Re: [R] Help request: highlighting R code on WordPress.com blogs

Hello D, Thanks for sharing your technique, nice work :) I hope the solution the people here are helping with will make it both cheaper and simpler for people with less CSS expreince. p.s: thank you for the kinds words regarding R-bloggers.com Best, Tal Contact

[R] Help request: highlighting R code on WordPress.com blogs

Hello dear R help members (and also Yihui and Romain), There are currently 28 R bloggers (out of the 117 R-bloggershttp://www.r-bloggers.com/I know of) that are using wordpress.com for publishing their R code (and I suspect this number will increase with time). WordPress.com doesn't support R

Re: [R] Help request: highlighting R code on WordPress.com blogs

. 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 Thu, Sep 9, 2010 at 3:02 AM, Tal Galili tal.gal...@gmail.com wrote: Hello dear R help members (and also Yihui

[R] Why is vector assignment in R recreates the entire vector ?

Hello all, A friend recently brought to my attention that vector assignment actually recreates the entire vector on which the assignment is performed. So for example, the code: x[10]- NA # The original call (short version) Is really doing this: x- replace(x, list=10, values=NA) # The original

[R] Where can the benchmark2 function be downloaded from?

Hello all, I am looking for the function benchmark2 ( a nice function for comparing the performance of two or more functions). I found online it exists in the butler package http://crantastic.org/packages/butler But for some reason, that package was removed from CRAN:

Re: [R] Where can the benchmark2 function be downloaded from?

(English) -- On Wed, Sep 1, 2010 at 6:37 PM, David Winsemius dwinsem...@comcast.netwrote: On Sep 1, 2010, at 11:13 AM, Tal Galili wrote: Hello all, I am looking for the function benchmark2

Re: [R] Why is vector assignment in R recreates the entire vector ?

: On 01/09/2010 11:09 AM, Tal Galili wrote: Hello all, A friend recently brought to my attention that vector assignment actually recreates the entire vector on which the assignment is performed. So for example, the code: x[10]- NA # The original call (short version) Is really doing

[R] Saving plot to tiff, with high resolution for publication ?

Hello all. A Journal we are sending an article to is asking for the following: To ensure the best reproduction quality of your figures we would appreciate high resolution files. All figures should preferably be in TIFF or EPS format... and should have the following resolution: Graph: 800 - 1200

Re: [R] Help making box plots in R when the x axis is a quantitative variable

Hi FishLover, I believe this will answer your question: # getting some dummy data seed(10) y - rnorm(100) x - sample(c(1,2,5.5), 100 , T) boxplot(y~x) # won't work boxplot(y~x, at = c(1,2,5.5), xlim = c(0,6)) # will work Cheers, Tal Contact

Re: [R] Delete rpart/mvpart cross-validation output

Hi Marie and Gavin, I do remember there is some command doing silent, so to suppress output (as if directing it to sink, but not really directing it anywhere). The problem is I don't remember the command at the moment - but some searching might yield you results. Cheers, Tal

Re: [R] Help with ANOVA

Hi Sneeketeeke, Did you happen to have a look at the example on ?aov and ?TukeyHSD Also, you might need to move your data from wide to long. For which you might wish to look at ?reshape (or better yet the ?melt ?cast commands from the reshape package) Tal Contact

Re: [R] Plotting K-means clustering results on an MDS

Hi trzeszutek, Another approach you might want to look at is the clustergram: http://www.r-statistics.com/2010/06/clustergram-visualization-and-diagnostics-for-cluster-analysis-r-code/ http://www.r-statistics.com/2010/06/clustergram-visualization-and-diagnostics-for-cluster-analysis-r-code/

Re: [R] Help with ANOVA

) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Thu, Aug 19, 2010 at 6:02 AM, Stephen Liu sati...@yahoo.com wrote: - Original Message From: Tal Galili tal.gal...@gmail.com

Re: [R] Displaying Results in Two Columns

You could find several good examples on the first several results here: http://www.google.com/search?sourceid=chromeie=UTF-8q=plot.ci+R Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me:

Re: [R] p.adjust( , fdr)

Hi Qing. I believe what you are referring to is: p.adjust(..., BH) The fdr option uses the method of Benjamini, Hochberg, and Yekutieli. (Not the original Benjamini, Hochberg article) It might be the method described here:

Re: [R] Is R GPL or LGPL (or can I write a commercial front end to R)?

