[R] Trouble getting rms::survplot(..., n.risk=TRUE) to behave properly

3.3 rpart_4.1-10 [25] sandwich_2.3-4 scales_0.4.0mvtnorm_1.0-5 [28] foreign_0.8-66 chron_2.3-47zoo_1.7-13 === Thanks, -steve -- Steve Lianoglou Computational Biologist Genentech __ R-help@r-project.org mailing list

Re: [R] Trouble getting rms::survplot(..., n.risk=TRUE) to behave properly

nk E Harrell Jr Professor and Chairman School of Medicine > > Department of *Biostatistics* *Vanderbilt University* > > On Thu, Jun 2, 2016 at 10:55 AM, Steve Lianoglou > wrote: > >> Hello foks, >> >> I'm trying to plot the number of patients a

Re: [R] Fastest way to calculate quantile in large data.table

EndTEST3-StartTEST3 > EndTEST4-StartTEST4 > EndTEST5-StartTEST5 > EndTEST6-StartTEST6 > EndTEST7-StartTEST7 > EndTEST8-StartTEST8 > > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://sta

Re: [R] Scraping HTML using R

tla* > *-* > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help >

Re: [R] NA's introduced by coercion

trying to do with your data after you convert it to a "numeric" -steve -- Steve Lianoglou Computational Biologist Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] NA's introduced by coercion

Hi Madhvi, First, please use "reply-all" when responding to emails form this list so that others can help (and benefit from) the discussion. Comment down below: On 26 Aug 2014, at 22:15, madhvi.gupta wrote: On 08/27/2014 10:42 AM, Steve Lianoglou wrote: Hi, On Tue, Aug 26, 20

Re: [R] loops in R

ect.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > Don McKenzie > Research Ecologist > Pacific Wildland Fire Sciences Lab > US Forest Service > > Affiliate Faculty > School of Environmental and Forest Sciences > University

Re: [R] howto get the number of columns and column names of multiply data frames

put of ls() into a list also does not work. How can I accomplish this task?? If you still want to do it this way, see: ?get for example: for (varName in paste('dataframe', 1:n, sep='')) { cat(colnames(get(varName))) } HTH, -steve -- Steve Lianoglou Graduate Student: C

Re: [R] problem selecting rows meeting a criterion

OK so the lesson so far is "use the subset function". Hopefully you're learning a slightly different lesson now :-) Does that clear things up at all? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center

Re: [R] R help from command line

ention, but are you working on a machine with a windowing system + browser? If so, set your help files to be seen in the browser: R> option(htmlhelp=TRUE) next time you ask for some ?help, it should pop up a browser window. Good enough? -steve -- Steve Lianoglou Graduate Student: Com

Re: [R] logged2

r package, but nothing else. If you can let us know where you're seeing this function used, we could likely provide more help. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornel

Re: [R] problem loading ncdf library on MAC

get the required libs and try again. Or are you getting different errors? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: ht

Re: [R] Nominal variables in SVM?

lor and height, your "feature matrix" for N examples would be N x 4 0,1,0,15 # blue object, height 15 1,0,0,10 # red object, height 10 0,0,1,5 # green object, height 5 ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer

Re: [R] request: Help

-- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing list https

Re: [R] Coding problem: How can I extract substring of function callwithin the function

me. But if you're trampling over some base:: function for something trivial like changing the value of one default parameter to something else, you might as well just get them to learn how to use the ? asap as well. -steve -- Steve Lianoglou Graduate Student: Computational Systems Bio

Re: [R] Coding problem: How can I extract substring of function callwithin the function

ou *might* be doing in the short term. Then again, it might not be. Everyone has their own style of teaching, and it's your prerogative to do it as you see fit. I wouldn't presume to know which way is best, so good luck with the upcoming semester :-) -steve -- Steve Lian

Re: [R] creating list of the from 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, . . ., n, n, n?

