[R] Simple suggestion for improvement

Hello, Being relatively new to R, I often find myself searching for functions using help.search(term). Why not have the command ??term invoke it in the same way as ?topic invokes index.search(topic)? Using a double question mark to invoke a wider search for a term seems relatively intuitive to

[R] Negative binomial regression for count data

Dear list, I would like to fit a negative binomial regression model as described in Byers AL, Allore H, Gill TM, Peduzzi PN., Application of negative binomial modeling for discrete outcomes: a case study in aging research. J Clin Epidemiol. 2003 Jun;56(6):559-64 to my data in which the

[R] Putting different colors on labels in plot (hclust)

Hi All R-helpers This is my first (but probartly not last ;-) mail to R-help, so hello to everybody. My problem: Is there a way to give colors to the labels (sample labels) in plots for a hclust object for better visualization? I have looked through plot, points, hclust and more but cannot

Re: [R] Simple suggestion for improvement

On 3 Mar 2005, at 10:08, Duncan Murdoch wrote: That's not a bad suggestion, but it might not be trivial to implement. Right now the ? is an operator that is parsed like other operators such as +: it becomes a function call . To have ?? mean something special would mean changes to the parser, or a

Re: [R] Putting different colors on labels in plot (hclust)

On Thu, 3 Mar 2005 11:00:10 +0100, JSPC (Jeppe Skytte Spicker) (J(SS) wrote: Hi All R-helpers This is my first (but probartly not last ;-) mail to R-help, so hello to everybody. My problem: Is there a way to give colors to the labels (sample labels) in plots for a hclust object for

[R] [R-pkgs] new package: ResistorArray

Announcing the release of a new R package ResistorArray. This package solves the (nontrivial) general problem of resistance on arbitrary (finite) resistor arrays. Outside electrical engineering, the problem has a wide range of applications to situations such as groundwater modelling; there is a

Re: [R] Putting different colors on labels in plot (hclust)

Le 03.03.2005 11:00, JSPC (Jeppe Skytte Spicker) a écrit : Hi All R-helpers This is my first (but probartly not last ;-) mail to R-help, so hello to everybody. My problem: Is there a way to give colors to the labels (sample labels) in plots for a hclust object for better visualization? I have

Re: [R] wilcox.test statistics

Hi, a value of 0 for the test statistic is possible. The test statistic is not just the sum of ranks, but this sum - n*(n+1)/2, where n is the number of observations of the group the rank sum is build. This statistic is equivalent to the ranks sums, since it differs only about a constant, which

[R] R Site Search Firefox Plugin

Hi! I have made a simple plugin for the Firefox search bar which searches via R Site Search. I submitted it weeks ago to Mozilla.org but they don't seem to respond. Thus, if anybody is interested, please let me know. Maybe we could also find some space on a ftp server for it. Best, Werner

[R] minimizing multivariate functions

Is there any implicit function in R to minimize a function with many variables? Many thanks Raquel -- R Granell, Rheumatology Unit School of Mathematics University of Bristol [EMAIL PROTECTED] Tel:07968079410 __

Re: [R] minimizing multivariate functions

maybe you could find `?optim' useful. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/16/336899 Fax: +32/16/337015 Web: http://www.med.kuleuven.ac.be/biostat/

Re: [R] Negative binomial regression for count data

Hi, I do not know the article. Notice that an excess of zeroes can lead to (spurious) overdispersion in data, therefore you should decide whether assuming a zip ( zero excess coming from a mixture) or a negBin (zero execess due to overdispersion) model. Of course some likelihood based criteria

[R] calculating of linkage-disequilibrium measures?

Hi , is it possible to calculate ld-measures D, D', r and perhaps corresponding p-values with r IF THE PHASE IS KNOWN? The genetics - package provides the LD function only for ambigious phase. Thank you very much Bettina Kulle __ R-help@stat.math.ethz.ch

[R] 3d plot of regression squared error

Hi. I'm trying to create a 3d plot for a teaching example of finding a least-squares estimate of the parameters to fit a line to some data. I was hoping to get a nice plot with a clear, single minima where the derivative of the surface is zero. No matter how much I tinker, I can't seem to get a

[R] Re: R Site Search Firefox Plugin

Hi again! someone has kindly provided webspace for the R Site Search plugin. You'll find it here: http://www.xyzump.de/rsitesearch.zip Just extract the files to the \Mozilla Firefox\searchplugins\ directory and restart Firefox. Best, Werner __

[R] Baffled by drop1

I've been experimenting with drop1 for my biostatistics class, to obtain the so-called Type III sums of squares. I am fully aware of the deficiencies of this method, however I feel that the students should be familiar with it. What I find baffling is that when applied to a fully balanced design,

[R] Baffled by drop1: Please ignore previous request!

