Re: [R] read sas data into R

Mary Royerr wrote: Hi I am having trouble using read.ssd. Can someone help? The code that I have written is *sashome-C:/Mary/Datasets* *read.ssd(read.ssd(file.path(sashome, core, sashelp), surv_1v,* *sascmd = file.path(sashome, sas.exe))* Here the path that I have given is correct,

Re: [R] Greek in vector

I have given an example in R News: Ligges, U. (2002): R Help Desk: Automation of Mathematical Annotation in Plots. R News 2 (3), 32-34. http://cran.r-project.org/doc/Rnews/Rnews_2002-3.pdf Uwe Ligges Todd A. Gibson wrote: Hello, I understand how to use substitute() to integrate Greek

Re: [R] saving simulation as .dat

Nigel.Walker wrote: I have simulated some data using the garchSim and would like to save the series as a .dat file. I am not sure how to do this unfortunately any help would be appreciated. Data import and export are described in the respective manual (R Data Import/Export).

Re: [R] A rebel boxplot question

Sorry, but I can't help you with your problem isntalling ggplot2. I'm a WinXP user and have no experience with R on Linux. Maybe Hadley Wickam could help you out on this one. Cheers, Thierry ir. Thierry Onkelinx

[R] histograms and significance values

Hi, I have a simulation with negative examples, and with R I can do quite easily a histogram and a density estimate. I have one positive example and I want some statistical significance value to see to what extent the positive example is part of the negative population. Does anyone have an

Re: [R] print Text on device

thank you Greg, this is just what I needed. On 10/8/07, Greg Snow [EMAIL PROTECTED] wrote: Look at the textplot function in the gplots package. Does that do what you want? -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801)

Re: [R] as.ordered

Hello Friedrich, thanks for your help and it is really not important that the solution is elegant. Important is only that there is a solution. But I still have some problems with this topic. #I tried as you suggested to order the vectors separately. My first problem is that my data is a

Re: [R] Linux editor for R+LaTeX, but not Emacs

is it only me or has anyone else the problem that running an R process within emacs is way much slower than in a regular terminal/ console? It's just you, and if you think some more about it, you'll see why we are all grinning. [ Hint: it can't be slower, outside of ridiculous corner

Re: [R] igraph and plotting connected components

On Mon, Oct 08, 2007 at 08:11:16PM -0500, [EMAIL PROTECTED] wrote: [...] Dot-file format is also *ridiculously simple* to generate , which I think of as a factor well in its favor. :-) This is just write.graph(g, format=dot, file=output.dot) in igraph. I hear that there's a tk-based

[R] Read in date fomat while colClasses=character

Hi R users, I am using xlsReadWrite to read a particular excel file. In one of the columns I have dates ( say col=5). Now date column is read by default as numeric. So I used dateTimeAs= isodatetime. This enables reading in the date format. However in the earlier column (say col=1) I have data

Re: [R] Linux editor for R+LaTeX, but not Emacs

On 10/9/07, Scionforbai [EMAIL PROTECTED] wrote: is it only me or has anyone else the problem that running an R process within emacs is way much slower than in a regular terminal/ console? It's just you, and if you think some more about it, you'll see why we are all grinning. [ Hint:

Re: [R] graph or svn

Paul, if you have large graphs the igraph package might help, it works very well with large sparse graphs. To convert an adjacency matrix (A) to an igraph graph object (g) you can simply use library(igraph) g - graph.adjacency(A) and then you can generate layouts with

[R] 16-way comparison.

Hi. I'm looking for a way to compare the following within and between each Year for each Season and number of Shifts in each Treatment. YearSeason Treatment Shifts (Log+1) I'm using R 2.6 (with R cmdr). I have difficulties as im a R-newbie. Could someoen guide me? Nicolai --

[R] Using Rexcel: How to work with a range of data?

