[R] plotmath overstrikes in output on a Linux system

2008-04-08 Thread Paul Johnson
I've been testing plotmath. But I'm getting some funny output one one computer. The problem is that characters are 'jumbled' and overstrike when symbols are introduced. Sample code: mu - 440.0 sigma - 12.5 myx - seq( mu - 4*sigma, mu+ 4*sigma, length.out=500) myDensity -

[R] error using method ls.ranking.capa.ident

2008-04-08 Thread Hazura Zulzalil
Good Day I'm trying to run the generalized least square approach for my 2-additive problem, unfortunately this error appeared. I have tried to figure out the error from the mailing list but couldn't find the solution. Any help is highly appreciated. This is my source code: a1 - c(76.18, 61.84,

Re: [R] pie graphic

2008-04-08 Thread Jim Lemon
Marco Chiapello wrote: Hi, My problem is: I have many data to plot as pie-chart, so the labels are not readable! Is there a way to solve my problem? For example is it possible move the labels more far to the graphic? Hi Marco, The essence of a pie chart is simplicity. You can do what you

Re: [R] Matching pairs from two data frame

2008-04-08 Thread solea
a so simple solution ... thanks a lot ! Henrique Dallazuanna wrote: Try: merge(DATA1, DATA2) On Mon, Apr 7, 2008 at 11:20 AM, solea [EMAIL PROTECTED] wrote: I am looking for a solution to match 2 dataframes from pairs of values (x and y) as indicated thereafter : First

Re: [R] plotmath overstrikes in output on a Linux system

2008-04-08 Thread Prof Brian Ripley
Looks likes the the laptop is using different fonts with incorrect font metrics. This could happen because it has a different screen resolution, or one of the systems is set to use scalable fonts or it is giving metrics for one fonts and using another or BTW, this is probably nothing to

[R] Legend on plots when using Cairo

2008-04-08 Thread audrey
Dear all, I am trying to use the Cairo package to avoid some X11 issues and it works very well. However, when I want to add a legend to my plots, I receive an error message from Cairo: library(Cairo) CairoPNG(file=test.png) plot(1:100) dev.off() null device 1 This works fine.

[R] question about nlminb

2008-04-08 Thread John Pitchard
Dear All, I wanted to post some more details about the query I sent to s-news last week. I have a vector with a constraint. The constraint is that the sum of the vector must add up to 1 - but not necessarily positive, i.e. x[n] - 1 -(x[1] + ...+x[n-1]) I perform the optimisation on the vector

[R] sample size for log-rank test with more than 2 groups

2008-04-08 Thread Essioux, Laurent
Hi everyone, I was wondering whether extension of the current spower function for Hmisc were existing? My current focus is to calculate sample size based on the log-rank test with more than 2 groups (with/without trend) Taking into account the loss of follow up and the accrual processes. A

Re: [R] How to access the attributes of a ggplot?

2008-04-08 Thread Tribo Laboy
Hi Hadley, Thanks for replying. I know that I can directly modify some of the properties of the plot object, but I was more interested in querying the current plot properties, something like: xlimits - getggopts(pobj, x_scale_limits) Is there anything like this implemented? I tried to drill

[R] Weibull maximum likelihood estimates for censored data

2008-04-08 Thread Nadia Theron
Hello! I have a matrix with data and a column indicating whether it is censored or not. Is there a way to apply weibull and exponential maximum likelihood estimation directly on the censored data, like in the paper: Backtesting Value-at-Risk: A Duration-Based Approach, P Chrisoffersen and D

Re: [R] tapply

2008-04-08 Thread Dimitris Rizopoulos
try this: mat - matrix(rnorm(1000), 100, 10) ind - gl(4, 25) rowsum(mat, ind) / rep(table(ind), each = ncol(mat)) I hope it helps. Best, Dimitris Dimitris Rizopoulos Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium

Re: [R] plotmath overstrikes in output on a Linux system

2008-04-08 Thread Peter Dalgaard
Paul Johnson wrote: I've been testing plotmath. But I'm getting some funny output one one computer. The problem is that characters are 'jumbled' and overstrike when symbols are introduced. Sample code: mu - 440.0 sigma - 12.5 myx - seq( mu - 4*sigma, mu+ 4*sigma, length.out=500)

[R] tapply

2008-04-08 Thread Manuel Montes
Does anyone have something like tapply for matrices? I would like to average the contents of columns according to factors but tapply works only with one column at each time. Is something available to do everything in one step? Many thanks. Manuel Montes

