[R] which data structure to choose to keep multile objects?

I have a function called nnmf which takes in one matrix and returns two matrices. for example, X [,1] [,2] [,3] [,4] [1,]147 10 [2,]258 11 [3,]369 12 z=nnmf(X,2) z$W [,1] [,2] [1,] 0.8645422 0.6643681 [2,] 1.7411863 0.5377504

Re: [R] another question: how to delete one of columes in two ones with high correlation(0.95)

thank you. I need learn it, after that, maybe I can understant it well. thank Nikhil Nikhil Kaza-2 wrote: You need dim(cor.matrix)[1] Following might be better instead of a loop, to to get the row ids of a matrix (which(cor.matrix =0.95) %/% dim(cor.matrix)[1])+1 for column ids

[R] a bug with Student t-value??

Hello, every one, Using the qt() function in R, I got a different Student t-value with the Student t table. e.g. the return value of function qt(0.95,9) is 1.833, while in table it is 2.262. I do not know why the difference exists. I guess it may be a bug in R. -- Íõ»¯Èå ²©Ê¿Ñо¿Éú

Re: [R] a bug with Student t-value??

Hi Huaru, Are you sure you are looking at 0.95 and NOT 0.975? as qt(0.975,9) = 2.262 generally tables are given for alpha/2 (alpha=0.05 in your case) significance. Please check carefully. Thx, S. On Sat, Nov 7, 2009 at 4:02 AM, huaru wang huaru.w...@gmail.com wrote: Hello, every one,

Re: [R] a bug with Student t-value??

Hi, Sunny, Sorry for my mistake. Thank you for your correction. Thx, Huaru 2009/11/7 Sunny Srivastava research.b...@gmail.com Hi Huaru, Are you sure you are looking at 0.95 and NOT 0.975? as qt(0.975,9) = 2.262 generally tables are given for alpha/2 (alpha=0.05 in your case)

Re: [R] a bug with Student t-value??

On 07-Nov-09 09:02:38, huaru wang wrote: Hello, every one, Using the qt() function in R, I got a different Student t-value with the Student t table. e.g. the return value of function qt(0.95,9) is 1.833, while in table it is 2.262. I do not know why the difference exists. I guess it may

Re: [R] a bug with Student t-value??

Sunny Srivastava wrote: Hi Huaru, Are you sure you are looking at 0.95 and NOT 0.975? as qt(0.975,9) = 2.262 generally tables are given for alpha/2 (alpha=0.05 in your case) significance. Please check carefully. Or, put differently, tables are often given for two-sided p-values (especially

Re: [R] map of a country and its different geographical levels

Hi Greg I downloaded the file france.shapefiles.zip Then i unziped it. There were 4 files interesting me: - france_administrative.dbf - france_administrative.prj - france_administrative.shp - france_administrative.shx How can i do to read the map france_administrative with R I tried this

Re: [R] Density estimate with bounds

Hi Greg, Thank you very much for your help. The logspline package seems to solve the problem. Best regards, Justine Original-Nachricht Datum: Thu, 5 Nov 2009 11:11:31 -0700 Von: Greg Snow greg.s...@imail.org An: Justine Rochon roc...@gmx.de, r-help@r-project.org

[R] Rpad and R 2.10.0

I have problems with Rpad and R 2.10.0 (Windows XP and Windows 7, browser is Firefox) Just starting Rpad by library(Rpad) Rpad() opens the browser and displays the .html files and the .Rpad files in my home directory, but these files do not have links and are not clickable. Doing the same in R

Re: [R] Error: cannot allocate vector of size 3.4 Gb

On Fri, Nov 6, 2009 at 8:19 PM, Benilton Carvalho bcarv...@jhsph.edu wrote: this is converging to bioc. let me know what your sessionInfo() is and what type of CEL files you're trying to read, additionally provide exactly how you reproduce the problem. Here is my sessionInfo(). pname is

Re: [R] map of a country and its different geographical levels

Perhaps asking on R-sig-geo might help (as well as reading the function help files, scripts found lying around somewhere may be stale ...)? If readShapePoly() (deprecated - use readShapeSpatial() instead) says that the data are not polygons, then they are not. If you want to fill administrative

Re: [R] map of a country and its different geographical levels

If readShapePoly() (deprecated - use readShapeSpatial() instead) says that the data are not polygons, then they are not. If you want to fill administrative boundaries polygons, you need polygons, not lines. The source you are using is based on OpenStreetMaps, so more likely to be lines, and as

Re: [R] Error: cannot allocate vector of size 3.4 Gb

you haven't answered how much resource you have available when you try reading in the data. with the mouse exon chip, the math is the same i mentioned before. having 8 GB, you should be able to read in 70 samples of this chip. if you can't, that's because you don't have enough resources

Re: [R] which data structure to choose to keep multile objects?

your could try something like this: xprocess-function(max_val) { result - list() for (iter in 2: max_val) { zz = sprintf( z%s, iter ) # use 'character' for indexing the list result[[as.character(iter)]] -nnmf(X,iter) } result } xprocess(10) On Fri, Nov 6, 2009 at 6:58

Re: [R] which data structure to choose to keep multile objects?