Hi, I am trying to use an R function over a column of data I have in my excel spreadsheet. I do the following:- 1) assign an object (calling it xaxis) to the data by typing in =Rput(xaxis,a1:a10), where my data is shown in cells a1:a10 Now I wish to arrive at the mean of these

[R] fit.contrast and interaction terms

Dear R-users, I want to fit a linear model with Y as response variable and X a categorical variable (with 4 categories), with the aim of comparing the basal category of X (category=1) with category 4. Unfortunately, there is another categorical variable with 2 categories which interact with x

[R] Unsere Empfehlung des Hauses persoenlich fuer [EMAIL PROTECTED]

Holen sie sich jetzt 2400 EUR in Cash ab Und gehen Sie dabei einen sicheren und koeniglichen Weg !!! Alles mehrsprachig und einfach erklaert, starten Sie jetzt !!! Für jeden erhaeltlich, ganz einfach: Anklicken, Registrieren, abholen !!! WO ERHALTEN SIE SONST 2400 Euro in 12 Monaten

[R] pseudo code

Hey there! I got a pseudo code and don't know how to apply it to R, maybe someone can help me: Input: A dataset X, kmax: maximum number of clusters, num_subsamples: number of subsamples. Output: S(i; k) - a distribution of similarities between partitions into k clusters of a reference

Re: [R] igraph and plotting connected components

Dieter, there are a couple of ways to do this in igraph, eg. you can decompose the graph into separate components with g - erdos.renyi.game(100, 1/100) graphs - decompose.graph(g) and then you will have a list of graphs. If you assign some vertex ids as vertex attributes then you can keep

Re: [R] window (x,y) co-ordinates of datapoints

On Tue, 9 Oct 2007, Samuel Kemp wrote: Hi, In the getGraphicsEvent function the (x,y) co-ordinates returned from the mouse move are in relation to where the mouse is located within the device window (i.e. the lower left corner of the window is '(0,0)', the upper right is '(1,1)'). You do

Re: [R] window (x,y) co-ordinates of datapoints

Prof Brian Ripley wrote: Read ?par and the descriptiuon in 'An Introduction to R'. din, fin, mai, omi, pin and usr are relevant. Is there any hope that, instead of fin, din, pin, etc someday we will have fmm, dmm, pmm? Alberto Monteiro __

Re: [R] window (x,y) co-ordinates of datapoints

On 10/9/2007 8:16 AM, Alberto Monteiro wrote: Prof Brian Ripley wrote: Read ?par and the descriptiuon in 'An Introduction to R'. din, fin, mai, omi, pin and usr are relevant. Is there any hope that, instead of fin, din, pin, etc someday we will have fmm, dmm, pmm? I don't think so (why

Re: [R] pseudo code

Requires: T = cluster(X): A hierarchical clustering algorithm L = cut-tree(T; k): produces a partition with k non-singleton clusters The functions you'll want to read the documentation to, here, are hclust() and cutree(). They're fairly straightforward and nicely documented. It looks like

Re: [R] window (x,y) co-ordinates of datapoints

Duncan Murdoch murdoch at stats.uwo.ca writes: On 10/9/2007 8:16 AM, Alberto Monteiro wrote: Prof Brian Ripley wrote: Read ?par and the descriptiuon in 'An Introduction to R'. din, fin, mai, omi, pin and usr are relevant. Is there any hope that, instead of fin, din, pin, etc

[R] read only certain parts of a file

Dear all, I would like to know how can I read a text file and create a data frame of only certain parts of the file. For instance, from this text file: === Matches For Query 0 (108 bases): 19_0070

[R] Trouble writing distance matrices to file

Hi all, I have a distance matrix, created in R (using vegdist). When I use write.matrix to write it to a file, it writes a matrix with values in the upper diagonal. Is it possible to get R to write only the lower diagonal values (since the matrix that it creates with vegdist actually only has

[R] extract year or month from date

Hi, I am having trouble extracting just the year or the month or the day from a date such as 5/7/2007 which is May 7th 2007. Is there any particular function to extract just the year from this format? When I am reading this data from a text file it is reading it correctly in the same format but

[R] lattice/xyplot: horizontal y-axis labels with scales(relation=free)

I would like to create an xyplot with varying y-axis limits and horizontal labels at the y-axis tickmarks. The following does not seem to work, although I think it should, going by the documentation for par. R version 2.5.1, Windows XP Prof. Thanks for a clue. Andreas Krause

[R] AlgDesign--exact and approximate design

Hi I am trying to generate a design using Algdesign and came across terms of exact design and approxiamte theory design, I did not find a reference to explain what they are, could some one shed some light about this on me? Another question is, I want to measure the main effects and at least

Re: [R] extract year or month from date

Highto convert strings into date use the:? strptime command, it converts data into POSIXlt classthis class provides direct access to some details of your date time information, likea-strptime(07/07/1992,format=%d/%m/%Y)a$mon+1 gives you the month (+1 because POSIXlt uses 0-11 for months