Re: [R] help

2008-04-08 Thread Jim Lemon
Partha Saha wrote: theil inequality measure with sub-group decomposability. Hi Partha, Are you referring to the Gini coefficient? If so, have a look at the ineq and reldist packages. Jim __ R-help@r-project.org mailing list

Re: [R] findGlobals on apply

2008-04-08 Thread Duncan Murdoch
Christophe Genolini wrote: f - function(x){apply(x,2,mean)} findGlobals(f) mean is a global variable, so findGlobals gets it right. That sound strange to me: a variable is something that vary... mean does not vary. maen will ge an argument that is a line of x and will make

Re: [R] How to pack my stuff into a package (library, collection)?

2008-04-08 Thread Uwe Ligges
Tribo Laboy wrote: Thanks all for the help and suggestions. I am little by little finding my way. I have another question to the people who use the R packaging system. Say I have a function called myfun.R. Where am I supposed to write the help to that function? When I use promt(myfun) or

[R] Install spatstat package on gentoo

2008-04-08 Thread Luca Penasa
Anybody know how to install R-spatstat package on a gentoo based system? Thanks you Luca -- Email.it, the professional e-mail, gratis per te: http://www.email.it/f Sponsor: Una BMW Z4 Roadster a 10€? Prova gratis su Bidplaza.it! * Clicca qui:

Re: [R] tapply

2008-04-08 Thread Chuck Cleland
On 4/8/2008 5:14 AM, Manuel Montes wrote: Does anyone have something like tapply for matrices? I would like to average the contents of columns according to factors but tapply works only with one column at each time. Is something available to do everything in one step? Many thanks.

Re: [R] Question Regarding 'pipe'

2008-04-08 Thread Jan T. Kim
On Mon, Apr 07, 2008 at 07:42:50PM -0500, [EMAIL PROTECTED] wrote: Can anyone point out why this is not working? y-read.table(pipe(' awk '{ n = $1; sub( .* $1 ,) ; while ( n-- ) ^ print }' temp.txt ')) ^ one problem is that your single-quoted R string

Re: [R] How to pack my stuff into a package (library, collection)?

2008-04-08 Thread Duncan Murdoch
Yesterday I wrote: I took a look at this today. You get an error message but the package is still installed without the CHM compiler, so that's less urgent. I did add a menu entry to install a source package from a directory: Packages | Install source package from local folder... to the

Re: [R] Legend on plots when using Cairo

2008-04-08 Thread Prof Brian Ripley
Why are you using Cairo 'to avoid some X11 issues' for an unreleased version of R that does not use X11 for its png() device? I see this under Cairo, but not under png(type =cairo) (the default). The R posting guide asked you to discuss package problems with the maintainer, so if you have not

[R] question about nlminb

2008-04-08 Thread John Pitchard
Dear All, I wanted to post some more details about the query I sent to s-news last week. I have a vector with a constraint. The constraint is that the sum of the vector must add up to 1 - but not necessarily positive, i.e. x[n] - 1 -(x[1] + ...+x[n-1]) I perform the optimisation on the vector

Re: [R] findGlobals on apply

2008-04-08 Thread Gabor Grothendieck
I think what he is referring to is that findGlobals lists mean under variables rather than functions when you do this with his f: findGlobals(f, FALSE) $functions [1] { apply $variables [1] mean On Tue, Apr 8, 2008 at 7:14 AM, Duncan Murdoch [EMAIL PROTECTED] wrote: Christophe Genolini

Re: [R] findGlobals on apply

2008-04-08 Thread Luke Tierney
On Tue, 8 Apr 2008, Christophe Genolini wrote: f - function(x){apply(x,2,mean)} findGlobals(f) mean is a global variable, so findGlobals gets it right. That sound strange to me: a variable is something that vary... mean does not vary. maen will ge an argument that is a line of x and will

Re: [R] Question Regarding 'pipe'

2008-04-08 Thread born . to . b . wyld
Reason, I need to do this in awk and not R: Let's say 'x' is the tabular representation of a sparse contingency table x x10 x11 x12 x13 x14 x15 x16 x17 x18 x19 Freq 10 0 0 2 2 2 0 2 0 2 54 51 0 0 2 2 2 0 2 1 21 61 0 1 0 2 2 0

Re: [R] sample size for log-rank test with more than 2 groups

2008-04-08 Thread Frank E Harrell Jr
Essioux, Laurent wrote: Hi everyone, I was wondering whether extension of the current spower function for Hmisc were existing? My current focus is to calculate sample size based on the log-rank test with more than 2 groups (with/without trend) Taking into account the loss of follow up