On Fri, Nov 6, 2009 at 11:58 PM, clue_less suhai_tim_...@yahoo.com wrote: I have a function called nnmf which takes in one matrix and  returns two matrices. for example, X     [,1] [,2] [,3] [,4] [1,]    1    4    7   10 [2,]    2    5    8   11 [3,]    3    6    9   12 z=nnmf(X,2)

Re: [R] map of a country and its different geographical levels

On Sat, 7 Nov 2009, hadley wickham wrote: If readShapePoly() (deprecated - use readShapeSpatial() instead) says that the data are not polygons, then they are not. If you want to fill administrative boundaries polygons, you need polygons, not lines. The source you are using is based on

Re: [R] The equivalence of t.test and the hypothesis testing of one way ANOVA

Hi, Student's T-test is a test that can be used to test ONE SINGLE linear restriction - which serves the as alternative hypothesis - on a linear model - which serves as the null hypothesis - AT THE SAME TIME. Fisher's F test is an extension of the T test. The F test can be used to test ONE

Re: [R] Error: cannot allocate vector of size 3.4 Gb

Most of the 8GB was available, when I run the code, because R was the only computation session running. On Sat, Nov 7, 2009 at 7:51 AM, Benilton Carvalho bcarv...@jhsph.edu wrote: you haven't answered how much resource you have available when you try reading in the data. with the mouse exon

[R] Scheffé's method?

Evidently my RSeek capabilities have once again failed me...By any chance is Scheffe's method (http://www.itl.nist.gov/div898/handbook/prc/section4/prc472.htm) implemented independently in any R base packages? If not, is it implemented independently in any of the add-on packages? Thanks

[R] after PCA, the pc values are so large, wrong?

rm(list=ls()) yx.df-read.csv(c:/MK-2-72.csv,sep=',',header=T,dec='.') dim(yx.df) #get X matrix y-yx.df[,1] x-yx.df[,2:643] #conver to matrix mat-as.matrix(x) #get row number rownum-nrow(mat) #remove the constant parameters mat1-mat[,apply(mat,2,function(.col)!(all(.col[1]==.col[2:rownum])))]

[R] cross-entity equation

vector1 vector2 vector3 vector4 h = 1.2345h = 1.2212h = 1.2065h = 1.3423 x1 = 0.8654y1 = 0.7525z1 = 1.3254x3 = 0.5746 x2 = 0.8642y2 = 0.2458

Re: [R] How to create multiple command windows of R on Windows?

You can start as many instances of R as you like (except for memory restrictions, perhaps), hence I do not get your point. Uwe Ligges Ivan wrote: Thanks for that. I seem to be able to only get one R console here though. Actually that is my question: how to get a different R console? On

Re: [R] Qtl - package - Question

Can you please try to ask the package maintainer who will certainly be happy to know if his function is broken and may know how to fix it. Best, Uwe Ligges Uwe Ligges Sunny Srivastava wrote: Dear R-Helpers, I am using qtl package to analyze qtl data from QTL cartographer. I have the map

Re: [R] Rpad and R 2.10.0

Yes I noticed the same problem since R 2.10.0, and I don't know why either. Let's forward the email to the maintainer. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-6609 Web: http://yihui.name Department of Statistics, Iowa State University 3211 Snedecor Hall, Ames, IA

[R] solution design for a large scale ( 50G) R computing problem

Hi, I am tackling a computing problem in R that involves large data. Both time and memory issues need to be seriously considered. Below is the problem description and my tentative approach. I would appreciate if any one can share thoughts on how to solve this problem more efficiently. I have

Re: [R] Error: cannot allocate vector of size 3.4 Gb

ok, i'll take a look at this and get back to you during the week. b On Nov 7, 2009, at 1:19 PM, Peng Yu wrote: Most of the 8GB was available, when I run the code, because R was the only computation session running. On Sat, Nov 7, 2009 at 7:51 AM, Benilton Carvalho bcarv...@jhsph.edu wrote:

[R] Conditional probability in Copula package?...

