Re: [R] logging messages

On Mon, 15 Nov 2004, Faber Fedor wrote: Hi all, I'm trying to learn R from an non-statistician's POV. I've got a statistician who uses R, but I'm the schmuck who has to integrate his R functions into an automated process. Defining a POV (undefined, as is `schmuck') as `not something' is really

Re: [R] Pairwise Distances -- How to vectorize the loop

Hi From what you write it seems to me a work for outer(). Did you try it? Cheers Petr On 15 Nov 2004 at 22:26, Timothy W. Victor wrote: R-List, I'm trying to compute pairwise distances among pairs of observations, which each pair containing data from 2 groups. There are more than

[R] Adding mean and SEM in Hmisc ecdf

Dear R Gurus, Sorry if this has been asked before but I did not find it in the archives. I would like to add a horizontal display of mean and SEM on Hmisc ecdf plots done by group (ie variate~treatment). Has anyone written some code to do that ? Thanks and kind regards, Jean-Louis

Re: [R] how can draw probability density plot?

I hope this is the direct operation you are looking for: curve(dnorm(x),from=-3,to=3) Best regards, Ales Ziberna - Original Message - From: LONG Yu [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Monday, November 15, 2004 1:26 PM Subject: [R] how can draw probability density plot?

[R] question about AIC

Hi everybody, we are a pool of phd students and we have a question about AIC. We are interested in calculating the AIC for a mixture model on galaxies data. So far we have found AIC works only for regression models, whereas we need AIC for a mixture of Normal with mean, sd and weights given by

[R] From S-Plus to R?

Dear collegues, I am using S-Plus for many years and is thinking of moving to R. In the FAQ I did not manage to find an answer to the following questions: Is it easy to move and transform functions, written under S-plus to functions under R? Furthermore, S-Plus has interesting functions to deal

[R] Multivariate Sampling

Dear Ales, I have found a matlab routine which does latin hypercube sampling with random distributions. It seem to be quite straightforward to transform it to R. If you or anybody else is interested - and it works - I am happy to send the R version to him. The method is from Iman and Conover

Re: [R] question about AIC

On Tue, 16 Nov 2004 [EMAIL PROTECTED] wrote: we are a pool of phd students and we have a question about AIC. We are interested in calculating the AIC for a mixture model on galaxies data. So far we have found AIC works only for regression models, whereas we need AIC for a mixture of Normal with

Re: [R] question about AIC

did you try google? e.g., with key word: `AIC mixture models'. Moreover, look at package `flexmix' (i.e., help(package=flexmix)) whose usage is illustrated in a recent article in JSS: http://www.jstatsoft.org/v11/i08/v11i08.pdf I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D.

[R] From S-Plus to R

Dear Isabelle, for most of my work I have switched from S-Plus to R, because it is easier to make scripts with due to the better documentation and some other more reasonable implementations. And there was also a cost issue with the S-Plus Server, which is not for free at all. In R I use the

[R] UML programming

hello, I'd like to know if it is possible to use R in a UML way by creating classes, methods,etc... If yes, can you please give me links for documentation and example ? thanks Accédez au courrier électronique de La Poste : www.laposte.net ; 3615 LAPOSTENET (0,34€/mn) ; tél : 08 92 68 13 50

Re: [R] question about AIC

I would also mention the mixreg package on CRAN. Regards m. ** Massimiliano Marinucci http://personales.ya.com/max_mar/ Ph.D Candidate in Economics Fundamentos del Analisis Económico II (Economía Cuantitativa) Facultad de CC.EE. Universidad Complutense

Re: [R] UML programming

Sure, you could do it in a UML way. But I know of no tools yet that will, and more importantly, the object-orientation style (generic functions, i.e. similar to CLOS) isn't the easiest to use in that way. On Tue, 16 Nov 2004 11:03:28 +0100, wayne [EMAIL PROTECTED] wrote: hello, I'd like to

Re: [R] How to remove x, y labels from a plot

try : plot(rnorm(20),rnorm(20),axes=F,xlab=,ylab=) Selon [EMAIL PROTECTED]: Hi there, I need to plot an illustrative figure without ticks, x, y labels in R. I managed to get the ticks removed, but had no luck with x, y labels. Any suggestions would be much appreciated. Jin Li