Re: [R] fit.contrast and interaction terms

Hello Berta, gmodels::fit.contrasts() simply performs a single-variable contrast using the model you have specified. To perform the more involved contrasts that you are describing, there are two approaches: 1) use the estimable() function in the gmodels package. gmodels::estimable()

Re: [R] lattice/xyplot: horizontal y-axis labels with scales(relation=free)

Andreas Krause: # still vertical despite las=1 xyplot(Sepal.Length ~ Sepal.Width | Species, data=iris, scales=list(relation=free), las=1) xyplot(Sepal.Length ~ Sepal.Width | Species, data=iris, scales=list(relation=free, las=1)) Try xyplot(Sepal.Length ~ Sepal.Width | Species, data=iris,

Re: [R] extract year or month from date

Read the help desk article on dates in R News 4/1. On 10/9/07, Mary Royerr [EMAIL PROTECTED] wrote: Hi, I am having trouble extracting just the year or the month or the day from a date such as 5/7/2007 which is May 7th 2007. Is there any particular function to extract just the year from this

[R] identify number of sequences from a vector

dear R users, I've got kind of strange problem that I can't solve, even though it's not that difficult. I need to compute the wald-wolfowitz run test on the residuals from a gee model, and I'm trying to build the quantities I need by hand. Whereas for the expected and the variance there's no

Re: [R] as.ordered

Birgit, First things first, stop trying to sort.list a data frame. This is why you are getting the error. It is still a dataframe whether it has 1 column or 100. ?sort.list clearly says argument 'x' is a vector, and as this shows, you are not passing it a vector dat0 - data.frame(var1 =

[R] [R-pkgs] new package ppls

A new package ppls is now available on CRAN. The ppls package implements penalized Partial Leasts Squares (PLS). In a nutshell, supervised dimensionality reduction via PLS is combined with penalization techniques. Features of the package include * estimation of linear regression models with

[R] problem with lower, upper triangles and diagonal

Hello R user! I have again a problem and sometimes I have the feeling that I will never learn to solve my problems by myself. But I found no solution in the searchable archieves or somewhere else. I have a square data.frame with distance values. In this special case the upper and the lower

Re: [R] AlgDesign--exact and approximate design

sun flyhyena at yahoo.com.cn writes: Another question is, I want to measure the main effects and at least two interactions, variables are factors, how do I ensure this in formula, ~.+v1:v2 +v3:v4 ? I would give something like the following a try (since you did not tell use where

Re: [R] window (x,y) co-ordinates of datapoints

On 10/9/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Tue, 9 Oct 2007, Alberto Monteiro wrote: Prof Brian Ripley wrote: Read ?par and the descriptiuon in 'An Introduction to R'. din, fin, mai, omi, pin and usr are relevant. Is there any hope that, instead of fin, din, pin,

Re: [R] read only certain parts of a file

Here are two possibilities. The first extracts all lines with 10 fields and then takes unique ones while the second extracts all lines that consist only of alphanumerics, space, underscore and period and then also takes unique lines. Both then read the result using read.table. The first one

Re: [R] identify number of sequences from a vector

On Tue, 2007-10-09 at 16:28 +0200, Niccolò Bassani wrote: dear R users, I've got kind of strange problem that I can't solve, even though it's not that difficult. I need to compute the wald-wolfowitz run test on the residuals from a gee model, and I'm trying to build the quantities I need by

Re: [R] How to create something between a script and a package

Mark, Moshe, Vladimir, Uwe, Thanks for the tips regarding -source- and -rprofile-. Best, Sergio On 10/9/07, Uwe Ligges [EMAIL PROTECTED] wrote: Sergio Correia wrote: (Before starting: I'm a total R noob so please bear with me in case of any error or faux pas). Hi, For a small

Re: [R] as.ordered

Hello Gavin, thanks for your answer. Answering to your sort.list a data frame. I tried to convert it to a vector but it was also not successful: bract.awnMin-as.vector(bract.awnMin) sort.list(bract.awnMin) Fehler in sort.list(bract.awnMin) : 'x' must be atomic for 'sort.list' Have you

[R] Summary vs fivenum results for Q3

I've just started using R and am still a neophyte, but I found the following curious result. I'm using the current version of R (2.5.1 (2007-06-27) ). Why are the results for the third quartile different in the output from the summary and fivenum commands? For the following data set 457

Re: [R] Summary vs fivenum results for Q3

Please read the relevant help pages: ?fivenum ?boxplot.stats Hint: Length of your data vector is an even number. Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of