Hello All, How would one go about getting Pr(Y ≤ y|X = x) for a Frank copula via the Copula or other package? Best Regards, David __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] Exhaustive search in leaps - Help Please

Dear R users, I'm new in R and couldn't find the solution to this in the postings. I want to be able to use the leaps package to perform an exhaustive regression. Most of my variables are categorical with many levels. I'd like to restrict the candidate subsets to either all levels included or all

[R] [R-pkgs] new dse package

With the release of R-2.10.0 I have divided the dse bundle into packages. The bundled package dse1 and part of dse2 are now in the new package dse. The remaining part of dse2 is in a new package EvalEst. The package dse does multivariate ARMA and state space time series modelling and

[R] lme4 and incomplete block design

Dear list members, I try to simulate an incomplete block design in which every participants receives 3 out of 4 possible treatment. The outcome in binary. Assigning a binary outcome to the BIB or PBIB dataset of the package SASmixed gives the appropriate output. With the code below, fixed

Re: [R] How to see any R package code?

You have a couple of options: 1) typing the name of the function will list the source within your R console. For example: ls will list the source code for the ls() function. So once you load your package, you can simply enter the name of the function whose source you wish to see and you will

Re: [R] How to create multiple command windows of R on Windows?

Well, the problem is that I want those console to be from the same session (i.e., they share same objects etc.). I do not think multiple instances of R could do it ... 2009/11/7 Uwe Ligges lig...@statistik.tu-dortmund.de You can start as many instances of R as you like (except for memory

[R] EM algorithm to fit circular mix of uniform+Von Mises

Hi all, I'm curious if anyone has coded an Expectation-Maximization algorithm that could help me model some circular data I have. I'd like to model it as a mixture of uniform and Von Mises centered on 0, so the only free parameters is the mixing proportion and the kappa of the Von Mises. I

Re: [R] plot.window arguments being ignored?

Hi Dan, I think it's because lines() is meant for you to add lines to a plot. Hence it does not make R redraw the plot. If you wish to set the limits of the y-axis (or x-axis for that matter), you should do it in the plot function call, and then call lines() without the ylim=ry part. So your

Re: [R] How to create multiple command windows of R on Windows?

On 07/11/2009 6:31 PM, Ivan wrote: Well, the problem is that I want those console to be from the same session (i.e., they share same objects etc.). I do not think multiple instances of R could do it ... No, there's only one console in each instance. That's pretty fundamental: there is one

[R] trend thresholds on time series

Dear all, I have several response variables estimated from some simulations, and I would like to identify the thresholds for trend changes. Fro example, below I forced two different response behaviours and on x is time unit. x-1:1500 y-x/exp(x^0.2) smaller15-y[y15]

Re: [R] EM algorithm to fit circular mix of uniform+Von Mises

Hi Mike, I have an EM algorithm code for a binary von Mises mixture with 5 parameters: mixing proportion (p), 2 locations (m1, m2), and 2 dispersion parameters (k1, k2). Of course, your model is nested within this one, where k1=Inf, m1 = arbitrary, m2=0. You should be able to modify my code

[R] Repeated measures on a factorial unbalanced in a blocks with split-plot design

Dear all, I am trying to analyze data from an experiment like this: Factors: Hormone - Levels: SH, CH (S = without; C=with; H=Hormone) Time - Levels: 19/08/09, 04/09/09, 18/09/09, 08/10/09, 20/10/09 (DD/MM/YY) Nutrition - Levels: Completa, Sem (without) Macronutrition - Levels: Ca, K, Mg, P, Sem

Re: [R] Conditional probability in Copula package?...

On Nov 7, 2009, at 3:50 PM, Tidal Wave wrote: Hello All, How would one go about getting Pr(Y ≤ y|X = x) for a Frank copula via the Copula or other package? Change the limits of integration? -- David Winsemius, MD Heritage Laboratories West Hartford, CT

Re: [R] which data structure to choose to keep multile objects?

If you use the replicate or lapply functions then this will be taken care of for you (a list will be created containing your function output). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From:

Re: [R] using xyplot to plot frequencies

histogram(~ standard | Year, data = all2) 2009/11/7 Lanna Jin lanna...@gmail.com: Hi all, First off, thank you for the overwhelming response last time.  I'm still trying to figure out the syntax of R to plot some distributions of some frequencies.  I've managed to plot histograms from the

[R] influence.measures(stats): hatvalues(model, ...)

Hello: I am trying to understand the method 'hatvalues(...)', which returns something similar to the diagonals of the plain vanilla hat matrix [X(X'X)^(-1)X'], but not quite.  A Fortran programmer I am not, but tracing through the code it looks like perhaps some sort of correction based on