10 -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing l

Re: [R] Replacing NA values in one column of a data.frame

_ 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. -- Steve Lianoglou Graduate Student: C

Re: [R] printing a dataframe summary to disk

rame) write.table(my.summary, quote=FALSE, file="summary.txt") -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info:

Re: [R] Remove columns

om the result. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-proje

Re: [R] lm.fit algo

ctor * ~ is used as "almost equals") You'll need some numerical/scientific/matrix library in java, perhaps this could be a place to start: http://commons.apache.org/math/userguide/stat.html#a1.5_Multiple_linear_regression Hope that helps, -steve -- Steve Lianoglou Graduate St

Re: [R] Newbie that don't understand R code

*t))/2) out } ) phi.inverse( - log(U)/Y, theta) phi.inverse was defined as the function returned by the switch statement. ``- log(U)/Y`` is passed in to the function's ``t`` argument. Does that help? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology |

Re: [R] value of nth percentile

the R code or command for this please let me know. I would appreciate your early response. R> dat <- rnorm(100, mean=10, sd=2) R> quantile(dat, .9) 90% 12.53047 R> sum(dat < quantile(dat, .9)) / length(dat) [1] 0.9 -steve -- Steve Lianoglou Graduate Student: Computational

Re: [R] open txt

oblema Tu file "plantula.txt" no esta aqui (I think). In short: you are passing some function the name of a file that doesn't exist. Try passing the absolute path to the plantula.txt file to your call to ``file()`` -steve -- Steve Lianoglou Graduate Student: Computational

Re: [R] Tr : create a table in the console!!

t understand what you want to do. From the code you've pasted, you already have extracted the numbers you wanted, so what do you mean when you say "I want to do a table" with them? Do you just want to put them in a data.frame, or something? -steve -- Steve Lianoglou Grad

Re: [R] Erros with RVM and LSSVM from kernlab library

ather than the matrix which you think you're passing in. Does that do the trick? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: h

Re: [R] Erros with RVM and LSSVM from kernlab library

therwise, can you provide something of a self- contained piece of code that you're using to invoke these functions such that it's giving you these errors? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill

Re: [R] Erros with RVM and LSSVM from kernlab library

b=1:10) R> is(df) [1] "data.frame" "list" "oldClass" "mpinput""vector" But R> is(df, 'list') [1] FALSE So, in short, I don't know if that's what's happening ... did it fix your problem, tho? -steve

Re: [R] a naive question

n, like so R> x[,1] You can use that to plot a histogram of the numbers in the first column: R> plot(hist(x[,1])) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contac

Re: [R] LASSO: glmpath and cv.glmpath

;t don't do them)[1] ... you might want to further divide your data into training/tuning/test (somewhere between steps 1 and 2) as another means of scoring models. HTH, -steve [1] http://hunch.net/?p=29 -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Slo

Re: [R] Convert list to data frame while controlling column types

RUE Can you check to see if your data's wonky somehow? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __

Re: [R] extra .

s any insight into that. I've always been curious and I seem to see it done in many different functions and packages, so I feel like I'm missing something ... Thanks, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kette

Re: [R] computation of matrices in list of list

) [,1] [,2] [,3] [,4] [,5] [1,] 5.003219 2.2498521 2.9065183 -2.7294155 5.5118195 [2,] 1.560042 -2.0677467 -1.5175750 3.1384472 1.7245805 [3,] -4.653988 -0.8043570 -1.3420022 -5.6794115 0.5077933 [4,] -7.433055 0.8248184 -0.8724350 -0.2229058 -3.7149176 [

Re: [R] Help on comparing two matrices

ttp://en.wikipedia.org/wiki/Divide_and_conquer_algorithm Perhaps you can take inspiration from some concrete sorting algorithms that are implemented this way: Merge sort: http://en.wikipedia.org/wiki/Merge_sort Quick sort: http://en.wikipedia.org/wiki/Quicksort Hope that helps, -steve -- S

Re: [R] Help on comparing two matrices

columns to a sorted matrix. > If you want to go about this by implementing the algo you described, I think > you'd be best suited via some divide-and-conquer/recursion route: Starting from step 2, that is. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Me

Re: [R] Help on comparing two matrices

can pad your matrices with zero rows or columns (depending on what's deficient) as an easy way out. Just an idea. Of course, if David's solution is what you need, then no need to bother with any of this. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology

Re: [R] Help on comparing two matrices

graph.isomorphic(g1, g2) # Or, using the (somehow fast) vf2 algorithm is.iso <- graph.isomorphic.vf2(g1, g2) HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http:

Re: [R] Filtering matrices

e three small example matrices and let us know what you'd like your indexing to return. Someone will provide the code to show you the correct way to do it. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical Co

Re: [R] Filtering matrices

ntersection, take an & of the two vectors, # but this is empty in this case. Either way, this would get # the points you're after my.data[good.cor & good.p] Does that make sense? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering C

Re: [R] GLMs

neralized mixed model") Will provide many answers. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __

Re: [R] rJava error for large XML object return in StatET plugin

Hi, On Aug 26, 2009, at 1:31 PM, Harsh wrote: Hi R List, I get this error using StatET R plugin in Eclipse. You might have more luck asking the StatET user mailing list: https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/statet-user -steve -- Steve Lianoglou Graduate Student

Re: [R] find numbers in a line with letters

t;, perl=T) [[1]] [1] 17 47 attr(,"match.length") [1] 4 5 R> gregexpr("(\\d+(\\.\\d+)?)", "this Item costs 3.32 Dollars, that item costs 10 dollars even, ", perl=T) [[1]] [1] 17 47 attr(,"match.length") [1] 4 2 R> gregexpr("(\\d+(\\.\\d+)?)&

Re: [R] SVM coefficients

uot; attribute, which I guess is what you're looking for (?) Run "example(svm)" to its end and type: R> m$coefs [,1] [1,] 1.00884130 [2,] 1.27446460 [3,] 2. [4,] -1. [5,] -0.35480340 [6,] -0.74043692 [7,] -0.87635311 [8,] -0.04857869 [9,

Re: [R] SVM coefficients

ing. SVMs are great for accuracy, but notoriously hard for interpretation. To try and squeeze some interpretability from your classifier in your feature space, you might try to look at the weights over your w vector: http://www.nabble.com/How-to-get-w-and-b-in-SVR--%28package-e1071%29-td24790413

Re: [R] Calling C funtion from R help Needed

ll would be: .C('checkstr_R_wrapper', n=as.character(n), n_length=length(as.character(n)), m=as.integer(m), result=integer(1)) ... or something ... perhaps. Does that help any? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sl

Re: [R] SVM coefficients

ich is already implemented for you in the penalized svm package (haven't used it myself): cran: http://cran.r-project.org/web/packages/penalizedSVM/index.html publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/25/13/1711 Does that help? -steve -- Steve Lianoglou Gra

Re: [R] Loading file in MAC-Syntax Error

sktop/test.txt/ 1. Where's your code? 2. Try to remove the trailing slash of your filename > It always gives me Syntax error message. What is the error message? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill

Re: [R] how to save an updated dataset

elp@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. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memori

Re: [R] foreach + snowfall for multicore situations

over using the foreach w/ multicore backend? Just curious because I've moved off of any snow* related packages since I only parallelize on the same box and find that the foreach/ doMC combo works just fine. -steve -- Steve Lianoglou Graduate Student: Computational Systems Bi

Re: [R] Regarding SVM using R

ries to send a sql query to your database and will be returned a data.frame of your results. You can manipulate that data.frame in the usual way to pick off your "target" column from. the predictor/feature columns and train your SVM accordingly (or use the entire data.frame along with the for

Re: [R] About BIC

I just ran ??bic to find it. Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___

Re: [R] using histogram to find cdf

Hi, On Sun, Sep 6, 2009 at 7:03 AM, maram salem wrote: > Dear all, > How can I use the histogram density estimate (hist) to find the value of the > cdf at a certain point? Can you just use the ecdf function on your original data? -steve -- Steve Lianoglou Graduate Student: Comp

Re: [R] Color index in image function

= terrain.colors(100), axes = FALSE) Right here: R> terrrain.colors(100) [1] "#00A600FF" "#03A700FF" "#07A800FF" "#0AAA00FF" "#0EAB00FF" ... Is that what you mean? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Mem

Re: [R] how do I draw this surface -- hand drawn in the attachemtn

y seen it in actio in the lattics vs. ggplot series of posts on the learnr.wordpress.com blog (very helpful). -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http

Re: [R] get the command line

(), collapse=" ") Can you give an example of what you're trying to get? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info:

Re: [R] get the command line

On Mon, Sep 7, 2009 at 12:00 AM, Peng Yu wrote: > On Sun, Sep 6, 2009 at 10:50 PM, Steve > Lianoglou wrote: >> Hi, >> >> On Sun, Sep 6, 2009 at 11:25 PM, Peng Yu wrote: >>> Hi, >>> >>> commandArgs gives me the arguments. I am wondering what comm

Re: [R] Averaging rows if a condition is true.

oblems using it, please post a small representative matrix of your data that we can paste into our own R session to slice and dice for you as an example. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of C

Re: [R] OT - Banker's Algorithum

on below to R: http://en.wikipedia.org/wiki/Banker%27s_algorithm#Pseudo-Code.5B3.5D Not really sure what else to say ... for instance, the line: P = P - {p} Might be: P <- setdiff(P, p) Maybe use lists to hold the stuff in P? Don't know what else you're looking for ... -steve -- Steve Lianoglo