My apologies to the list for sending this without adequate research. I have found my answer; please ignore! Thanks. I've been experimenting with drop1 for my biostatistics class, to obtain the so-called Type III sums of squares. I am fully aware of the deficiencies of this method, however I feel

[R] creating a formula on-the-fly inside a function

I have a function that, among other things, runs a linear model and returns r2. But, the number of predictor variables passed to the function changes from 1 to 3. How can I change the formula inside the function depending on the number of variables passed in? An example: get.model.fit -

RE: [R] creating a formula on-the-fly inside a function

as.formula(paste(response.dat ~ , paste(pred.dat, collapse= +))) pred.dat is a list of predictors Sandip -Original Message- From: Dr Carbon [mailto:[EMAIL PROTECTED] Sent: Thursday, March 03, 2005 10:28 AM To: [EMAIL PROTECTED] Subject: [R] creating a formula on-the-fly inside a

Re: [R] creating a formula on-the-fly inside a function

On Thu, 2005-03-03 at 10:28 -0500, Dr Carbon wrote: I have a function that, among other things, runs a linear model and returns r2. But, the number of predictor variables passed to the function changes from 1 to 3. How can I change the formula inside the function depending on the number of

Re: [R] creating a formula on-the-fly inside a function

Dr Carbon drcarbon at gmail.com writes: : : I have a function that, among other things, runs a linear model and : returns r2. But, the number of predictor variables passed to the : function changes from 1 to 3. How can I change the formula inside the : function depending on the number of

[R] Hot to _set_ an xmlAttr XML xmlAttr set

Dear R-Gurus! I have read an xml document with xmlTreeParse and can access that attribute value by xmlGetAttr or xmlAttrs What I want to do is to set a new value and to write the modified DOM tree into an XML file. But until now I have not found an setter method equivalent to the getter method?

[R] plot question

I have the following simple situation: tt - data.frame(c(0.5, 1, 0.5)) names(tt) - a plot(tt$a, type = 'o') gives the following plot ('I' and '.' represent the axis): I I I X I I I X X I... 1 2 3 what do I have to change to get the following: I I I X I I I X

Re: [R] 3d plot of regression squared error

On Thursday 03 March 2005 13:04, Ross Clement wrote: Hi. I'm trying to create a 3d plot for a teaching example of finding a least-squares estimate of the parameters to fit a line to some data. I was hoping to get a nice plot with a clear, single minima where the derivative of the surface is

RE: [R] creating a formula on-the-fly inside a function

If these are nested models, see ?drop.terms. -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA The business of the statistician is to catalyze the scientific learning process. - George E. P. Box -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL

Re: [R] plot question

On Thu, 2005-03-03 at 17:29 +0100, Christoph Lehmann wrote: I have the following simple situation: tt - data.frame(c(0.5, 1, 0.5)) names(tt) - a plot(tt$a, type = 'o') gives the following plot ('I' and '.' represent the axis): I I I X I I I X X I... 1 2

Re: [R] plot question

tt - data.frame(c(0.5, 1, 0.5)) names(tt) - a plot(tt$a, type = 'o',xlim=c(0,4)) __ James HoltmanWhat is the problem you are trying to solve? Executive Technical Consultant -- Office of Technology, Convergys [EMAIL PROTECTED]

Re: [R] plot question

On Thu, 2005-03-03 at 10:44 -0600, Marc Schwartz wrote: See ?par for more information. Correction, that should have been ?plot.default for more information, though ?par has other relevant information on plot parameters as well. Marc __

Re: [R] plot question

On Mar 3, 2005, at 5:29 PM, Christoph Lehmann wrote: I have the following simple situation: tt - data.frame(c(0.5, 1, 0.5)) names(tt) - a plot(tt$a, type = 'o') gives the following plot ('I' and '.' represent the axis): I I I X I I I X X I... 1 2 3 what do I have to change