Re: [R] How to remove x, y labels from a plot

Hi Jin Li, does plot( 1:100, rnorm(100), ann=FALSE, xaxt=n, yaxt=n ) produce what you want? Arne On Tuesday 16 November 2004 13:06, [EMAIL PROTECTED] wrote: Hi there, I need to plot an illustrative figure without ticks, x, y labels in R. I managed to get the ticks removed, but had no

Re: [R] Barplot difficulties

Heather J. Branton wrote: Hello. I am an R newbie struggling to learn and use R . I have read many portions of the R Reference Manual, as well as the FAQs. Given that I learn something new each time, I know I might be missing something obvious. But I appeal to your good nature to help me

Re: [R] Adding mean and SEM in Hmisc ecdf

Jean-Louis Abitbol wrote: Dear R Gurus, Sorry if this has been asked before but I did not find it in the archives. I would like to add a horizontal display of mean and SEM on Hmisc ecdf plots done by group (ie variate~treatment). Has anyone written some code to do that ? Thanks and kind regards,

[R] violinplot options

Hi, I am using the function vioplot() to generate violin plots. Now I would like to add a label to the y axix and a title to the diagram. Just setting ylab didnt work. Is it possible to set such options for the function ? I tried also with the function simple.violinplot, but also with this I

[R] Simple plot() question

Hi First a simple question to do with plot(). How do I change the x-axis labels on a plot? For example, I am plotting each row of a matrix, and I want each row to be a line on my graph. Simple really. Eg: plot(sg[1,], type=l) When I do this, the x-axis is labelled 1:38, as I have 38 columns

[R] Difference between two correlation matrices

Hi Now a more theoretical question. I have two correlation matrices - one of a set of variables under a particular condition, the other of the same set of variables under a different condition. Is there a statistical test I can use to see if these correlation matrices are different? Thanks

Re: [R] Simple plot() question

michael watson (IAH-C) wrote: Hi First a simple question to do with plot(). How do I change the x-axis labels on a plot? For example, I am plotting each row of a matrix, and I want each row to be a line on my graph. Simple really. Eg: plot(sg[1,], type=l) When I do this, the x-axis is labelled

Re: [R] Simple plot() question

try something like plot(..., axes=FALSE) axis(2); axis(1, labels=c(your labels)) Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/16/396887 Fax: +32/16/337015 Web:

RE: [R] Simple plot() question

Hi Mick: I'm a little unsure if this is what you are after but does this do it? foo.mat - matrix(rnorm(100), nrow = 10, ncol = 10) plot(foo.mat[1,], type=l, xlab = Crud, ylab = More Crud) plot(foo.mat[1,order(foo.mat[1,])], type=l, xaxt = n, xlab = Crud, ylab = More Crud) axis(1,

Re: [R] Difference between two correlation matrices

Hello, I don't know if it is applicable in your case, but have you tried Mantel test? You can use it to determine significant correlation between two matrices, using Pearsion, Spearman or Kendal correlation indices. Hope it helps, All the best, Marta - Original Message - From: michael

[R] deleting a file

Dear all, I have a very simple question. Simple, that is, if you know the answer. I wish to delete a file in a given directory after having first checked its existence. I issue the following commands path-'c:example/R/' Thus creating the directory. indicator-length(grep(filename,path)) If

Re: [R] deleting a file

In Linux I would issue the command system('rm paste(path,'filename',sep='')') and this works just fine. It does not however work for windows, and I have no idea whether it would work on a mac. Is there a single command thay escapes me? Yes. help(file.remove)

[R] memory allocation

Dear sirs, I'm using the Splancs package to compute standard errors of the estimates of a spatio-temporal k function. When I use as spatial and temporal distances too long vectors (respectively 60 and 80 entries) for a dataset of 1000 observations, R gives me the message Error: cannot

[R] User package - Simple Ports

R experts, I created a package X for R 1.8 that I want to re-install for 2.0.1. In addition to downloading/installing Perl and Rtools as directed in the README.packages file and ensuring that they appear in my path, I have modified X's DESCRIPTION file to include all required fields.