Re: [R] About " create dataset permanently in package "

nd Settings\YOU\RainRainGoAway \rain1.rda", then load it from there in R: R> load("C:\Documents and Settings\YOU\ RainRainGoAway\rain1.rda") That should do the trick ... let us know if you need more help. -steve -- Steve Lianoglou Graduate Student: Computational Syste

Re: [R] Regarding SVM using R

from your validation set when you pass it into the predict function? ie: predict(model.ksvm, validation[, -length(validation)] should probably be predict(model.ksvm, validation, ...) That should work ... but if you're using this for anything serious, be sure you understand why.

Re: [R] sparse vectors

ng-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___

Re: [R] Regarding SVM using R

replies on list 2 . Please post your new code along with the error. Thank, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] Regarding SVM using R

t. In short -- stop removing the features (columns) from your training/ testing data and it should work. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskc

Re: [R] Linux R version: best?

the latest version when it's released. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/co

Re: [R] memory limit problem

er 16384*16384 > Error: cannot allocate vector of size 512.0 Mb > I not have other objects in R memory. > what I do? Get a 64 bit system and ditch windows? http://thread.gmane.org/gmane.comp.lang.r.general/64637 Or maybe the bigmemory package can help? http://cran.r-project.org/web/packages

Re: [R] Graph visualization

) mat <- rbind(c(0, 0, 1, 1), c(0, 0, 1, 1), c(1, 1, 0, 1), c(1, 1, 1, 0)) dimnames(mat) <- list(LETTERS[1:4], LETTERS[1:4]) graph <- graph.adjacency(mat) tkplot(graph) (you can specify different layouts, too). HTH, -steve -- Steve L

Re: [R] transposing a distance matrix in R

o now: R> who.vs.who[lower.tri(m),] Var1 Var2 2BA 3CA 6CB ... almost there, no just put it together: R> dist <- m[lower.tri(m)] R> who <- who.vs.who[lower.tri(m),] R> names(dist) <- paste(who[,1], who[,2], sep=".vs.") R> dist B.vs.A C.vs.A

Re: [R] Moving to Mac OS X

at's all I really need as I spend most of my time in the terminal then sourcing some file that has the functions I'm trying to refine anyway ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Me

Re: [R] Working with large matrix

the lm. I am using LINUX 64 bit with 32G mem. Is there an elegant and fast way of completing this task? Do bigmemory and biglm help? http://cran.r-project.org/web/packages/bigmemory http://cran.r-project.org/web/packages/biglm -steve -- Steve Lianoglou Graduate Student: Computational Systems

Re: [R] help with plotting

ou see how length(a) > 1 -- what should ``if (a)`` evaluate to? R is telling you that it's just evaluating a[1]. So, maybe your data isn't what you expect it to be? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center

Re: [R] Moving to Mac OS X

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. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering

Re: [R] Moving to Mac OS X

R.app GUI, you can get it from here: http://r.research.att.com/#GUI For some reason the 2.9-leopard.dmg is missing (though the 2.10-devel is there). This was just noticed on R-sig-mac earlier today and, AFAIK, it should be back soon. -steve On 9/11/09 12:38 PM, Steve Lianoglou wrote:

Re: [R] help with for loop

each row of your matrix, yes? Look at the ``apply`` function, with MARGIN set to 1. Here I'm just calling the ``mean`` function over every row of my matrix: R> m <- matrix(1:100, 10, 10) R> apply(m, 1, mean) [1] 46 47 48 49 50 51 52 53 54 55 Substitute your own function f

Re: [R] Way to iteratively change line color and line style

Hi, On Fri, Sep 11, 2009 at 8:12 PM, Jason Rupert wrote: > I would like to have a way to automatically change the line color and line > style. For auto-generating colors, try ?rainbow Not sure about what you can do about alternating the line style ... -steve -- Steve Lianoglou Gr

Re: [R] linear regression, exclude a datum

doesn't make sense to you, please post some code we can comment on. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~l

Re: [R] Location of Packages?

s. 32 bit, look at the size of the pointer: R> .Machine$sizeof.pointer [1] 8 8 means 64 bit, 4 means 32 bit. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info:

Re: [R] call for input

e. See: ?readline -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-pro

Re: [R] Eliminate cases in a subset of a dataframe

them). Refer to them by their position in the data.frame as you would if you didn't create a subset. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell Universit

