subject: Re: [R] Multiple plots; single x(y) labels > >

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 > To: "Shi, Tao" ; 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 scrip

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