Re: [R] Simple suggestion for improvement

How will you deal with multiple word searches such as help.search(eps dev) One way to implement would be ??eps dev but this looks awkward to me. Regards, Adai On Thu, 2005-03-03 at 10:21 +, Yan Wong wrote: On 3 Mar 2005, at 10:08, Duncan Murdoch wrote: That's not a bad

[R] image() z-values beyond zlim

Dear useRs, When plotting with image(), I would like the z-values that extend beyond the upper zlim to be indicated with one colour, or preferably with som sort of hatching, as I'm printing in black and white. By default these values just show up as blank areas in the image. I've tried all

[R] Plotting of 3D Point Sets

Hi, Trials have generated a vast number of points, which I would like to have plotted in 3D. They are in no particular order. I would be satisfied with just being able to see the points in a graph, much nicer, though, would be something as shown on the R Aqua screenshot page. Thanx in advance

[R] Need suggestions for plotting 3D plot

Hi Everybody, I am a newbie in R. I have a data in the form of a matrix which I want to make some 3D plots using R. There is some functions for instance hist() for 2D plots, but I cant find any function for 3D plots. Is there any function available in R for 3D plots? If so, is there any

Re: [R] image() z-values beyond zlim

On Thu, 3 Mar 2005, Mikkel Grum wrote: Dear useRs, When plotting with image(), I would like the z-values that extend beyond the upper zlim to be indicated with one colour, or preferably with som sort of hatching, as I'm printing in black and white. By default these values just show up as

Re: [R] Need suggestions for plotting 3D plot

Hi, http://www.stat.ucl.ac.be/ISpersonnel/lecoutre/stats/fichiers/_gallery.pdf The document above starts showing 3 different types of 3D graphics persp scatterplot3d wireframe A few days ago there was a discussion here on the list about providing a graph library. During this discussion several

Re: [R] Plotting of 3D Point Sets

Try scatterplot3d() in the scatterplot3d package. Alternatively try searching http://maths.newcastle.edu.au/~rking/R/ Regards, Adai On Thu, 2005-03-03 at 17:45 +, Stephan Freyberger wrote: Hi, Trials have generated a vast number of points, which I would like to have plotted in 3D.

[R] stdev, skew, kurtosis, ACF from summary function?

The summary() function shows the min, median, mean, max, and 25th and 75th percentiles, but not the standard deviation, skew, and kurtosis (at least by default). Is there are an option of summary() that does this, or has someone written code for this? Since the columns of my table are time

[R] reading row vectors from file

Hi, New to R, using version 2.0.1 (2004-11-15) on debian Linux (sid), kernel 2.6.8-2-686. I have data in files with separate vectors on each row of the file, e.g., $ cat /tmp/stats freq,0,1,2,3,4,5,6,7,8,9,16,17,18,19,20,... noise,49,47,48,48,50,47,48,47,46,50,48,54,49,47,49,...

[R] German Map Data?

Hello! Is there a more accurate map of germany than the one included in the world map of the map package available? I am using R 2.0.1 under win2k. Thanks, Werner __ R-help@stat.math.ethz.ch mailing list

Re: [R] reading row vectors from file

Ken Irving fnkci at uaf.edu writes: : : Hi, : : New to R, using version 2.0.1 (2004-11-15) on debian Linux (sid), kernel : 2.6.8-2-686. : : I have data in files with separate vectors on each row of the file, : e.g., : : $ cat /tmp/stats : freq,0,1,2,3,4,5,6,7,8,9,16,17,18,19,20,... :

Re: [R] stdev, skew, kurtosis, ACF from summary function?

