[R] group comparison for ordinal variable

st in package "coin" can do this job or not? Thanks, Weiwei -- Weiwei Shi, Ph.D Research Scientist "Did you always know?" "No, I did not. But I believed..." ---Matrix III -- Weiwei Shi, Ph.D Research Scientist "Did you always know?" &qu

[R] group comparison for ordinal variable

this job or not; or maybe pwilcox? 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]] __ R-help@r-project.or

[R] heatmap for plotting categorical matrix

atmap.2(a4[1:40,], Rowv=NA, Colv=NA, col=c("grey", "blue", "purple", "red"), trace="none") Thanks, Weiwei -- Weiwei Shi, Ph.D Research Scientist "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Re: [R] network package in R

ough the latter has a link while B and C do not. I hope I explained my question clear this time. Weiwei On Sat, May 28, 2011 at 11:51 AM, Weiwei Shi wrote: > Thank you, Steve. > > Initially I tried to choose b/w cytoscape and pajek, among other bunch of > software. I did n

Re: [R] network package in R

> Hi, > > On Fri, May 27, 2011 at 5:32 PM, Weiwei Shi wrote: > > 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

Re: [R] network package in R

tion to find if network package can do that or not. Or, there is another package which can do the similar job. So I did _any_ search. Thank you for tabulating the searched results, though useless for me. Weiwei On Fri, May 27, 2011 at 4:44 PM, David Winsemius wrote: > > On May 27, 2011, a

[R] network package in R

-- Weiwei Shi, Ph.D Research Scientist "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r

[R] variable selection

Hi there, Can anyone suggest some packages in R doing variable selections in predictive modeling besides randomForest? Faster, better. Any also in clustering analysis? Thanks, Weiwei -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not.

Re: [R] how to save plots automatically

ld have 5 graphs in each > single pdf. > > Regards, > Yihui > -- > Yihui Xie > Phone: 515-294-6609 Web: http://yihui.name > Department of Statistics, Iowa State University > 3211 Snedecor Hall, Ames, IA > > > > On Tue, Sep 22, 2009 at 10:23 PM, David Winsemius

[R] how to save plots automatically

s pdf? Thanks, W. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]] __ R-help@r-project.org mailing list htt

[R] get NA from outlier{randomForest}

,]) t1 = outlier(t0) > summary(t1) Min. 1st Qu.Median Mean 3rd Qu. Max. NA's -1.09600 0.09848 0.90990 1.34400 2.61000 4.67200 971.0 Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I

[R] graph data mining

Hi I am wondering if R or some others provide free-to-use graph mining tools, like mining some frequent structure in a x-y plot data? thanks, Weiwei -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed...

[R] margins defined in randomForest and supclust

ch is very inconvenient, any clever way? Thanks, Weiwei -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]] __ R-help@r-

[R] how to keep row name if there is only one row selected from a data frame

by myself after I used A[1,] manually. > A[1,] [1] 1 6 Thanks, W. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]] _

Re: [R] cohen's kappa

one more question, "The third value (kappa (2*PA-1)) is adjusted for prevalence using the method proposed by Byrt, Bishop and Carlin (1993)" --- from ?cohen.kappa What does the "prevalence" refer to? On Sun, Sep 7, 2008 at 10:43 PM, Weiwei Shi <[EMAIL PROTECTED]> wrot

[R] cohen's kappa

looking at some output, for example, cohen.kappa{concord} ? One more, could anyone explain in brief, what's the difference between kappa(Cohen) and kappa(Siegel)? Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did no

Re: [R] [BioC] similarity between two gene lists with varied length

cine > Washington University School of Medicine > > President-Elect, Classification Society > > > From: [EMAIL PROTECTED] [ > [EMAIL PROTECTED] On Behalf Of Weiwei Shi [ > [EMAIL PROTECTED] > Sent: Saturday, August 23, 2008 7:55 PM >

[R] similarity between two gene lists with varied length

Dear listers, a little off-topic: I am looking for and compare algorithms which can calculate "distance" or "similarity" between two gene lists with different lengths. Any paper, any implementation in R and any suggestion is welcome! Thanks, -- Weiwei Shi, Ph.D Research S

[R] svm: is this right?