Re: [R] Install spatstat package on gentoo

2008-04-08 Thread Uwe Ligges
Luca Penasa wrote: Anybody know how to install R-spatstat package on a gentoo based system? Same as on any other system, see the manual R Installation and Administration and please do read the posting guide. Best, Uwe Ligges Thanks you Luca -- Email.it, the professional e-mail,

[R] Metropolis acceptance rates

2008-04-08 Thread Michael Margolis
Is there a way to recover Metropolis-step acceptance rates AFTER completing posterior draws? The immediate application is in the probit.bayes and logit.bayes models used by Zelig... which I believe is merely calling MCMCpack. So one strategy, to which I am fixing to resort, is to call, say,

Re: [R] How to pack my stuff into a package (library, collection)?

2008-04-08 Thread Duncan Murdoch
On 08/04/2008 7:08 AM, Tribo Laboy wrote: Thanks all for the help and suggestions. I am little by little finding my way. I have another question to the people who use the R packaging system. Say I have a function called myfun.R. I guess you mean you have a source file myfun.R, containing a

Re: [R] How to pack my stuff into a package (library, collection)?

2008-04-08 Thread Tribo Laboy
okey-dokey, one more problem resolved. Keeping one documentation .Rd file for each R source file. Thanks! TL __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] permutation test assumption?

2008-04-08 Thread João Fadista
Dear all, Can I do a permutation test if the number of individuals in one group is much bigger than in the other group? I searched the literature but I didin´t find any assumption that refers to this subject for permutation tests. Best regards João Fadista Ph.d. student

Re: [R] permutation test assumption?

2008-04-08 Thread ONKELINX, Thierry
Dear João, You can do permutation tests on an unbalanced design. HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en

[R] basehaz and newdata

2008-04-08 Thread Terry Therneau
The 'basehaz' function is just a wrapper for survfit, and includes only some of the arguments of the former. It's main reason for existence is that another more well known (but inferior :-) package uses that term. I don't understand the final comment in the exchange, however: I had been

[R] Change the position of panel strips in a lattice plot.

2008-04-08 Thread Gustaf Rydevik
Hi all, In lattice plots, is there any option to position the panel strips with text below each subgraph, instead of above? i.e. in: Depth - equal.count(quakes$depth, number=8, overlap=.1) xyplot(lat ~ long | Depth, data = quakes) ,is there any way to make Depth appear below the subgraphs,

Re: [R] How to access the attributes of a ggplot?

2008-04-08 Thread hadley wickham
Thanks for replying. I know that I can directly modify some of the properties of the plot object, but I was more interested in querying the current plot properties, something like: xlimits - getggopts(pobj, x_scale_limits) Is there anything like this implemented? Ah, that's much more

[R] Practical Data Limitations with R

2008-04-08 Thread Jeff Royce
We are new to R and evaluating if we can use it for a project we need to do. We have read that R is not well suited to handle very large data sets. Assuming we have the data prepped and stored in an RDBMS (Oracle, Teradata, SQL Server), what can R reasonably handle from a volume perspective?

Re: [R] Practical Data Limitations with R

2008-04-08 Thread ajay ohri
Dear Jeff, R works fine for 22 rows that i tested on a home PC with XP . Memory is limited to hardware that you have. I suggest beefing up RAM to 2 GB and hard disk space and then working it out. I evaluated R too on my site www.decisionstats.com and I found it comparable if not better to

Re: [R] Practical Data Limitations with R

2008-04-08 Thread Philipp Pagel
On Tue, Apr 08, 2008 at 09:26:22AM -0500, Jeff Royce wrote: We are new to R and evaluating if we can use it for a project we need to do. We have read that R is not well suited to handle very large data sets. Assuming we have the data prepped and stored in an RDBMS (Oracle, Teradata, SQL

Re: [R] Question Regarding 'pipe'

2008-04-08 Thread Jan T. Kim
On Tue, Apr 08, 2008 at 06:52:33AM -0500, [EMAIL PROTECTED] wrote: Reason, I need to do this in awk and not R: Let's say 'x' is the tabular representation of a sparse contingency table x x10 x11 x12 x13 x14 x15 x16 x17 x18 x19 Freq 10 0 0 2 2 2 0 2 0 2 54 51