From what I've seen on other OSS project, GPL can be a bit viral, making it (purposefully) difficult for someone to close the source code for free reuse. My tip for you would be to try and see what REvolution computing has been doing with their product (which is a repackaging of R with more code

Re: [R] data.frame: return all rows where at least one...

One solution - let's say our data.frame is xx Then: xx - matrix(rnorm(9), 3,3) apply(xx 0, 1, any) Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) |

Re: [R] applying strsplit to a whole column

Have a look at the stringr package It simplifies such things... Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com

Re: [R] applying strsplit to a whole column

In such cases (which I don't think must happen), consider using ?lapply and also ?unlist Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il

Re: [R] Output (graphics and table/text)

Fun question. Here is one solution that has come to mind: # graphics output test a - c(1,3,2,1,4) b - c(2,1,1,1,2) c - c(4,7,2,4,5) d - rnorm(500) e - rnorm(600) op - par(mfrow=c(2,2)) pie(a) pie(b) pie(c) txt - capture.output(ks.test(d,e)) txt - txt[txt != ] txt - paste(txt, collapse = \n )

Re: [R] Kruskal Walllis test

I would suggest to you the following: 1) Run the same thing, but with a loop instead of apply 2) add the to loop a printing that shows you on what cycle of the loop the function breaks 3) see if that vector has any Inf or NA values (although in general I think you are using a numeric instead of a

Re: [R] How to extract ICC value from irr package?

And in general, you can use: str(NameOfObject) To understand it's *str*ucture, and where the value resides. Cheers. Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) |

Re: [R] R: classification tree model!

People who speak only English and Hebrew (like myself), can't help you. Consider reposting in English. Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) |

Re: [R] Is there paid support for R?

As others have mentioned, A simple place to start looking at would be to go through the list on the wiki page: http://en.wikipedia.org/wiki/R_(programming_language)#Commercialized_versions_of_R And contacting the companies one by one. The other alternative I would check is to contact the

Re: [R] multiple graphics windows open

...@gmail.comwrote: This will work. I was hoping for 3 distinct graphs so the user would be able to click on them. Thanks, Erin On Fri, Jul 30, 2010 at 11:07 PM, Tal Galili tal.gal...@gmail.com wrote: Hello Erin. I think I understand. Those the following code solve your issue

Re: [R] hi! l have a question please help me

Is this a question from your homework? Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English)

Re: [R] logos and goodies

Interesting topic and question. I hope someone who knows will answer this. Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |

Re: [R] multiple graphics windows open

Hi Erin, Could you please add a simple self contained code for us to try and help you with? (giving us code with doesn't help) Best, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me:

Re: [R] hi! l have a question please help me

Then please read this: http://www.r-project.org/posting-guide.html *Basic statistics and classroom homework:* R-help is not intended for these. If you want learning materials for R you can check out: http://stats.stackexchange.com/questions/138/resources-for-learning-r And:

Re: [R] Reading .eps file created in Illustrator

Hi Patrick, I don't have an answer for you. But thought it might be worth to have a look at this: http://www.r-bloggers.com/getting-data-from-an-image-introductory-post/ Also, there was someone who presented a really simple GUI system in useR2010. Where his code gave a GUI based on R base

Re: [R] multiple graphics windows open

with a line segment between the two points. The second is the graph of the subset. The third is the EWMA of the subset data. Thanks, Erin On Fri, Jul 30, 2010 at 10:13 AM, Tal Galili tal.gal...@gmail.com wrote: Hi Erin, Could you please add a simple self contained code for us to try

Re: [R] Statistical mailing list

This is the new and exiting kid on the block: http://stats.stackexchange.com/ There is also: http://metaoptimize.com/qa For more machine learning type questions. Best, Tal http://stats.stackexchange.com/ Contact Details:---

Re: [R] New Open Source Community

You mean along with: http://stats.stackexchange.com/ and http://stats.stackexchange.com/http://metaoptimize.com/qa/ We have passed the online-over-proliferation stage for out topic of interest... :) Tal Contact Details:---

Re: [R] as.dendrogram for DICE coefficient.