Re: [R] deleting a file

You may be interested in one of dir.create(), file.exists(), or unlink(). -roger Roger Gill wrote: Dear all, I have a very simple question. Simple, that is, if you know the answer. I wish to delete a file in a given directory after having first checked its existence. I issue the following

Re: [R] Difference between two correlation matrices

One solution is to use procruste analysis. Perform a principal coordinate analysis on your data (cmdscale) to obtain two individuals by variables tables. Then, you can perform procruste rotation and test to know if the two matrice tell the same thing. It is more powerful than mantel test. As you

[R] Rggobi-color maps and colors

Hello, I was wondering if the function get(set)ColorMap.ggobi() is working for anyone.. The function is not defined when I tried to work on it. Also, I would really like to know, if I can increase the number of colors in any of the color scheme, if possible. We only got 12 colors (maximum?) to

[R] Fourier analysis

Dear colegues, Is there any function in R for calculating the four coefficients of each harmonic in fourier analysis, from a set of x,y coordinates is given? Is it possible to do Fourier analysis? Has anyone done contour analysis using R? Any help wil be apretiated, Thank you very much, All the

Re: [R] memory allocation

There is more to that message you have not reproduced. I am pretty sure you are on Windows, and you need to read the rw-FAQ (as the posting guide asks you too). See Q2.7. On Tue, 16 Nov 2004, Massimiliano Copetti wrote: I'm using the Splancs package to compute standard errors of the estimates

Re: [R] deleting a file

On Tue, 16 Nov 2004 15:43:12 - Roger Gill wrote: Dear all, I have a very simple question. Simple, that is, if you know the answer. Yes, look at ?file.remove Z I wish to delete a file in a given directory after having first checked its existence. I issue the following commands

[R] Changing zeros to NAs in a data frame

Dear R People: I have a data frame with some columns that are numeric and some which are factors. There are zeros in the numeric columns and I would like to change them to NAs. However, there are zeros in some of the factor columns, and I would like them to be left alone. Is there a global

[R] R 2.0.0 Installation Problem

I and my students have been having an odd problem with this release, which is that packages are disappearing. After installation the package is found with the library command, but later in the same session or in a later session, the library command returns a not found error. Then later it is back.

[R] changing character to a vector name

Dear R People: I would like to generate a vector/variable name from within a loop to be passed to a table function. This is what I have so far: assign(p1,paste(raw3.df$,rw2$V1[3],sep=)) p1 [1] raw3.df$CITIZEN Essentially, I want to use the raw3.df$CITIZEN along with another value to generate a

[R] R: Changing zeros to NAs in a data frame

Hi, see this example. I hope I helped you a little bit. Bye Vito dati X YZ 1 10 0 0 2 0 20 60 3 30 40 50 4 11 12 3 dati[dati==0]-NA dati X YZ 1 10 NA 0 2 NA 20 60 3 30 40 50 4 11 12 3 = Diventare costruttori di soluzioni Became solutions' constructors The

[R] help on EM Algorithm for bivariate normal

Hi, I woul like to know if it is possible to have a R code to generate EM Algorithm for a normal bivariate mixture. Best regard, S.F. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide!

[R] Please help using SQL with R SQL Server

I cannot get a database connection in R to my MS SQL Server database. In S-Plus 6.2 I have used the following successfully: rawdata - importData(type=DIRECT-SQL, user=xfl2, password=xfl2, server=rinnycs0059, database=xf, table=, sqlQuery=select * from testTbl) In R I have tried both DBI

Re: [R] Changing zeros to NAs in a data frame

Laura Holt wrote: Dear R People: I have a data frame with some columns that are numeric and some which are factors. There are zeros in the numeric columns and I would like to change them to NAs. However, there are zeros in some of the factor columns, and I would like them to be left alone.