Re: [R] 64-bit OSX binary for 2.9.2

acked in the root (e.g. tar fvxz R*.tar.gz -C /), but doesn't contain the GUI (see below for a separate download).""" You'll have to install the R.app GUI separately if you want to use the 2.9.2 install, otherwise I think the 2.9.0 *.pkg installer includes

Re: [R] (no subject)

Hi, On Sep 14, 2009, at 10:19 AM, asie soheili wrote: I want to comput prime component of a graph. please guide mi. If you're working with graphs, you'll want to check out the igraph package: http://cran.r-project.org/web/packages/igraph/ http://igraph.sourceforge.net/ -steve

Re: [R] average for files and graph

type of plot do you expect to see? ?plot ?barchart ?barplot ?boxplot ?points ?lines ... -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/co

Re: [R] Strange question/result about SVM

t then it just seems to look like line noise ... infer them as you see fit ... -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: ht

Re: [R] Is there an equivalent of "echo"

hz.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. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medica

Re: [R] Boost in R

mcr: 0 achieved after 20 boosting step(s) What is "mcr" mean? Third link down: http://www.google.com/search?hl=en&q=logitboost+mcr&spell=1 Looks like MCR == misclassification rate? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial S

Re: [R] identical(length(x), 1) returns FALSE, but print(length(x)) is 1, length(x)==1 is TRUE, and is.integer(lenght(x)) is TRUE????

), 1L) is TRUE ... ouch ... I guess the lesson learned is that: identical() != == -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos

[R] Putting together a constantly evolving package

ight do eventually down the road, anyway), but I'm wondering if there are other alternatives. Thanks, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info:

Re: [R] Turnpoints

ave count less than 4000 2. You can use it to select out of the vector. R> df[less4000,] You can also use the subset function R> subset(df, count < 4000) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill

Re: [R] T-test to check equality, unable to interpret the results.

he p- value (in any statistical test), the less confident you should be that rejecting the null hypothesis is a good idea. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University

Re: [R] T-test to check equality, unable to interpret the results.

han measured: sorry. Thanks for wearing the stats prof hat, though. It's good that someone stepped up to lay down the law. With white flag raised, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College

Re: [R] SVM

the Examples section of ?svm .. it's pretty straight forward. Let us know what problems you're having understanding those examples and we can try to offer some insight. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Cente

Re: [R] SVM

? I'm not really sure where to begin ... what are you trying to do, exactly? Why do you think you want to build an SVM? What do you expect it to do for you? -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical Co

Re: [R] SVM

learning more about SVMs and other machine learning approaches, you can watch Andrew Ng's intro to machine learning classes online. The relevant links are at the top of this page: http://ai.stanford.edu/~ang/courses.html -steve -- Steve Lianoglou Graduate Student: Computational Systems B

Re: [R] Updating R-code in own package

find anything about updating R-code in the package. I'm pretty sure the only "correct" thing to do is just fix the code in your package's source tree then reinstall the package wholesale to replace the bad code with the fixed code. -steve -- Steve Lianoglou Graduate Stude

Re: [R] R on browser

e happy to help. Thanks, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-hel

Re: [R] Emacs and ESS help

directory which emacs will find. The "~" abbreviation is required and is interpreted to be your home directory. In emacs C-x C-f ~/.emacs And for what it's worth "~" translated to C:\Documents and Settings \YOURACCOUNT on your windows box ... I think. -steve --

Re: [R] Any concept of 'by reference' or 'address of' in R?

lements in the matrix/data.frame, then you shouldn't have to worry, and look to optimize elsewhere ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio

Re: [R] Working around 256 byte variable names? + trouble opening large file

not an excel guru, so I don't know how it handles data export when certain cells are missing in a row -- each row should have as many demarcated data points as any other. So if its a CSV, there should be just as many ","'s in line 397 as there are in the preceding lines

Re: [R] How to sort the elements in a matrix?

ements in column 2, by the sequence of the elements in column 1 in ascending order? R> ab[order(ab[,1]),2] [1] 3 4 2 1 -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University

Re: [R] svm and RMSE

vior? Is the different RMSE over different folds of cross validation. Over the same data? With the same parameters? Is the RMSE significantly different? Providing an example that shows this behavior would help. Thanks, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Me

Re: [R] for loop Vs apply function Vs foreach (REvolution enhancement)

MC" is a foreach backend that parallelizes over the cpus/cores of 1 machine, others parallelize over different machines in a cluster), then it will just run the code in the %dopar% block sequentially. Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems B

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