Hello Shubha, To my understanding, Once you get a dist matrix, you would wish to put it into a clustering algorithm, who's output you would then put into a plot (which will produce a dendrogram). You might want to have a look at the steps given here:

Re: [R] UseR! 2010 - my impressions

Dear Ravi - I echo everything you wrote, useR2010 was an amazing experience (for me, and for many others with whom I have spoken about it). Many thanks should go to the wonderful people who put their efforts into making this conference a reality (and Kate is certainly one of them). Thank you for

Re: [R] Help with Reshaping from Wide to Long

Hi John, 1) Read the help for the reshape package. What you want is to use the melt function. 2) There are various ways of doing Repeated measures Anova in R, you might want to have a look at this: http://www.r-statistics.com/2010/04/repeated-measures-anova-with-r-tutorials/ (I especially like

Re: [R] Help with Reshaping from Wide to Long

Hi John, Try posting a sample of your data in reply to this e-mail by using: dput(head(accuracy)) And me (or someone else) will be sure to fix your command. Regarding the ANOVA, read more :) Tal Contact Details:--- Contact

Re: [R] package for rank ordered logit

Did you try: library(MASS) ?polr ? Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English)

Re: [R] Summing over intervals

You might find it useful to look at rollmean from the zoo package. Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |

Re: [R] boxplot on all the columns

Actually, boxplot (bhtest1) Should do what you want... Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com

[R] Is there a Mixed effect model for regression/classification trees?

Hello all, This is more a statistical question then an R question, but I am sure it will have an R interpretation to it. If I wish to predict an outcome based on some potential features, I could (in some cases) use either regression or regression-tree. However, if my observations are divided to

Re: [R] Non-parametric regression

From reviewing the first google page result for Non-parametric regression R, I hope this link will prove useful: http://socserv.mcmaster.ca/jfox/Courses/Oxford-2005/R-nonparametric-regression.html Contact Details:--- Contact

Re: [R] Plotting text in existing plot?

see ?text Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English)

Re: [R] Plotting text in existing plot?

Possible fortune. :) Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English)

Re: [R] How can i draw a graph with high and low data points

Hi Nathaniel , Could you give us a simple example of your data using the ?dput Function? Basically you might want to draw the axis yourself, and connect the lines is possible through using points(..., type = l) But I'd rather try and answer this with simple example data to be sure I understand

Re: [R] Calling Gnuplot from R

Dear Greg, I keep on being amazed at the abundance of functions you have packed into the TeachingDemos package - thank you! Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com

Re: [R] How can i draw a graph with high and low data points

Hi Nathaniel, Here are a few links for (short) articles that can help you get comfortable in doing such tasks: http://www.statmethods.net/graphs/line.html http://www.statmethods.net/graphs/scatterplot.html Here is a tiny example: x - 1:100 y - rnorm(100) plot(y~x) lines(loess(y~x)$fitted ~ x)

Re: [R] Brewer.pal error

Hi there, For me the package is working. Try to install.packages(RColorBrewer) It. And then library(RColorBrewer) Then something like: brewer.pal(7,Greens) Write in the mailing list what errors you got (if any) at any of these commands. Tal Contact

Re: [R] Histogram Principal component analysis in R

Hello Dhiman , I have never tried doing it on such data, so I am not sure how this methodology applies or what covets it may hold. However, R wise, it sounds to me like simply reusing the code here: http://www.statmethods.net/advstats/factor.html Would do the trick. p.s: you wrote It would be

Re: [R] Visualization of coefficients

) points(cf, 1:k, pch = pch, col = col) abline(v = 0, lty = lty[2], lwd = lwd[2]) axis(1) axis(2, at = 1:k, labels = labels, las = las) box() } On Fri, 2 Jul 2010, Tal Galili wrote: Specifically this link: http://tables2graphs.com/doku.php?id=04_regression_coefficients Great

Re: [R] Visualization of coefficients

) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Wed, Jul 7, 2010 at 12:10 PM, Achim Zeileis achim.zeil...@uibk.ac.atwrote: On Wed, 7 Jul 2010, Tal Galili wrote: Hello David, Thanks

Re: [R] Visualization of coefficients

: On Wed, 7 Jul 2010, Tal Galili wrote: Hi Achim and Allan,I updated the post with Allan's example (thanks Allan). Thanks! Achim, you wrote: Finally, the Poisson model in comparison with the binomial models does not make much sense, I guess. I agree. I wanted something to showcase

Re: [R] Visualization of coefficients

-statistics.com (English) -- On Wed, Jul 7, 2010 at 5:19 PM, Michael Friendly frien...@yorku.ca wrote: Tal Galili wrote: Hello David, Thanks to your posting I started looking at the function in the arm

Re: [R] LatticeExtra Parallel

Hi Ben, You can also experiment with matlines Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English)

[R] Why doesn't my change of Renviron.site work on windows 7 ?