Vivek Rao vivekrao4 at yahoo.com writes: : : The summary() function shows the min, median, mean, : max, and 25th and 75th percentiles, but not the : standard deviation, skew, and kurtosis (at least by : default). Is there are an option of summary() that : does this, or has someone written code

[R] regression on a matrix

Hi - I am doing a monte carlo experiment that requires to do a linear regression of a matrix of vectors of dependent variables on a fixed set of covariates (one regression per vector). I am wondering if anyone has any idea of how to speed up the computations in R. The code follows: #regression

Re: [R] reading row vectors from file

Why not simply read it as an csv file, then transpose it. If you also store it as a data frame, you can use attach() or detach() the object to the search path whenever you want to access the variables directly. df - read.csv( tmp.txt, header=FALSE, row.names=1 ) df - data.frame( t( df ) ) df

Re: [R] reading row vectors from file

Gabor Grothendieck ggrothendieck at myway.com writes: : : Ken Irving fnkci at uaf.edu writes: : : : : : Hi, : : : : New to R, using version 2.0.1 (2004-11-15) on debian Linux (sid), kernel : : 2.6.8-2-686. : : : : I have data in files with separate vectors on each row of the file, : : e.g.,

[R] Rank-based p-value on large dataset

I have a fairly simple problem--I have about 80,000 values (call them y) that I am using as an empirical distribution and I want to find the p-value (never mind the multiple testing issues here, for the time being) of 130,000 points (call them x) from the empirical distribution. I typically

RE: [R] regression on a matrix

You might use lsfit instead and just do the whole Y matrix at once. That saves all the recalculation of things involving only X. Reid Huntsinger -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Eduardo Leoni Sent: Thursday, March 03, 2005 5:16 PM To:

RE: [R] Rank-based p-value on large dataset

When you say the 130,000 points are from the empirical distribution, how did you get them? Is each one really one of the values of y? If you sorted y first, would you know which one (ie which index) each x is? (Sorting 80,000 elements took essentially no time at all on my sub-gigahertz Pentium

Re: [R] German Map Data?

There is a shapefile at: http://www.vdstech.com/map_data.htm The maptools package can read and plot shapefiles. Greg Snow, Ph.D. Statistical Data Center [EMAIL PROTECTED] (801) 408-8111 Werner Wernersen [EMAIL PROTECTED] 03/03/05 02:35PM Hello! Is there a more accurate map of germany than

Re: [R] Rank-based p-value on large dataset

The x's and y's are different sets--210,000 values altogether. That is really the issue--they can't just be sorted, at least that I can see Sean On Mar 3, 2005, at 5:38 PM, Huntsinger, Reid wrote: When you say the 130,000 points are from the empirical distribution, how did you get

Re: [R] Rank-based p-value on large dataset

On Thursday 03 March 2005 16:22, Sean Davis wrote: I have a fairly simple problem--I have about 80,000 values (call them y) that I am using as an empirical distribution and I want to find the p-value (never mind the multiple testing issues here, for the time being) of 130,000 points (call them

[R] ESS

Hi all, I am running R 2.0.1 under Windows XP in German. I configured my path as follows: C:\Programme\R\rw2001\bin;C:\Programme\xemacs-packages\lib-src\;C:\Programme\XEmacs-21.4.13\i586-pc-win32 I can not start R proccess or ESS from within XEmacs. What is going wrong? I can not start S. M-x

Re: [R] Need suggestions for plotting 3D plot

Am Donnerstag, 3. März 2005 19:03 schrieb Soumyadeep nandi: Hi Everybody, I am a newbie in R. I have a data in the form of a matrix which I want to make some 3D plots using R. There is some functions for instance hist() for 2D plots, but I cant find any function for 3D plots. Is there any

Re: [R] Rank-based p-value on large dataset

On Thursday 03 March 2005 16:32, Deepayan Sarkar wrote: On Thursday 03 March 2005 16:22, Sean Davis wrote: I have a fairly simple problem--I have about 80,000 values (call them y) that I am using as an empirical distribution and I want to find the p-value (never mind the multiple testing

[R] how to capture a series of plots

Hi, there I am trying to capture a series of plots into jpeg or png files so that I can create gif animation later. However, my plot background generation is very slow, and I create the background plot only at the very beginning, and at each step I only refresh the foreground points and symbols

Re: [R] Rank-based p-value on large dataset

One solution is to cut() 'x' according to the breaks defined by 'y'. Using cut with labels=FALSE is really fast. See a simulation below. However the accuracy depends on the number of ties you have in your empirical distribution. I have tried to simulate with the round() function below. #

[R] Rconsole wishlist

Hi all, Wouldn't it be nice (??!!) if R automatically issued a warning message when the R console buffer was about to fill so that you could save all your output into a text file? (I know about sink(), but I think it would be good to have an easier mechanism to save a complete record of messages

Re: [R] Rank-based p-value on large dataset

On 3/3/05 19:04, Adaikalavan Ramasamy [EMAIL PROTECTED] wrote: One solution is to cut() 'x' according to the breaks defined by 'y'. Using cut with labels=FALSE is really fast. See a simulation below. However the accuracy depends on the number of ties you have in your empirical distribution.