[R] how to check if a variable is preferentially present in a sample

2008-04-08 Thread Tania Oh
Dear All, I do apologise if this question is out of place for this list but I've tried searching mailing lists and read Introductory Statistics with R by Peter Dalgaard, but couldn't find any hints on solving my question below: I have a data frame (d) of values which I will rank in

Re: [R] Practical Data Limitations with R

2008-04-08 Thread hadley wickham
We are new to R and evaluating if we can use it for a project we need to do. We have read that R is not well suited to handle very large data sets. Assuming we have the data prepped and stored in an RDBMS (Oracle, Teradata, SQL Server), what can R reasonably handle from a volume

[R] Help me about singular error nls

2008-04-08 Thread jarod_v6
Dear List I have that problem: this is file : PBS.txt TimeRFU 0. 27.3021 0.0800 26.1565 0.1600 25.4836 0.2400 25.2104 0.3200 24.7967 0.4000 24.6310 0.4800 24.3472 0.5600 24.2905 0.6400 24.1394 0.7200 24.0244 0.8000 23.8532 0.8800 23.7908 0.9600 23.6668 1.0400 23.7458 1.1200

Re: [R] Change the position of panel strips in a lattice plot.

2008-04-08 Thread Deepayan Sarkar
On 4/8/08, Gustaf Rydevik [EMAIL PROTECTED] wrote: Hi all, In lattice plots, is there any option to position the panel strips with text below each subgraph, instead of above? No. -Deepayan i.e. in: Depth - equal.count(quakes$depth, number=8, overlap=.1) xyplot(lat ~ long | Depth,

Re: [R] re garding Garch prediction mechanism

2008-04-08 Thread Spencer Graves
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. In particular, I suggest you use a published data set from a package like tseries, fEcofin, or FinTS. If you want to compare results with

[R] RSPerl threads

2008-04-08 Thread J Greenbaum
Hi all, I'm trying to use the RSPerl module in a script that uses threads. I am able to call R functions without a problem when I don't use threads. However, using threads, I get varying errors depending on how I call the R functions. If I call the R::initR function in the boss thread and then

[R] RSPerl threads II

2008-04-08 Thread J Greenbaum
My previous post seems to have been eaten by the server because of embedded code. You can now find that code at: http://tinyurl.com/3o88j2 I aoplogize for the double-posting... -Jay Hi all, I'm trying to use the RSPerl module in a script that uses threads. I am able to call R functions

Re: [R] Practical Data Limitations with R

2008-04-08 Thread Sankalp Upadhyay
Millions of rows can be a problem if all is loaded into memory, depending on type of data. Numeric should be fine but if you have strings and you would want to process based on that column (string comparisons etc) then it would be slow. You may want to combine sources outside - stored

Re: [R] post hoc statistical power

2008-04-08 Thread Charles C. Berry
On Tue, 8 Apr 2008, Yuelin Li wrote: I remember reading about post hoc statistical power on R-help. But I can't seem to find them with RSiteSearch(post hoc statistical power) and variations of it. I would like to learn more about post hoc statistical power, its meaningfulness, advantages

Re: [R] Help me about singular error nls

2008-04-08 Thread Dieter Menne
jarod_v6 jarod_v6 at libero.it writes: I have that problem: this is file : PBS.txt Time RFU 0.27.3021 0.080026.1565 rm(list=ls()) print(ls()) #carica Dati con file di testo b -read.table(PBS.txt, sep=\t, header= TRUE) print(b) b nlmod1 - nls(RFU ~ A +

Re: [R] findGlobals on apply

2008-04-08 Thread Gabor Grothendieck
Yes, based on that it seems understandable although initially suprising. On Tue, Apr 8, 2008 at 12:56 PM, Duncan Murdoch [EMAIL PROTECTED] wrote: On 4/8/2008 7:42 AM, Gabor Grothendieck wrote: I think what he is referring to is that findGlobals lists mean under variables rather than

Re: [R] Metropolis acceptance rates

2008-04-08 Thread Anup Nandialath
Hi Michael, If you are using the standard logit or probit model, it is fairly easy to save the acceptance rate after each draw. I would recommend using the bayesm package as the source code is easy to manipulate. For instance in the probit function (rbprobitGibbs), you need to include a

Re: [R] lme and confidence intervals

2008-04-08 Thread Dieter Menne
Cristian Carranza cristiancarranza_1 at hotmail.com writes: After fitting a mixed effects model to repeated measurements data set, and after several unsuccessful atempts to make a simple plot of the confidence interval for the fitted model, I gave up and now I am asking for help in this useful