Re: [R] memory allocation

On Tue, 16 Nov 2004, Massimiliano Copetti wrote: Dear sirs, I'm using the Splancs package to compute standard errors of the estimates of a spatio-temporal k function. When I use as spatial and temporal distances too long vectors (respectively 60 and 80 entries) for a dataset of 1000

RE: [R] Changing zeros to NAs in a data frame

This isn't pretty but it's a way to do it: foo - data.frame(x = c(1,0,1,1,0,2,4), y = as.factor(c(0,2,1,1,0,3,1))) Zero2NA - function(x){ if(is.numeric(x)) { x[x == 0] - NA; } return(x) } foo2 - as.data.frame(lapply(foo, Zero2NA)) foo foo2 HTH, Andy -Original Message- From:

[R] R help

Hi, I was wondering as to how I could convert SPSS data imported to R into tabular form. In the sense, direct usage of read.table( ) doesnt help. Thanks - Meet the all-new My Yahoo! – Try it today! [[alternative HTML version deleted]]

Re: [R] Changing zeros to NAs in a data frame

On Tue, 16 Nov 2004, Laura Holt wrote: Dear R People: I have a data frame with some columns that are numeric and some which are factors. There are zeros in the numeric columns and I would like to change them to NAs. However, there are zeros in some of the factor columns, and I would like them

Re: [R] help on EM Algorithm for bivariate normal

take a look at: flexmix mixreg mclust packages on CRAN You may also define your own M-step in some of these packages... EM is used to find the parameters of the mixture. Ciao M. ** Massimiliano Marinucci http://personales.ya.com/max_mar/ Ph.D

RE: [R] User package - Simple Ports

If I'm not mistaken, I believe you need to do make pkg-X or R CMD INSTALL X Andy From: Keith J Sabol R experts, I created a package X for R 1.8 that I want to re-install for 2.0.1. In addition to downloading/installing Perl and Rtools as directed in the README.packages

Re: [R] R help

I don't understand your question. PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html;. In particular, have you read the R Data Import / Export documentation that some with R [available, from www.r-project.org - Manuals or R - help.start()]? Have you tried read.spss

[R] problems with compiling a package

Hello, I am trying to compile packages for R2.0.0 patch in a win XP machine. Most of the packages compile without problems, with C or FTG or only R. Now some packeges give the following error which I do not understand how to correct ... preparing package xxx for lazy loading Error in names -

Re: [R] help on EM Algorithm for bivariate normal

The three packages that someone else mentioned in response to your post flexmix mixreg mclust may be usefule in real applications. On the other hand, if your interest is in teaching EM or developing your own EM by using a simple example, the most recent issue of The American Statistician

Re: [R] problems with compiling a package

On Tue, 16 Nov 2004 [EMAIL PROTECTED] wrote: Hello, I am trying to compile packages for R2.0.0 patch in a win XP machine. What exactly is `R2.0.0 patch'? If you mean 2.0.0 patched, it has a date, and the date is crucial. Most of the packages compile without problems, with C or FTG or only R.

Re: [R] changing character to a vector name

Laura Holt lauraholt_983 at hotmail.com writes: . I would like to generate a vector/variable name from within a loop to be . passed to a table . function. . . This is what I have so far: . assign(p1,paste(raw3.df$,rw2$V1[3],sep=)) . p1 . [1] raw3.df$CITIZEN . . Essentially, I want to use the

Re: [R] problems with compiling a package

r.ghezzo at staff.mcgill.ca writes: : One other question, this npreparing package for lazy loading does not occur for : all packages, although their DESCRIPTION and folders are similar, When does a : package goes to lazy loading and when it does not? You can use LazyLoad: no in the

Re: [R] Difference between two correlation matrices

If you have the data that created the correlation matrices, then you can do a permutation test. The first question to ask is, What does 'different' mean? Some choices include: max(abs(cor1 - cor2)) max(abs(eigen(cor1 - cor2)$values)) Once you have decided what metric makes most sense, you can

[R] gcrma package

Hi ! I would like to understand where do affinity.spline.coefs used in function compute.affinities come from ? library(gcrma) data(affinity.spline.coefs) affinity.spline.coefs X1 X2 X3 X4 X5 X1 -0.55004171 -0.58579091 -0.08870557

[R] CDs for R?