Hi all, I added the following line on the Renviron.site file: R_LIBS=C:\Program Files (x86)\R\library And when I start R and run: .libPaths() I don't see this path. On windows XP it worked for me. I am now using windoes 7 (64 bit) with R 32. Is there a reason this shouldn't work? Thanks,

Re: [R] Why doesn't my change of Renviron.site work on windows 7 ?

in Windows to certain directories makes my life much easier. HTH, Josh On Fri, Jul 2, 2010 at 12:48 AM, Tal Galili tal.gal...@gmail.com wrote: Hi all, I added the following line on the Renviron.site file: R_LIBS=C:\Program Files (x86)\R\library And when I start R and run: .libPaths

[R] Combining several plots besides a dendrogram?

Hello all, I would like to recreate the plot shown here (from a useR 2009 presentation): http://www.agrocampus-ouest.fr/math/useR-2009/abstracts/pdf/Hocking.pdf I downloaded the code for that image, and discovered that it relies on external web services, and also having PERL installed on the

Re: [R] Combining several plots besides a dendrogram?

. And these regions can be customized depending on the size of the objects you want to plot. Regards, Carlos. On Fri, Jul 2, 2010 at 1:34 PM, Tal Galili tal.gal...@gmail.com wrote: Hello all, I would like to recreate the plot shown here (from a useR 2009 presentation): http://www.agrocampus-ouest.fr/math

Re: [R] Why doesn't my change of Renviron.site work on windows 7 ?

/depts/ncb/home.shtml -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Tal Galili Sent: Friday, July 02, 2010 12:49 AM To: r-help@r-project.org Subject: [R] Why doesn't my change of Renviron.site work on windows 7 ? Hi all

Re: [R] Visualization of coefficients

Specifically this link: http://tables2graphs.com/doku.php?id=04_regression_coefficients Great reference Bernd, thank you. Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com

Re: [R] Combining several plots besides a dendrogram?

that transcend panels in the figure. Have a look at some of the code in this package, it is on R-Forge: http://aqp.r-forge.r-project.org/ Cheers, Dylan On Fri, Jul 2, 2010 at 4:34 AM, Tal Galili tal.gal...@gmail.com wrote: Hello all, I would like to recreate the plot shown here (from a useR 2009

Re: [R] Visualization of coefficients

BTW, another visualization that might be useful in your case is Nomogramhttp://en.wikipedia.org/wiki/Nomogram : http://lib.stat.cmu.edu/S/Harrell/help/Design/html/nomogram.html (I remember first encountering it on a lecture by Frank Harrell lecture and being very happy for the discovery) Tal

Re: [R] ROC curve in R

Regarding search, There is also the sos packege. And yesterday someone wrote a nice R code to enable searching inside the description of all packages: http://www.r-bloggers.com/cran-search/ Cheers, Tal Contact Details:---

Re: [R] plot focus

Good question pdb, I would suggest you to use: par(bg = white) In the beginning of the code, But it doesn't solve the general problem of how to get the lines to be properly aligned. I am curious for the answer from betteR people. Best, Tal Contact

Re: [R] Export Results

Do you have an open word file ? Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English)

Re: [R] Export Results

See ?pdf ?png ?sink There is also R2wd (about which I wrote here: http://www.r-statistics.com/2010/05/exporting-r-output-to-ms-word-with-r2wd-an-example-session/ ) And there are also the brew, and Sweave packages (as Henrique mentioned). Best, Tal Contact

Re: [R] best way to plot a evolution in time

Hi Nana, The question is not fully clear to me. Are you looking to plot the (let's call it) family tree of the genes ? (if so, then using plot(hclust(gene.dist)) Might be a direction for you) Tal Contact Details:--- Contact

Re: [R] Handouts / Reports or just simply printing text to PDF?

Hi Ralf, ?pdf and ?png are good places to start. There is also R2wd: http://cran.r-project.org/web/packages/R2wd/index.html For exporting R output to word. I wrote a short tutorial session for it here:

Re: [R] boxplot width

Does: boxplot(data$site~data$chr, varwidth=TRUE) (notice I removed the ' ' from the 'TRUE') Work ? Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) |

Re: [R] Euclidean Distance Matrix Analysis (EDMA) in R?