Re: [R] as.ordered

On Tue, 2007-10-09 at 17:12 +0200, Birgit Lemcke wrote: Hello Gavin, thanks for your answer. Answering to your sort.list a data frame. I tried to convert it to a vector but it was also not successful: bract.awnMin-as.vector(bract.awnMin) Why did you expect that to work? I guess you

[R] skill scores

Hi, I'm a new R-user. I want to use some skill scores for weather forecast purpose. Are there packages or functions in R with some skill scores (POD, FAR, TSS, CSI, HEIDKE, ecc)? Thanks in advance Gianni -- Gianni Messeri La.M.M.A (Laboratorio Meteorologia e Modellistica Ambientale) CNR-IBIMET

Re: [R] problem with lower, upper triangles and diagonal

Hello Fernando, I have two problems with you suggestion: First what I get back if I use lowerTriangle is this: (f2.low-lowerTriangle(f2, diag = TRUE)) [1] 0 1 1 1 1 0 1 0 0 1 1 1 1 1 0 But I need a triangle and I need an object of class dist to use afterwards the mantel.rtest function. So I

[R] Plotting two distance matrices

Hi all, I'm trying to plot two distance matrices against each other (74x74,phylogenetic distance and phenotypic distances). However R gives an error message:Error in plot.new() : figure margins too large. Is it because I have too many points to plot? Thanks in advance, Muri

Re: [R] A rebel boxplot question

Rolf Turner wrote Your example is a bit confusing --- Sorry, maybe I can provide a better example above of what I want. ``add'' and ``col'' do not seem to be arguments for boxplot(). Are you sure? ;-) Maybe you could want to take a look to this: clyde - rnorm(100) melvin -

Re: [R] continue for loop in case of erros

Hi, See ?try On 09/10/2007, Irene Mantzouni [EMAIL PROTECTED] wrote: Dear all, I have a for loop which includes nls model estimation. The loop breaks after the first non-convergence error. How can I make the loop continue and try to estimate all models? I suppose it should be sth like:

Re: [R] continue for loop in case of erros

Thank you all! Yes, try works! __ 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

[R] 00LOCK error on site-library

I am experiencing an OOLOCK error when attempting to update packages to my site-library. I have an identical setup on my local Linux machine, but this problem on the remote Linux machine (PPC cluster) started about 3 weeks ago and is present whether I used R-devel or R-2.6.0 or R-2.5.1. Also,

Re: [R] as.ordered

Hello Gavin, I am so sorry that I haven´t read your mail accurately. Now I tried all and it works very well and is exactly what I need. Many thanks for your help. And also many thanks to all the other people helping me. Greetings Birgit Am 09.10.2007 um 17:38 schrieb Gavin Simpson: On

Re: [R] window (x,y) co-ordinates of datapoints

On Tue, 9 Oct 2007, hadley wickham wrote: On 10/9/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Tue, 9 Oct 2007, Alberto Monteiro wrote: Prof Brian Ripley wrote: Read ?par and the descriptiuon in 'An Introduction to R'. din, fin, mai, omi, pin and usr are relevant. Is there any

[R] Help with gamm errors

Dear All Hopefully someone out there can point out what I am missing! I have a (large, several hundred) dataset of gardens in which over two years the presence/absence of a particular bird species is noted each week. I have good reason to believe there is a difference between the two years in the

Re: [R] How put description under the graph (using different lines)

Thank you very much, Grew. It help me a lot, but I still have a doubt. How can I reduce the height between layout. I try something as: layout( rbind( 1,2,c(3,4)), height=c( 2, 0.5, 0.5)), but I don't achieve reduce it. For example, I need a something as:

Re: [R] How to create something between a script and a package

IMHO: When in doubt (or even when not) --- create a package. It's not that hard, and it focuses the mind wondrously. Particularly writing help files for the functions that you create. cheers, Rolf Turner

Re: [R] continue for loop in case of erros

It's a FAQ: 7.32. -thomas On Tue, 9 Oct 2007, Irene Mantzouni wrote: Dear all, I have a for loop which includes nls model estimation. The loop breaks after the first non-convergence error. How can I make the loop continue and try to estimate all models? I suppose it should be sth

[R] Multivariate chi-square distribution function

Dear All, Is there any function in R for computing multivariate chi-square distribution? How about multivariate gamma distribution? I appreciate any comment on this subject. Thank you, Amin Zollanvari PhD student Department of Electrical and Computer Engineering, Texas AM University, College