Hi Folks, I'm sure I'm speaking for more than a few (though possibly a minority) here. There's something of a hidden assumption that R users can readily download whatever they need from CRAN. Some of us are on narrow bandwidth dialup connections, so downloading large quantities of stuff is out

Re: [R] deleting a file

Achim Zeileis wrote: On Tue, 16 Nov 2004 15:43:12 - Roger Gill wrote: Dear all, I have a very simple question. Simple, that is, if you know the answer. Yes, look at ?file.remove Z ... and file.path() in order to specify the location in an OS independent way. Uwe Ligges I wish to

Re: [R] gcrma package

This question is more for the BioConductor mailing list. If you type in library(gcrma) help(affinity.spline.coefs) at the command prompt, it suggests you to see compute.affinities. Doing a help(compute.affinities), you will see under References section : Hekstra, D.,

RE: [R] How to remove x, y labels from a plot

Hi Arne, It works. It produced what I wanted. y-rnorm(1000, 2, 0) plot(density(y), ylab=Abundance of species, xlab=Environmental gradient, main= , lty=2, col=4, xaxt=n, yaxt=n) Thanks, Arne. And also thanks to other responses. Regards, Jin -Original Message- From: Arne Henningsen

Re: [R] CDs for R?

(Ted Harding) [EMAIL PROTECTED] writes: [...] There's something of a hidden assumption that R users can readily download whatever they need from CRAN. [...] What I'd like to suggest, for consideration, is that along with the stirling work done at many centres to set up and maintain

Re: [R] CDs for R?

There was a similar thread earlier this year http://tolstoy.newcastle.edu.au/R/help/04/03/1785.html I think I previously made the suggestion that you could download this from an internet cafe. I am not sure if these cafes allow you to plug in your own laptop or burn it for you. If you have a

Re: [R] CDs for R?

On Tue, 16 Nov 2004 21:39:14 - (GMT), (Ted Harding) [EMAIL PROTECTED] wrote: Hi Folks, I'm sure I'm speaking for more than a few (though possibly a minority) here. There's something of a hidden assumption that R users can readily download whatever they need from CRAN. Some of us are on

[R] beginner's problem in displaying large data

I got a sample data (let's call it sample.data), which is about 2200 by 15. I tried to take a look of all data sample.data It shows only a part of data that I thought was a corner. It does not really affect my job, but I thought it is nice to have a look of all data. I can see individual

[R] plot question

Say y and z are two time series (functions of date). What is the R command to plot y and z together on a graph with date on the x-axis? DISCLAIMER: This e-mail message and any attachments are inte...{{dropped}} __ [EMAIL PROTECTED] mailing list

Re: [R] beginner's problem in displaying large data

1. Did you try dim(sample.data)? Is it actually 2200 by 15? Or are you reading in just some subset of the data? If it is 2200 by 15, could you also please do class(sample.data)? 2. I just got a full listing from the following: (tst - data.frame(array(rnorm(2200),

[R] Cross-correlated variables in kernel density estimation

Hi, I am wondering if the kde2d 2-D kernel density estimation function in the MASS package can take into account the effect of correlations between the variables. I couldn't find any achieved information on this issue. Unfortunately, I don't have the 2002 edition of Modern Applied Statistics with

RE: [R] Cross-correlated variables in kernel density estimation

From: Adam Gobena Hi, I am wondering if the kde2d 2-D kernel density estimation function in the MASS package can take into account the effect of correlations between the variables. I couldn't find any achieved information on this issue. Unfortunately, I don't have the 2002 edition of

[R] about 2 color variance stabilization

Hello sir: A paper of you namedExact and Approximate Variance-Stabilizing Transformations for Two-Color Microarrays is very helpful for my work. A question which needs your help.Thanks a lot. For instance,cy3~control cy5~treatment And after calculating the htransformation for each channel,we can

Re: [R] plot question

Apoian, Zack Zack.Apoian at sac.com writes: Say y and z are two time series (functions of date). What is the R command to plot y and z together on a graph with date on the x-axis? There are several time series classes (ts, zoo in zoo, irts in tseries, its in its, timeDate in fBasics) and its