Re: [R] ESS

There is an ESS mailing list that might be more appropriate. I use emacs rather than Xemacs, but I think you need to point the path to ess in init.el file which is located on the home directory. E.g. : (setq ess-icon-directory C:/Programme/xemacs-packages/etc/ess) (require 'ess-site)

RE: [R] Rconsole wishlist

I'm guessing you're talking about Rgui on Windows, but please don't leave us guessing. If you run R under Ess/(X)Emacs, you have the entire session that can be saved in a (transcript) file. Does your OS not put date stamps on file? file.info(.Rhistory) size isdir mode

[R] Question about density()

If I integrate over the result of the density() funcion, is the result 1? For example x - rnorm(1000) plot(density(x)) Does the area under the curve I see sum to 1? What I really want to know is if I can directly compare two particular curves, generated like this x - rnorm(1000)

Re: [R] Question about density()

Dan Bolser dmb at mrc-dunn.cam.ac.uk writes: : : If I integrate over the result of the density() funcion, is the result 1? : : For example : : x - rnorm(1000) : plot(density(x)) : : Does the area under the curve I see sum to 1? : : What I really want to know is if I can directly compare two

[R] fitting pareto to data?

hi i have an experimental dataset which i think is coming from a pareto/powerlaw distribution. i am trying to use the 2 parameter pareto distribution from Jim Lindsey's rmutil package (i am open to using any package however.) i would like R to compute estimates for the 2 pareto parameters

RE: [R] Rconsole wishlist

Sorry, yes, Rgui under WinXP (SP2). But while Windows date stamps the history file file.info(.Rhistory) size isdir mode mtime ctime .Rhistory 5377 FALSE 666 2005-03-04 10:37:52 2005-03-04 10:37:52 atime .Rhistory 2005-03-04 13:54:11

[R] (no subject)

Dear R help Is there a way for R to ignore NA entries in a data set. I find I can do box plots for certain columns that have no NA entries but cannot do histograms or boxplots for the other columns that have NA entries Brett Stansfield __

Re: [R] Rconsole wishlist

Duncan Mackay wrote: Sorry, yes, Rgui under WinXP (SP2). But while Windows date stamps the history file file.info(.Rhistory) size isdir mode mtime ctime .Rhistory 5377 FALSE 666 2005-03-04 10:37:52 2005-03-04 10:37:52 atime

Re: [R] fitting pareto to data?

r help r_hlp at yahoo.com writes: : : hi : : i have an experimental dataset which i think is coming : from a pareto/powerlaw distribution. : : i am trying to use the 2 parameter pareto distribution : from Jim Lindsey's rmutil package (i am open to using : any package however.) : : i would

Re: [R] Rconsole wishlist

The problem is that the commands history is GUI-specific (there are four mechanisms, readline on Unix, one for the GUI MacOS X (I believe), one for RGui and one for rterm. And we will have to cope with both GNU and BSD readline shortly). We try to keep them consistent, and that means a

Re: [R] (no subject)

Am Freitag, 4. März 2005 05:08 schrieb Brett Stansfield: Dear R help Is there a way for R to ignore NA entries in a data set. Yes, what about na.omit, try help.search(missing values), there are some very good examples for handling missing values Please, have a look at the posting guide and use

Re: [R] how to capture a series of plots

See ?dev.copy Uwe Ligges Weijie Cai wrote: Hi, there I am trying to capture a series of plots into jpeg or png files so that I can create gif animation later. However, my plot background generation is very slow, and I create the background plot only at the very beginning, and at each step I

[R] Is aggregate() what I need here?

I'm pretty new to R, and I've been given a script by a user who wants some help with it. I know enough about the way R works to know that this is a very inefficient way to do what the user wants (the LSB_JOBINDEX stuff is added by me so that this can work on many hundreds of input data files