Isn't this what ?dist Does ? Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English)

Re: [R] Clustering

Hi Ralph, In case of hclust, the dendrogram does show the steps (they are the heights presented in the graph). You can present them also in a matrix using cutree, for example: dat - (USArrests) n - (dim(dat)[1]) hc - hclust(dist(USArrests)) cutree(hc, k=1:n) You might then visualize the

Re: [R] About normality tests (2) ...

look at: ?qqnorm and ?qqline Examples are in their help. Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com

Re: [R] R vs SAS and Revolution R

Regarding R and REvolution, there was a post published recently comparing the two: http://www.r-bloggers.com/comparing-standard-r-with-revoutions-for-performance/ Regarding the rest, I don't know... Tal Contact Details:---

Re: [R] Drawing paths through a grid

Hi Rex, It sounds like something that can be done with ?lines If you would supply with a simple self contained data that represents what you are trying to plot, then we might be able to better help you. If you have the data in R, use dput to be able to copy paste it into the email. Cheers, Tal

Re: [R] Is there a non-parametric repeated-measures Anova in R ?

. Regards, Maciej -Ursprüngliche Nachricht- Message: 117 Date: Thu, 17 Jun 2010 20:12:54 -0400 From: David Winsemius dwinsem...@comcast.net To: Tal Galili tal.gal...@gmail.com Cc: r-help@r-project.org Subject: Re: [R] Is there a non-parametric repeated-measures Anova in R

[R] Invitation to a new QA statistical-analysis website

There is a new initiative to open a community based QA website which is based on the StackOverFlow engine - to answer data-analysis (and obviously R) related Questions. After good several months of using StackOverFlow (see the R tagged questions here http://stackoverflow.com/questions/tagged/R),

Re: [R] Graphics question: How to create a changing smudge factor for overlapping lines?

%s, x)), each = 100)) dat$y = dat$y + rnorm(length(dat$y), 3, 3) # Without alpha ggplot(aes(x = x, y = y, group = grp), data = dat) + geom_line() # With alpha ggplot(aes(x = x, y = y, group = grp), data = dat) + geom_line(alpha = 0.04, size = 2) cheers, Paul On 06/15/2010 12:57 PM, Tal

[R] Is there a non-parametric repeated-measures Anova in R ?

Hello Prof. Harrell and dear R-help mailing list, I wish to perform a non-parametric repeated measures anova. If what I read online is true, this could be achieved using a mixed Ordinal Regression model (a.k.a: Proportional Odds Model). I found two packages that seems relevant, but couldn't find

Re: [R] Is there a non-parametric repeated-measures Anova in R ?

. The standard non-parametric test is the Friedman test. ?friedman.test Jeremy On 16 June 2010 10:22, Tal Galili tal.gal...@gmail.com wrote: Hello Prof. Harrell and dear R-help mailing list, I wish to perform a non-parametric repeated measures anova. If what I read online is true

Re: [R] Parallel computing on Windows (foreach) (Sergey Goriatchev)

Hi all, Just for the record, this is the link to the blog post: http://www.r-statistics.com/2010/04/parallel-multicore-processing-with-r-on-windows/ You can run work in parallel in multiple processors. Although it is only worthwhile when each task takes a long time to run (I give an example to

Re: [R] dendrogram

Hi Elyakhlifi, You can try this: hc - hclust(dist(USArrests), ave) plot(hc, cex = .5) Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il

[R] Graphics question: How to create a changing smudge factor for overlapping lines?

Hello all, I am trying to create a Clustergram in R. (More about it here: http://www.schonlau.net/clustergram.html) And to produce a picture similar to what is seen here: http://www.schonlau.net/images/clustergramexample.gif I was able (more or less) to write the R code for creating the image,

Re: [R] Graphics question: How to create a changing smudge factor for overlapping lines?

Hi Hadley, Thanks for replying. The glitches are the cases where you would have a bundle of lines belonging to a specific cluster, but had spaces between them (because the place of one of the lines was saved for another line that in the meantime moved to another cluster). I just came up with a

Re: [R] Graphics question: How to create a changing smudge factor for overlapping lines?

Hi Hadley, I wrapped the code into a function. I made it so all the lines would always start from the cluster mean. And I tried to give more meaning to the colors by giving the color according the the order of the first principal component of that observation. What do you think ? Tal #

Re: [R] Graphics question: How to create a changing smudge factor for overlapping lines?

: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Tue, Jun 15, 2010 at 5:04 PM, Tal Galili tal.gal

Re: [R] Finding an order for an hclust (dendrogram) object without intersections

-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Sun, Jun 13, 2010 at 8:42 PM, Tal Galili tal.gal...@gmail.com wrote: o.k, I found

[R] How to write a customized hclust algorithm in R?