[R] Non-Linear Regression on a Matrix

Hi, I'm terribly sorry for submitting my primitive question, I'm a beginner in R and was hoping to get some help re: non-linear fit. I have a 2D data with the following structure: A BC 1 1 111 1 2 121 1 3 131 2 1 141 2 2 151 2 3

RE: [R] Cross-correlated variables in kernel density estimation

Hi Andy, Sorry about the vague subject line. I think I overlooked a lot of things including the description of the function itself. Anyway, you have got the essence of my question. Thanks for the reply. I am using kernel density estimation to estimate the pdf some data. The pdf estimation is an

Re: [R] Non-Linear Regression on a Matrix

If your non-linear function (A, B) is parametric nls should do it for you. If you have R version 2 (perhaps even 1.9) do ?nls to see the help page. Older versions of R require library(nls) first. Hope this helps, Andy __ Andy Jaworski 518-1-01 Process

[R] how to estimate conditional density

Hi, there. Suppose I have a bivariate data set y1 and y2. Can anybody tell me how to estimate the conditional density of f(y1|y2) and vice versa? Thanks. Yulei $$$ Yulei He 1586 Murfin Ave. Apt 37 Ann Arbor, MI 48105-3135 [EMAIL PROTECTED] 734-647-0305(H)

Re: [R] CDs for R?

Ted, On Tue, Nov 16, 2004 at 09:39:14PM -, Ted Harding wrote: Hi Folks, I'm sure I'm speaking for more than a few (though possibly a minority) here. There's something of a hidden assumption that R users can readily download whatever they need from CRAN. Some of us are on narrow

[R] Search engine for LINUX MOZILLA

Hi, I am looking for help on searc engine at R htmlhelp page. Here is the system settings: R 2.0.0 (2004-10-04). Installed at Linux RH 9.0 (kernal 2.4.20-8) and FC2 (kernal 2.5.8). The web broswer is Mozilla 1.7 Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7) Gecko/20040616 From

[R] persp grid

I've got a 4x4 matrix of points from a 2-way ANOVA I'd like to plot. The x,y correspond to the treatment groups and look like this ((1,1),(1,2),(1,3),(1,4),(2,1),...). The z is the 4x4 matrix. How can I get persp to grid the x,y axis with only the numbers 1-4 on both? Regards, Joel Bremson UC

Re: [R] CDs for R?

On 16 Nov 2004, at 23:39, (Ted Harding) wrote: Some of us are on narrow bandwidth dialup connections, so downloading large quantities of stuff is out of the question (e.g. at approx. 5min/MB, it would take over 2 days to download a single CD). The meat of CRAN (including contributed packages and

[R] How to plot this

Hi there, I produced a plot using the following codes: y-rnorm(1000, 2, 0) x0-c(0, 0) y0-c(0, 0) y1-c(0, 1) x1-c(0, 4) plot(density(y), ylab=Abundance of species, xlab=Environmental gradient, main= , xlim=c(0, 4), ylim=c(0, 1), lty=2, col=4, xaxt=n, yaxt=n, frame.plot=F)

[R] Re: variations on the theme of survSplit

Danardono [EMAIL PROTECTED] wrote: While waiting for 2.1, for those who need function[s] for this survival-splitting business, as I do, this 'survcut' function below might be helpful. It is not an elegant nor efficient function but it works, at least for some examples below. Ditto the

Re: [R] Search engine for LINUX MOZILLA

This is covered in the R-admin manual, linked to from that HTML page. Please follow carefully the advice there. In particular ensure that you have a version of Java that is said to work (preferably the latest, 1.5.0). On Wed, 17 Nov 2004, Yuandan Zhang wrote: Hi, I am looking for help on searc

Re: [R] Cross-correlated variables in kernel density estimation

Yes it can and it is in the reference. On Tue, 16 Nov 2004, Adam Gobena wrote: Hi, I am wondering if the kde2d 2-D kernel density estimation function in the MASS package can take into account the effect of correlations between the variables. I couldn't find any achieved information on this issue.

RE: [R] How to plot this

If this is a quick and dirty process you want rather than learning all the capabilities that are in R then I would copy the density curve (or the bits you like) into your favourite image editor, and use it's capabilities to pretty it up. However there are a number of options. Firstly you have