[R] plot function / par() settings

2008-04-08 Thread Pedro Mardones
Dear all; I'm trying to create a 2 x 3 plot (something I know like lattice can do better) using the plot function. However; I'm not sure how to make the width of the plots to be the same on each column. I guess the answer maybe obvious but I haven't been able to figure it out. I'll appreciate any

Re: [R] plotmath overstrikes in output on a Linux system

2008-04-08 Thread Paul Johnson
On Tue, Apr 8, 2008 at 4:29 AM, Prof Brian Ripley [EMAIL PROTECTED] wrote: Looks likes the the laptop is using different fonts with incorrect font metrics. This could happen because it has a different screen resolution, or one of the systems is set to use scalable fonts or it is giving metrics

[R] fit points to plane

2008-04-08 Thread Luca Penasa
Is there a function for obtaining the best-fitting plane from a large number of points (something like 25.000 points)? Thank you... Luca -- Email.it, the professional e-mail, gratis per te: http://www.email.it/f Sponsor: Gioca con i Supereroi Marvel sul cellulare! Clicca qui:

[R] diagonally fill a rectangle with color gradient

2008-04-08 Thread tom soyer
Hi, Is it possible to diagonally fill a rectangle with a color gradient? I noticed that the gradient.rect of plotrix could fill a rect either up and down or from side to side. I am looking for something similar but fills diagonally instead, e.g., from the upper left corner to the bottom right.

[R] distance matrix as text file - how to import?

2008-04-08 Thread Hans-Jörg Bibiko
Dear all, I have -hopefully- a tiny problem. I was sent a text file containing a distance matrix à la: 1 2 3 4 5 6 Now I wanted to import these data into a dist object to, let's say, do 'plot(hclust(v))'. My first naïve approach was to scan the text file in order to get a vector v. Then I

[R] Combining many csv files into one and adding a column with an id of each csv file read

2008-04-08 Thread Judith Flores
Dear R experts, I have been looking into the help-pages and old questions from the R-Help site, but the options offered there don't seem to work in my case. First of all, I am working on Windows XP, using R version 2.6.2. I am attaching two csv files as an example of how the data I am

[R] reading in a Fortran binary array

2008-04-08 Thread Alexy Khrabrov
Greetings -- I'd like to avoid converting a Fortran array of floats into ASCII and back reading it in R. Furthermore it's much faster to dump large arrays in binary, as they take up much less space with full precision -- many decimal points take up many bytes in ASCII versus four or eight

[R] simple graphing question

2008-04-08 Thread stephen sefick
#copy and paste this into R f - (structure(list(TKN = c(0.103011025, 0.018633208, 0.104235702, 0.074537363, 0.138286096), RM = c(215, 198, 148, 119, 61)), .Names = c(TKN, RM), class = data.frame, row.names = 25:29)) plot(f$TKN~f$RM, type=b) I would like to reverse the X-Axis. How do I do this?

Re: [R] plot function / par() settings

2008-04-08 Thread Paul Johnson
On Tue, Apr 8, 2008 at 12:47 PM, Pedro Mardones [EMAIL PROTECTED] wrote: Dear all; I'm trying to create a 2 x 3 plot (something I know like lattice can do better) using the plot function. However; I'm not sure how to make the width of the plots to be the same on each column. I guess the

Re: [R] simple graphing question

2008-04-08 Thread Henrique Dallazuanna
Try: plot(f$RM~f$TKN, type=b) On Tue, Apr 8, 2008 at 4:18 PM, stephen sefick [EMAIL PROTECTED] wrote: #copy and paste this into R f - (structure(list(TKN = c(0.103011025, 0.018633208, 0.104235702, 0.074537363, 0.138286096), RM = c(215, 198, 148, 119, 61)), .Names = c(TKN, RM), class =

Re: [R] simple graphing question

2008-04-08 Thread stephen sefick
On Tue, Apr 8, 2008 at 3:52 PM, stephen sefick [EMAIL PROTECTED] wrote: Sorry, to have the x-axis to go from 200 to 0 or to reverse the x points- the line starts on the left hand side of the graph at x=215, y=0.10301103 ... and end with x=61, y=0.13828610. does this make sense?

Re: [R] simple graphing question

2008-04-08 Thread benlafleche
This is maybe not the most elegant way, but it does de job. You first put f$RM values in negative form. Then you plot your graph without the x axis labels. After, you create the labels you want. Try this : f - (structure(list(TKN = c(0.103011025, 0.018633208, 0.104235702, 0.074537363,

Re: [R] fit points to plane

2008-04-08 Thread Rolf Turner
On 9/04/2008, at 8:28 AM, Luca Penasa wrote: Is there a function for obtaining the best-fitting plane from a large number of points (something like 25.000 points)? ?lm ## Attention:\ This e-mail message is privileged and

[R] Split

2008-04-08 Thread Kris Ghosh
I have data in the form of a column such as 1234. 2345. 3435. 4343. I want to have the data in this form ..i.e to remove the dot at the end of each number above. 1234 2345 3435 4343 I am trying to use split but it is not working. Any suggestions? [[alternative HTML version deleted]]

[R] save multiple pages lattice-plot

2008-04-08 Thread Katell HAMON
Dear R-helper, I am trying to save some plots I made with lattice, but I have several pages printed for each call. My layout is something like c(col=2,row=4,pages=12) and I didn't find a way to save those plots, because I am usually using savePlot() which from what I saw can only save one

[R] Separate y-limits in xYplot panels II

2008-04-08 Thread John Poulsen
Hello, I have been trying to use xYplot in Hmisc to graph plots, allowing each panel to have a y-axis dependent on the data in the panel. Following the advice from the R-Help list, message: [R] separate y-limits in xYplot panels on Wed, 30 May 2007 08:12:06 -0700 (PDT), I used

[R] Problem with NA data when computing standard error

2008-04-08 Thread LeCzar
Hey, I want to compute means and standard errors as two tables like this: se-function(x)sqrt(var(x)/length(x)) object1-as.data.frame.table(tapply(Data[Year==1999],na.rm=T,list(Group[Year==1999],Season[Year==1999]),mean))

Re: [R] fit points to plane

2008-04-08 Thread Bert Gunter
But probably not a good idea, as there are likely to be some scientfically interesting local inhomogeneities that an appropriate nonparametric smoother (e.g. splines,...) could reveal. -- Bert Gunter -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Rolf

Re: [R] simple graphing question

2008-04-08 Thread Paul Johnson
On Tue, Apr 8, 2008 at 2:18 PM, stephen sefick [EMAIL PROTECTED] wrote: #copy and paste this into R f - (structure(list(TKN = c(0.103011025, 0.018633208, 0.104235702, 0.074537363, 0.138286096), RM = c(215, 198, 148, 119, 61)), .Names = c(TKN, RM), class = data.frame, row.names = 25:29))

[R] Smoothing 3 D data

2008-04-08 Thread Ruby_Stanford
Hey. I have a set of data points (x1,y1,z1; x2,y2,z2;...xn,yn,zn). I need to smooth these in 3D. For example if these were in 2 D then one would use inverse distance weighting or moving averages. Does anyone know of any funtion in R that can be used to do this (Using 3D

Re: [R] diagonally fill a rectangle with color gradient

2008-04-08 Thread Paul Murrell
Hi tom soyer wrote: Hi, Is it possible to diagonally fill a rectangle with a color gradient? I noticed that the gradient.rect of plotrix could fill a rect either up and down or from side to side. I am looking for something similar but fills diagonally instead, e.g., from the upper left

Re: [R] fit points to plane

2008-04-08 Thread Luca Penasa
Rolf Turner wrote: On 9/04/2008, at 8:28 AM, Luca Penasa wrote: Is there a function for obtaining the best-fitting plane from a large number of points (something like 25.000 points)? ?lm what does it mean? ##

Re: [R] fit points to plane

2008-04-08 Thread Luca Penasa
Bert Gunter wrote: But probably not a good idea, as there are likely to be some scientfically interesting local inhomogeneities that an appropriate nonparametric smoother (e.g. splines,...) could reveal. ok... im working on laser scanner cloud of points... the model im working with is

Re: [R] how to check if a variable is preferentially present in a sample

2008-04-08 Thread Jorge Velez
Hi Tania, I think it could be. I tried a solution based on your data set using a chi-squared approach. Here is what I got: # # Data set set.seed(123) d - data.frame(cbind(val=rnorm(1:10)^2, group=sample(LETTERS[1:5],100,repl=TRUE))) d[,val]-as.numeric(as.character(d$val)) #

Re: [R] distance matrix as text file - how to import?

2008-04-08 Thread Paul Johnson
On Tue, Apr 8, 2008 at 1:50 PM, Hans-Jörg Bibiko [EMAIL PROTECTED] wrote: Dear all, I have -hopefully- a tiny problem. I was sent a text file containing a distance matrix à la: 1 2 3 4 5 6 Try this! I put your test data in text.txt and voila: mat - matrix(0, 3,3) mat[row(mat) =

Re: [R] Problem with NA data when computing standard error

2008-04-08 Thread Jorge Velez
Hi there, Perhaps se-function(x)sqrt(var(x,na.rm=T)/sum(!is.na(x))) object1-as.data.frame.table(tapply(Data[Year==1999],list(Group[Year==1999],Season[Year==1999]),mean)) object2-as.data.frame.table(tapply(Data[Year==1999],list(Group[Year==1999],Season[Year==1999]),se)) Hope this helps, Jorge

Re: [R] reading in a Fortran binary array

2008-04-08 Thread Prof Brian Ripley
See ?readBin The format of a Fortran unformatted file is compiler- and OS-dependent, but if you know what it is, readBin() can read it. On Tue, 8 Apr 2008, Alexy Khrabrov wrote: Greetings -- I'd like to avoid converting a Fortran array of floats into ASCII and back reading it in R.

Re: [R] save multiple pages lattice-plot

2008-04-08 Thread Deepayan Sarkar
On 4/8/08, Katell HAMON [EMAIL PROTECTED] wrote: Dear R-helper, I am trying to save some plots I made with lattice, but I have several pages printed for each call. My layout is something like c(col=2,row=4,pages=12) and I didn't find a way to save those plots, because I am usually using

Re: [R] Problem with NA data when computing standard error

2008-04-08 Thread Paul Johnson
On Tue, Apr 8, 2008 at 12:44 PM, LeCzar [EMAIL PROTECTED] wrote: Hey, I want to compute means and standard errors as two tables like this: se-function(x)sqrt(var(x)/length(x)) The missings are not your main problem. The command var computes the variance-covariance matrix. Some

Re: [R] findGlobals on apply

2008-04-08 Thread Christophe Genolini
Hi Luke Thanks for all these explanation, things are clearer. Let me go back on my initial problem, that was, as a programmer, I would like to have a tool to detect typo by detecting globals variables: I get that findGlobals is not design for that. I did not realy understand the use of

Re: [R] permutation test assumption?

2008-04-08 Thread João Fadista
Dear Thierry, Thanks for the reply. But as you may read in the paper http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/18/2244 when the sample sizes are not the same there may be an increase in the Type I error rate. Comments will be appreciated. Best regards, João Fadista

Re: [R] permutation test assumption?

2008-04-08 Thread Achim Zeileis
On Wed, 9 Apr 2008, João Fadista wrote: Dear Thierry, Thanks for the reply. But as you may read in the paper http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/18/2244 when the sample sizes are not the same there may be an increase in the Type I error rate. No, this is false

[R] Overlapping distributions (populations) - assigning an individual to a population?

2008-04-08 Thread Phil Rhoades
People, Say a particular measure of an attribute for individuals in different populations gives a set of overlapping normal distributions (one distribution per population). If I then measure this attribute in a new individual - how do I assess the likelihood of this new individual belonging to

[R] Separate y-limits in xYplot panels II

2008-04-08 Thread John Poulsen
Hello, I have been trying to use xYplot in Hmisc to graph plots, allowing each panel to have a y-axis dependent on the data in the panel. Following the advice from the R-Help list, message: [R] separate y-limits in xYplot panels on Wed, 30 May 2007 08:12:06 -0700 (PDT), I used

Re: [R] permutation test assumption?

2008-04-08 Thread João Fadista
But in that paper they refer to another (http://www.bepress.com/cgi/viewcontent.cgi?article=1053context=ucbbiostat) where they say that permutation distribution produces an asymptotically correct null distribution if (i) the sample sizes are equal Best regards, João

Re: [R] findGlobals on apply

2008-04-08 Thread Luke Tierney
On Wed, 9 Apr 2008, Christophe Genolini wrote: Hi Luke Thanks for all these explanation, things are clearer. Let me go back on my initial problem, that was, as a programmer, I would like to have a tool to detect typo by detecting globals variables: I get that findGlobals is not design for

Re: [R] Separate y-limits in xYplot panels II

2008-04-08 Thread Christoph Meyer
Hi John, I think even with scales=list(y=list(relation=free) you have to specify the y-limits for each panel, i.e. add something like ylim=list(c(0,1200),c(0,1)) to your code. Best regards, Christoph Wednesday, April 9, 2008, 12:37:43 AM, you wrote: Hello, I have been trying to use

Re: [R] Combining many csv files into one and adding a column with an id of each csv file read

2008-04-08 Thread jim holtman
Here is one way of doing it. Read the data into a list and then use 'do.call(rbind...': filenames - Sys.glob(*.csv) # however you get the list of file allData - lapply(filenames, function(.file){ dat-read.csv(filename, header=F) dat-dat[c(-1:-3),c(-1,-4,-5,-6,-7,-9,-10,-11,-12)]

Re: [R] Combining many csv files into one and adding a column with an id of each csv file read

2008-04-08 Thread jim holtman
I blew it. Forgot to use the parameter. Here is the revised copy: filenames - Sys.glob(*.csv) # however you get the list of file allData - lapply(filenames, function(.file){ dat-read.csv(.file, header=F) dat-dat[c(-1:-3),c(-1,-4,-5,-6,-7,-9,-10,-11,-12)]

Re: [R] Split

2008-04-08 Thread jim holtman
Assuming that this data is character, then this will work: (it removes the last period in the string) x - scan('clipboard', what='') Read 4 items x [1] 1234. 2345. 3435. 4343. sub(\\.$, , x) [1] 1234 2345 3435 4343 On Tue, Apr 8, 2008 at 11:30 AM, Kris Ghosh [EMAIL PROTECTED] wrote: I have

Re: [R] permutation test assumption?

2008-04-08 Thread Achim Zeileis
On Wed, 9 Apr 2008, João Fadista wrote: But in that paper they refer to another (http://www.bepress.com/cgi/viewcontent.cgi?article=1053context=ucbbiostat) where they say that permutation distribution produces an asymptotically correct null distribution if (i) the sample sizes are equal

Re: [R] preferred version of Linux for R?

2008-04-08 Thread Simon Blomberg
There are binaries on CRAN for several distros. There is the R-sig-debian list for debian users. As far as I know, there are no mailing lists for other distros. This may indicate a preference for debian among R users. Or it may mean that debian is so difficult to use with R that it requires a

Re: [R] preferred version of Linux for R?

2008-04-08 Thread Mitchell Maltenfort
If your criterion is use of resources, then you might be more interested in which flavor of Linux makes it easy to turn the X-window server off. No windows or mouse, more RAM and CPU cycles for R. As I recall, the only Linux where that might be a problem is Ubuntu, because there's no convenient

[R] chi-square test

2008-04-08 Thread Roslina Zakaria
Hi R-users, I would like to find the goodness of fit using Chi-suare test for my data below: xobs=observed data, xtwe=predicted data using tweedie, xgam=predicted data using gamma xobs - c(223,46,12,5,7,17) xtwe - c(217.33,39,14,18.33,6.67,14.67) xgam - c(224.67,37.33,12.33,15.33,5.33,15)

Re: [R] Overlapping distributions (populations) - assigning an individual to a population?

2008-04-08 Thread Phil Rhoades
Rolf, On Wed, 2008-04-09 at 10:57 +1200, Rolf Turner wrote: On 9/04/2008, at 10:30 AM, Phil Rhoades wrote: People, Say a particular measure of an attribute for individuals in different populations gives a set of overlapping normal distributions (one distribution per population). If

Re: [R] post hoc statistical power

2008-04-08 Thread John Fox
Dear Yuelin, Another paper critical of post-hoc power calculations is Hoenig and Heisey, 2001. The Abuse of Power: The Pervasive Fallacy of Power Calculations for Data Analysis. The American Statistician, 55, 19-24. Hoenig and Heisey show that so-called observed power is simply a re-expression of

Re: [R] Overlapping distributions (populations) - assigning an individual to a population?

2008-04-08 Thread Ruben Roa Ureta
Rolf, On Wed, 2008-04-09 at 10:57 +1200, Rolf Turner wrote: On 9/04/2008, at 10:30 AM, Phil Rhoades wrote: People, Say a particular measure of an attribute for individuals in different populations gives a set of overlapping normal distributions (one distribution per population).

Re: [R] preferred version of Linux for R?

2008-04-08 Thread Dirk Eddelbuettel
On 8 April 2008 at 19:06, Mitchell Maltenfort wrote: | If your criterion is use of resources, then you might be more | interested in which flavor of Linux makes it easy to turn the X-window | server off. No windows or mouse, more RAM and CPU cycles for R. As I | recall, the only Linux where

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