Hello dear R-help mailing list members, I wish to create an hclust object which will be based on a customized hierarchical clustering algorithm, programmed in R. After looking into the hclust function, I noticed that the algorithms themselves are implemented in Fortran. In order for me to

[R] Finding an order for an hclust (dendrogram) object without intersections

Hello all, I manually created an hclust object. Now I am looking to reorder the leafs so they won't intersect with each other, and would be happy for advises on how to do that. Here is an example code: #- a - list() # initialize empty object # define

Re: [R] Finding an order for an hclust (dendrogram) object without intersections

) -- On Sun, Jun 13, 2010 at 7:08 PM, Charles C. Berry cbe...@tajo.ucsd.eduwrote: On Sun, 13 Jun 2010, Tal Galili wrote: Hello all, I manually created an hclust object. Now I am looking to reorder the leafs so they won't intersect with each other, and would be happy

Re: [R] Finding an order for an hclust (dendrogram) object without intersections

) -- On Sun, Jun 13, 2010 at 7:39 PM, Tal Galili tal.gal...@gmail.com wrote: Thanks Charles. In the meantime, I found out the following code does the trick. But I am wondering if: 1) I might have made a mistake in it somewhere 2) If there are other (smarter) ways of going about this. Here

Re: [R] Compiling R with multi-threaded BLAS math libraries - why not actually ?

commercially or academically. Maybe a short tutorial using free software, such as ATLAS would be suitable content for an r-bloggers post :) ? Matt Shotwell Graduate Student Div. Biostatistics and Epidemiology Medical University of South Carolina On Fri, 2010-06-11 at 19:21 -0400, Tal Galili wrote

[R] Displaying homogeneous groups in aov post-hoc results ?

Hello dear R-help mailing list, A friend of mine teaches a regression and experimental design course and asked me the following question. She is trying to find a way to display the homogeneous groups (after performing tukey test on an aov object). here's an example for what she means by

Re: [R] Compiling R with multi-threaded BLAS math libraries - why not actually ?

, Tal Galili tal.gal...@gmail.com wrote: Hello Gabor, Matt, Dirk. Thank you all for clarifying the situation. So if I understand correctly then: 1) Changing the BLAST would require specific BLAST per computer configuration (OS/chipset). It's BLAS (Basic Linear Algebra Subroutines

Re: [R] Can one get a list of recommended packages?

Hello David, I am not sure I understood your question. Are you asking what are the packages that the R release comes with? Or are you asking what recommended packages one should have when installing R? (There is a good list to start with

Re: [R] Displaying homogeneous groups in aov post-hoc results ?

Thank you very much Hadley, exactly what I was looking for. Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com

[R] Compiling R with multi-threaded BLAS math libraries - why not actually ?

Hello all, I came acrosshttp://www.r-bloggers.com/performance-benefits-of-linking-r-to-multithreaded-math-libraries/ David Smith's new post Performance benefits of linking R to multithreaded math librarieshttp://blog.revolutionanalytics.com/2010/06/performance-benefits-of-multithreaded-r.html

[R] non-parametric repeated measures anova using Proportional Odds Model - examples?!

Hello dear R-help mailing list, I wish to perform a non-parametric repeated measures anova. If what I read online is true, this could be achieved using a mixed Ordinal Regression model (a.k.a: Proportional Odds Model). I found two packages that seems relevant, but couldn't find any vignette on

Re: [R] Using R with Web services

I refer to several resources on the subject here: http://www.r-statistics.com/category/r-and-the-web/ But the first I would suggest you to look at is this: http://www.r-statistics.com/2010/02/web-development-with-r-an-hd-video-tutorial-of-jeroen-ooms-talk/ It won't answer all of yor questions

Re: [R] Replacing NAs with 0 for a list of data frames

I would consider trying the plyr package using the llply function. With something like: require(plyr) func - function(xx) { xx[is.na(xx)] - 0 return(xx) } llply(your.df.list, func) What I wondering is why you want to do this. Best, Tal Contact

Re: [R] What does LOESS stand for?

Hi Peter, If this article is correct: http://www.r-bloggers.com/abbreviations-of-r-commands-explained-250-r-abbreviations/ Loess stands for: [LO]cally [E]stimated [S]catterplot [S]moothing Best, Tal Contact Details:---

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