Re: [R] bug: wireframe and tcltk

Lafaye de Micheaux Pierre wrote: Dear R users, When i call the wireframe function from within a tcltk widget, it does not work. Here is a sample program that shows the bug. When you try: is.it.a.bug() You can see that the curve instruction is run but not the wireframe one. Do you

[R] Visualize cox proportional hazards

Hello all I would like to visualize the hazard ratios of a cox proportional hazards model. I have seen some good examples in the New England Journal of Medicine: http://content.nejm.org/cgi/content/short/353/26/2747/F3 http://content.nejm.org/cgi/content/short/350/26/2654/F2 (I hope these are

Re: [R] window (x,y) co-ordinates of datapoints

Look at the cnvrt.coords function in the TeachingDemos package, it does this type of thing for you. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL

Re: [R] Visualize cox proportional hazards

There are at least a couple of versions of such plots. Search for forest plots: help.search(forest plot) -Christos Christos Hatzis, Ph.D. Nuvera Biosciences, Inc. 400 West Cummings Park Suite 5350 Woburn, MA 01801 Tel: 781-938-3830 www.nuverabio.com -Original Message- From:

Re: [R] How put description under the graph (using different lines)

How does it not work? The following produces a graph that looks like your drawing. layout( rbind(1,2,c(3,4)), heights = c(2,.5,.5) ) plot(1:10) library(gplots) textplot('Descrip. A', cex=1) textplot('Descrip. B', cex=1, col='red') textplot('Descrip. C', cex=1, col='red') -- Gregory

Re: [R] how to use \Sexpr{} with sweave

Just goes to show, it helps to search the archives! I discovered this in the R-help archives: https://stat.ethz.ch/pipermail/r-help/2004-July/053920.html And similarly, in the Sweave manual: A.16 After loading package R2HTML Sweave doesn’t work properly! Package R2HTML registers an Sweave

[R] 2 Sample Confidence Interval - Formatting Data?

Hello all, I have to run a 2 Sample Confidence Interval on some data; the command for such intervals is confint(...), but in the help documentation it says that you need a fitted model object in order to run this command. What does that mean? The data is very small, it's:

[R] R dynamic memory management

I have a loop that processes all the raw data files in agiven directory. It should allocate only the memory to accomodate the filenames list. Each file is loaded into RAM one at a time and saved to another directory after processing. The R script runs fine but it had some memory problems so it was

Re: [R] Summary vs fivenum results for Q3

On Tue, 9 Oct 2007, Schaefer, Robert L. Dr. wrote: I've just started using R and am still a neophyte, but I found the following curious result. I'm using the current version of R (2.5.1 (2007-06-27) ). Why are the results for the third quartile different in the output from the summary

Re: [R] 2 Sample Confidence Interval - Formatting Data?

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Wayne Aldo Gavioli Sent: Tuesday, October 09, 2007 3:37 PM To: [EMAIL PROTECTED] Subject: [R] 2 Sample Confidence Interval - Formatting Data? Hello all, I have to run a 2 Sample Confidence

Re: [R] 2 Sample Confidence Interval - Formatting Data?

On Tue, 2007-10-09 at 18:37 -0400, Wayne Aldo Gavioli wrote: Hello all, I have to run a 2 Sample Confidence Interval on some data; the command for such intervals is confint(...), but in the help documentation it says that you need a fitted model object in order to run this command. What

Re: [R] regression by groups

Jiong Zhang, PhD wrote: Hi All, I want to run regression (lm) on my dependant variable by gender and race. How do I integrate the by function in lm? thanks. Here is an example using the iris data: by(iris, iris$Species, function(x){ summary(lm(Sepal.Length ~ Sepal.Width +

Re: [R] silhouette: clustering labels have to be consecutive intergers starting from 1?

that happened to me with R-2.4.0 (alpha) and was fixed on R-2.4.0 (final)... http://tolstoy.newcastle.edu.au/R/e2/help/06/11/5061.html then i stopped using... now, the problem seems to be back. The same examples still apply. This fails: require(cluster) set.seed(1) x - rnorm(100) g -

Re: [R] R dynamic memory management

On Tue, 9 Oct 2007, Maura E Monville wrote: I have a loop that processes all the raw data files in agiven directory. It should allocate only the memory to accomodate the filenames list. Without seeeing the script (see the footer of this and every R-help message, including the second copy you

[R] Studentized maximum distribution

Has anyone written a function to find the quantiles for the studentized maximum distribution, and the studentized maximum modulus distribution? Thanks for any help. Kostas - [[alternative HTML version deleted]]