17 0 My question is, is there anything wrong with the following call: m2 <- best.svm(class~., data=x1, gamma=2^(-3:3), cost=2^(0:5)) # x1 is training data pred1 <- predict(m2, x3) # x3 is test data Thanks! -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?&

Re: [R] Date formats

shound, and > > __ > 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-con

Re: [R] editor under MAC system

ml > and provide commented, minimal, self-contained, reproducible code. > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]]

Re: [R] logistic regression using "glm",which "y" is set to be "1"

commented, minimal, self-contained, reproducible code. > > > > > > > - > Best regards, > Bin Yue > > * > student for a Master program in South Botanical Garden , CAS > > -- > View this message in context: > http://www.nabble.com/logi

Re: [R] anyway to force rpart() to include a specific predictor

ted, minimal, self-contained, reproducible code. > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III __ R-help@r-project.org mailing list https://stat.ethz.ch

Re: [R] Reg : using two different matrix : how to do t.test

guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

[R] biplot

Hi, I am wondering how to draw biplot with the same scales on both plots? For example, if the two plots have much different scales, generally the two x-y's are scaled so that the two plots are sitting in the center automatically. How to disable this? Thanks -- Weiwei Shi, Ph.D Res

Re: [R] diagonal LDA

s prediction without details of > the model and the posterior probabilities like the > lda() function in MASS. Is there an equivalent to the > lda() for diagonal linYOUear discriminant analysis? > > Thanks > > > --- Weiwei Shi <[EMAIL PROTECTED]> wrote: > > &

Re: [R] diagonal LDA

ilman/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. > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?"

Re: [R] how to split data.frame by row?

t; dim(df) <- c(10,6) > dim(df) <- c(5,12) > > On 29/10/2007, Weiwei Shi <[EMAIL PROTECTED]> wrote: > > > > hi, > > > > if I have 20 x 3 data.frame, how to split it into > > 10 x 6 (moving the lower part of 10x3 to column) > > > > or &g

[R] how to split data.frame by row?

hi, if I have 20 x 3 data.frame, how to split it into 10 x 6 (moving the lower part of 10x3 to column) or 5 x 12 thanks -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed...

Re: [R] retrieve version information for a package?

ttps://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. > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "N

Re: [R] alignment algorithm or pattern frequency calculation

frequent itemset, yeah.. I did not use that for a while thanks. On 10/19/07, Gad Abraham <[EMAIL PROTECTED]> wrote: > Weiwei Shi wrote: > > Hi, > > > > I am looking for an algorithm (better if it is implemented in R) which > > can do the following: > >

Re: [R] alignment algorithm or pattern frequency calculation

freq. Best, Weiwei On 10/18/07, Nordlund, Dan (DSHS/RDA) <[EMAIL PROTECTED]> wrote: > > > -Original Message- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of Weiwei Shi > > Sent: Thursday, October 18, 2007 3:32 PM > > T

Re: [R] alignment algorithm or pattern frequency calculation

4]] [1] "a" "b" "c" "d" "e" On 10/18/07, Nordlund, Dan (DSHS/RDA) <[EMAIL PROTECTED]> wrote: > > -Original Message- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of Weiwei Shi > > Sent: Thursday, Octo

Re: [R] alignment algorithm or pattern frequency calculation

the naive way is to exhausive search, but too bad for large and real situation. On 10/18/07, Weiwei Shi <[EMAIL PROTECTED]> wrote: > for example, > > a,b: 3 which means a and b appear together 3 times in my input list. > > On 10/18/07, jim holtman <[EMAIL PROTECTED]

Re: [R] alignment algorithm or pattern frequency calculation

for example, a,b: 3 which means a and b appear together 3 times in my input list. On 10/18/07, jim holtman <[EMAIL PROTECTED]> wrote: > It would be helpful if you explained what the numbers mean. > > On 10/18/07, Weiwei Shi <[EMAIL PROTECTED]> wrote: > > Hi, > >

[R] alignment algorithm or pattern frequency calculation

Hi, I am looking for an algorithm (better if it is implemented in R) which can do the following: from the following list: a,b,c,d a,b,c b,c a,b,c,d,e to calculate a,b,c,d: 2 a,b,c: 3 a,b: 3 a,c: 3 b,c: 4 b,c,d:2 here, the order is not important. Thanks. -- Weiwei Shi, Ph.D Research

[R] class weight

Hi, I am wondering which classification algorithms in R have implemented class weight for imbalanced data prediction? Thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed...