Re: [R] The Origins of R AND CALCULUS

2009-02-05 Thread Wacek Kusnierczyk
Ajay ohri wrote: An amusing afterthought : What is a rival software (ahem!) was planting this, hoping for a divide between S and R communities.or at the very minimum hoping for some amusement. an assumption or even a pretense of stealing credit is one of the easiest ways of sparking

[R] R memory usage and size limits

2009-02-05 Thread Tom Quarendon
I have a general question about R's usage or memory and what limits exist on the size of datasets it can deal with. My understanding was that all object in a session are held in memory. This implies that you're limited in the size of datasets that you can process by the amount of memory you've

Re: [R] Problem installing ad administrating packages

2009-02-05 Thread Birgitle
It is also not possible if I use this commands install.packages(analogue,/Library/Frameworks/R.framework/Versions/2.8/Resources/library,repos=http://R-Forge.R-project.org;) Fehler in .readRDS(pfile) : unbekanntes Eingabeformat Error in .readRDS(pfile) : unknown enter format also

Re: [R] The Origins of R AND CALCULUS

2009-02-05 Thread Thomas Lumley
Wacek, If you have bug reports for a contributed package please take them up with the maintainer, not the list. -thomas On Thu, 5 Feb 2009, Wacek Kusnierczyk wrote: Ajay ohri wrote: An amusing afterthought : What is a rival software (ahem!) was planting this, hoping for a divide

Re: [R] Sweave and \Sexpr{}

2009-02-05 Thread Dieter Menne
Felipe Carrillo mazatlanmexico at yahoo.com writes: I am trying to create a dynamic latex table using \Sexpr{} but it's not evaluating it. I also tried the example below without Sweave and also fails. I have also copied the Sweave.sty to my working directory but nothing seems to work. Do I

Re: [R] Sweave and \Sexpr{}

2009-02-05 Thread Eric R.
Felipe: See Leisch's FAQ A18. http://www.statistik.lmu.de/~leisch/Sweave/FAQ.html#x1-2A.18 You likely have R2HTML loaded (likely because you are using Tinn-R) and that causes some difficulties for Sweave that are easily solved as described in the FAQ. Felipe Carrillo wrote: Hi: I

[R] eliminating control characters from formatted data files

2009-02-05 Thread David Epstein
I have a few hundred files of formatted data. Unfortunately most of them end with a spurious CONTROL-Z. I want to rewrite the files without the spurious character. Here's what I've come up with so far, but my code is unsafe because it assumes without justification that the last row of df contains

Re: [R] R memory usage and size limits

2009-02-05 Thread Prof Brian Ripley
Please read ?Memory-limits and the R-admin manual for basic information. On Thu, 5 Feb 2009, Tom Quarendon wrote: I have a general question about R's usage or memory and what limits exist on the size of datasets it can deal with. My understanding was that all object in a session are held in

Re: [R] The Origins of R AND CALCULUS

2009-02-05 Thread Mark Difford
If you have bug reports for a contributed package please take them up with the maintainer, not the list. Of course, Wacek is right. His observations being made with a customary needle-like precision. It's that old conundrum about how to have your cake and still eat it. Regards to all, Mark.

Re: [R] non linear regression with nls

2009-02-05 Thread lauramorg...@bluewin.ch
Thank you a lot Mr. Ritz! I've tried the loop you suggested and I added a list for lower and upper limits of the parameters, but there is still a problem... I have a list of functions, which works... fz1-function(Portata, a, b){a+(b/Portata)} fz2-function(Portata, a, b){a*exp(b*Portata)}

[R] UNIX Installation of package systemfit fails

2009-02-05 Thread Yong Wang
Dear list I am trying to install the systemfit package under unix, install.packages(systemfit) the installation failed. I am attaching the error and version information below, (if dependencies=TRUE, much more error) any help appreciated best, yong

Re: [R] non linear regression with nls

2009-02-05 Thread lauramorg...@bluewin.ch
Hello, thanks for the advice of nlsList! I tried to look at the help page of nlsList, but I didnt understand how to use the subset argument of the function and it's not clear to me if this only allows you to choose one subset or if it run the regression for every given subset, in this case how

Re: [R] UNIX Installation of package systemfit fails

2009-02-05 Thread Uwe Ligges
Please read your output which tells you several times: Try removing '/usr/home/d/068/wangyong/R/x86_64-unknown-linux-gnu-library/2.7/00LOCK' Uwe Ligges Yong Wang wrote: Dear list I am trying to install the systemfit package under unix, install.packages(systemfit) the installation

[R] help regarding storing time difference values in same unit?

2009-02-05 Thread Suresh_FSFM
Dear R-Experts, Seek your help. In a List object e.g. Time_duration[[]], I am storing differece between two time-stamps (start-time and end-time) for a certain event. Time difference does not remain constant for, say, 10 observations. Each time, the time difference is given in different time

Re: [R] The Origins of R AND CALCULUS

2009-02-05 Thread Richard . Cotton
Does any student, or teacher for that matter care whether Newton or Leibntiz invented calculas. Students or teachers may not care, but Newton and Leibniz themselves were pretty bitter about who should get credit for what. http://en.wikipedia.org/wiki/Newton_v._Leibniz_calculus_controversy I

[R] How to do ICC

2009-02-05 Thread pgseye
Hi, I'm essentially wanting to calculate intra- and inter-observer variabilities for the first principal component of an optic disc shape measure of a sample of individuals, so from what I can work out I need to work out an intraclass correlation coefficient(s). For the intra-data, I have 2

Re: [R] How do I get my IT department to bless R?

2009-02-05 Thread S Ellison
Rolf: I'm in the odd position of having run the modest IT department at my lab for five years, which (when I took it over) included my small statistics team, since split out. So I'm a gamekeeper turned poacher. Stavros wasn't wrong; these are all genuine issues for an IT manager. I can think of a

Re: [R] Problem installing ad administrating packages

2009-02-05 Thread Birgitle
Solved: I reinstalled R 2.8.1. B. Birgitle wrote: It is also not possible if I use this commands install.packages(analogue,/Library/Frameworks/R.framework/Versions/2.8/Resources/library,repos=http://R-Forge.R-project.org;) Fehler in .readRDS(pfile) : unbekanntes Eingabeformat Error

[R] split dataset randomly in prediction and validation set

2009-02-05 Thread Els Verfaillie
For a geostatistical analysis, I would like to split my dataset randomly into 2 parts: a prediction set (with 2/3 of my data) and a validation set (with 1/3 of my data). Both datasets will thus contain different data. Any suggestions? [[alternative HTML version deleted]]

[R] basic question: Linear model

2009-02-05 Thread Stefan Kraemer
Hey, I try to understand a basic statistic question. I am modelling a linear regression Y=X*B+E. To compute the effect of “group” the B-values of the regressors/columns that code the interaction effects (col. 5-8 and col. 11-14, see below) have to be weighted with non-zero elements within the

[R] Chi-squared test adjusted for multiple comparisons? Harbe's test?

2009-02-05 Thread Laura Lucia Prieto Godino
Hi! I have some data that looks like this up downpercentaje uew_21 20 14 58.82 uew_20_527 40 40.29 uew_20 8 13 38.09 uew_19_517 42 28.81 So I have 4 experimental conditions and I am counting number of animals in the up and

[R] Unexpected mfrow, layout behavior (pdf still has multiple pages)

2009-02-05 Thread Paul Johnston
My goal is to create a graph with one column and three rows into a single graphic. The mfrow, mfcol, and layout functions all have the same effect: three graphs are produced in a single pdf file, having one graph per page. This is not what I want (I didn't want multiple pages). Just before I

Re: [R] UNIX Installation of package systemfit fails

2009-02-05 Thread Peter Dalgaard
Yong Wang wrote: Dear list I am trying to install the systemfit package under unix, install.packages(systemfit) the installation failed. I am attaching the error and version information below, (if dependencies=TRUE, much more error) any help appreciated ERROR: failed to lock

[R] confidence interval for roc curves

2009-02-05 Thread marc bernard
Dear all, I am looking for an R package that allows me to calculate and plot the confidence limits for the roc curve using for example some bootstrapping. I tried ROCR who seems doing such work but i couldn't find the right option to do it. Many thanks Bests Marc

[R] Roc curves confidence intervals

2009-02-05 Thread marc bernard
Dear all, I am looking for an R package that allows me to calculate and plot the confidence intervals for the roc curve using for example some bootstrapping. I tried ROCR who seems doing such work but i couldn't find the right option in it. Many thanks Bests Marc

Re: [R] The Origins of R AND CALCULUS

2009-02-05 Thread Peter Dalgaard
Mark Difford wrote: It would have been very easy for Mr. Vance to have written: John M. Chambers, a former Bell Labs researcher who is now a consulting professor of statistics at Stanford University, was an early champion. At Bell Labs, Mr. Chambers had helped develop S, THE PROTOTYPE OF R,

Re: [R] Unexpected mfrow, layout behavior (pdf still has multiple pages)

2009-02-05 Thread Peter Dalgaard
Paul Johnston wrote: My goal is to create a graph with one column and three rows into a single graphic. The mfrow, mfcol, and layout functions all have the same effect: three graphs are produced in a single pdf file, having one graph per page. This is not what I want (I didn't want multiple

Re: [R] help regarding storing time difference values in same unit?

2009-02-05 Thread jim holtman
If you are using 'difftime', you can specify the units: x - as.POSIXct(c('2009-01-01 10:00', '2009-03-04 13:00')) x [1] 2009-01-01 10:00:00 GMT 2009-03-04 13:00:00 GMT difftime(x[2], x[1]) Time difference of 62.125 days difftime(x[2], x[1], units='secs') Time difference of 5367600 secs On

[R] maptools: Test if point is in polygon

2009-02-05 Thread Aleksandr Andreev
In R's maptools package, is there a built-in function to test if a given point is inside a given polygon on the map? The map was loaded from an ESRI Shapefile. The point's latitude and longitude are known. Thank you! Aleks -- Aleksandr Andreev Fulbright Fellow

[R] plotrix::thigmophobe could usefully coerce to numeric...

2009-02-05 Thread S Ellison
thigmophobe.labels() fails with error when supplied with an array resulting from tapply (example below). The error originates in thigmophobe() I know the help page says 'numeric vector' but it would be kind of nice if it worked with numeric things of class array too. I think it would need no

Re: [R] question about running multiple R windows

2009-02-05 Thread milton ruser
On Thu, Feb 5, 2009 at 6:31 AM, Uwe Ligges lig...@statistik.tu-dortmund.dewrote: milton ruser wrote: Dear George, I think it will depends on the amount of memory that each your session will need. Case each session use a big amount of memory, may be your some of your sessions will get

Re: [R] question about running multiple R windows

2009-02-05 Thread Uwe Ligges
milton ruser wrote: Dear George, I think it will depends on the amount of memory that each your session will need. Case each session use a big amount of memory, may be your some of your sessions will get error. I also think that you will not save time if you start several dataset at same time,

Re: [R] The Origins of R AND CALCULUS

2009-02-05 Thread Mark Difford
Peter Dalgaard wrote: This of course does not mean that the current R should not acknowledge its substantial S heritage, just that if you want to describe the early history of R accurately, you do need to choose your words rather more carefully. Point taken, Peter. But I wan't trying to

[R] Installing package RODBC error - please help

2009-02-05 Thread Vaz Joao (QPT TO EPA)
Hi, I have R version 2.8.1 running on Windows 2000 and can't seem to be able to install package RODBC. I've tried reinstalling R but that wasn't successful. Can some one please help? This is the command I'm using and the subsequent error message: install.packages(RODBC, .Library,

[R] Problem with plotting data from within a function

2009-02-05 Thread Marie Sivertsen
Dear List, I try to develop code where plotting functions are embeded in my own functions. The following is simplified example: test - function() { data - data.frame(x=rep(1:2, each=50), y=rnorm(100)) library(lattice) attach(data) xyplot(y~x) detach() } test() As far as I

[R] optimal control, maximization with several variables?

2009-02-05 Thread Frederik Noack
Dear all, I would like to solve the following problem, which can be done with optimal control theory or dynamic programming: max(x,y) a*u1+b*u2+c*f1(u2) s.t. 0u1x, 0u2f2(x,u2), x'=f3(u1,u2,x) which can be rewritten if optimal control theory should be applied as

Re: [R] eliminating control characters from formatted data files

2009-02-05 Thread jim holtman
Here is one way of doing it. You can read it in as raw and then either replace/delete the control character and write the file back out: # read in as 'raw' and delete the control-Z from the string x - readBin('/tempyy.txt', 'raw', n=10) x [1] 54 68 69 73 20 69 73 20 61 20 74 65 73 74 20

Re: [R] Problem with plotting data from within a function

2009-02-05 Thread Peter Dalgaard
Marie Sivertsen wrote: Dear List, I try to develop code where plotting functions are embeded in my own functions. The following is simplified example: test - function() { data - data.frame(x=rep(1:2, each=50), y=rnorm(100)) library(lattice) attach(data) xyplot(y~x)

Re: [R] Roc curves confidence intervals

2009-02-05 Thread David Freedman
Would you be interested in the cross-validation that's on pp 3 and 4 of the ROCR package PDF? plot(perf,lwd=3,avg=vertical,spread.estimate=boxplot,add=TRUE) there are various options for the 'spread.estimate' David Freedman marc bernard-2 wrote: Dear all, I am looking for an R package

Re: [R] split dataset randomly in prediction and validation set

2009-02-05 Thread jim holtman
?sample x - 1:100 # test data y - split(x, sample(1:2, length(x), replace=TRUE, prob=c(1,2))) y $`1` [1] 4 6 7 13 15 17 18 20 21 29 35 36 37 39 41 43 46 49 50 52 61 68 70 72 76 77 79 80 82 85 87 94 95 96 99 $`2` [1] 1 2 3 5 8 9 10 11 12 14 16 19 22 23 24 25 26 27

Re: [R] help regarding storing time difference values in same unit?

2009-02-05 Thread Suresh_FSFM
Thank you, Jholtman ! :-) Regards, Suresh jholtman wrote: If you are using 'difftime', you can specify the units: x - as.POSIXct(c('2009-01-01 10:00', '2009-03-04 13:00')) x [1] 2009-01-01 10:00:00 GMT 2009-03-04 13:00:00 GMT difftime(x[2], x[1]) Time difference of 62.125 days

Re: [R] eliminating control characters from formatted data files

2009-02-05 Thread Murray Cooper
David, This may be a case of If all you have is a hammer, everything looks like a nail. If all you want to do is remove the last line if it contains a CONTROL-Z, why not use something like perl to process the files? Murray M Cooper, Ph.D. Richland Statistics 9800 N 24th St Richland, MI, USA

Re: [R] Numeric class and sasxport.get

2009-02-05 Thread Sebastien Bihorel
Ok, just so as I get that straight, is the 'labelled' class something that you created in your package or a readily available class in base R? *Sebastien Bihorel, PharmD, PhD* PKPD Scientist Cognigen Corp Email: sebastien.biho...@cognigencorp.com mailto:sebastien.biho...@cognigencorp.com

Re: [R] Problems in Recommending R

2009-02-05 Thread hadley wickham
I don't think you should completely rule out javascript. It's possible to use it in ways that add to the utility of a page, while not detracting from it if not available. OK, what particularly do you have in mind? Here's a few of examples off the top of my head. These are things that

Re: [R] Problems in Recommending R

2009-02-05 Thread hadley wickham
On Thu, Feb 5, 2009 at 8:32 AM, hadley wickham h.wick...@gmail.com wrote: I don't think you should completely rule out javascript. It's possible to use it in ways that add to the utility of a page, while not detracting from it if not available. OK, what particularly do you have in

[R] change individual label colours in a cluster plot?

2009-02-05 Thread Jim Ottaway
I am doing some bibliometric analysis of interdisciplinarity using cluster analysis of co-authorship. I'd like to be able to specify the colour of individual authors in the labels to show a prior grouping by discipline (red for sociology authors, blue for economics authors, ..., that sort of

[R] Three questions about DSE

2009-02-05 Thread Rebecca Sela
I have been using the dse1 and dse2 packages to estimate a model in which the underlying state is an ARMA(2,2) and the observed variables are equal to the state plus noise. I am describing this model using a state space model. First, in estimation, is there a way to restrict two of the

Re: [R] overlay plot question

2009-02-05 Thread Doran, Harold
Did you want something like this: library(lattice) x - plogis(.x, location=0, scale=1) y - plogis(.x, location=2, scale=4) xvals - seq(-7.6, 7.6, length=100) xyplot(x+y ~ xvals, type = c(g, l)) -Original Message- From: r-help-boun...@r-project.org

Re: [R] change individual label colours in a cluster plot?

2009-02-05 Thread patricia garcía gonzález
Hi, If you have a variable, that defines what you want to differentiate (sociology, economics etc.) then you can add color depending on the value of that variable. You will have to convert it to numeric if it is not. An example would be plot( iris[ , 1 ], iris[ , 2], col = iris[ , 3 ] )

Re: [R] maptools: Test if point is in polygon

2009-02-05 Thread baptiste auguie
I don't know about the maptools package but one general way to do this would be to compute the convex hull (?chull) of the augmented set of points and test if the point belongs to it. Hope this helps, baptiste On 5 Feb 2009, at 13:21, Aleksandr Andreev wrote: In R's maptools package,

Re: [R] maptools: Test if point is in polygon

2009-02-05 Thread Rainer M Krug
On Thu, Feb 5, 2009 at 3:21 PM, Aleksandr Andreev aleksandr.andr...@gmail.com wrote: In R's maptools package, is there a built-in function to test if a given point is inside a given polygon on the map? The map was loaded from an ESRI Shapefile. The point's latitude and longitude are known.

Re: [R] The Origins of R

2009-02-05 Thread Duncan Murdoch
On 2/5/2009 1:05 AM, Mark Difford wrote: I think that all appeared on January 8 in Vance's blog posting, with a comment on it by David M Smith on Jan 9. So those people have -27 days Then there was no need for vituperative comments (not from you, of course): simply point doubters to the

Re: [R] eliminating control characters from formatted data files

2009-02-05 Thread David Epstein
Murray Cooper wrote: This may be a case of If all you have is a hammer, everything looks like a nail. If all you want to do is remove the last line if it contains a CONTROL-Z, why not use something like perl to process the files? My first thought was to use perl, and this would have

Re: [R] The Origins of R

2009-02-05 Thread Mark Difford
Duncan Murdoch wrote: So I'm not complaining, but the main problem I saw in his article was that it didn't mention me. I knew Robert Gentleman (even had an office next to him!) before he started R: surely that must have been a key influence. I am sorry to hear that. If I understand you

Re: [R] change individual label colours in a cluster plot?

2009-02-05 Thread Jim Ottaway
patricia garcía gonzález kurtney...@hotmail.com writes: Hi, If you have a variable, that defines what you want to differentiate (sociology, economics etc.) then you can add color depending on the value of that variable. You will have to convert it to numeric if it is not. An example would

Re: [R] The Origins of R

2009-02-05 Thread Roy Mendelssohn
Can we give this a rest (or take it offline)? This is the R-Help mail list, and I fail to grasp how anyone is being helped to use R by this endless discussion. -Roy M. ** The contents of this message do not reflect any position of the U.S. Government or NOAA.

[R] A way to lock down the order of bars for ggplot dodged histogram

2009-02-05 Thread Jason Rupert
It appears that ggplot reorder the data for a dodged histogram based on whether or not a specific variable has a value in the first bin.   I would like to be able to absolutely force the order of the variables in the bin.  For example, say I have three variables Me, You, and Them.  

Re: [R] The Origins of R

2009-02-05 Thread Murray Cooper
Consider yourself lucky! I'm sure there are many people who would prefer not to see their name in the NYT. ;-) Murray Coooper - Original Message - From: Duncan Murdoch murd...@stats.uwo.ca To: Mark Difford mark_diff...@yahoo.co.uk Cc: r-help@r-project.org Sent: Thursday, February 05,

Re: [R] A way to lock down the order of bars for ggplot dodgedhistogram

2009-02-05 Thread ONKELINX, Thierry
Dear Jason, Convert Person to a factor with the levels in the order that you want. Group_df$Person - factor(Group_df$Person, levels = c(Them, You, Me)) HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en

Re: [R] Chi-squared test adjusted for multiple comparisons? Harbe'stest?

2009-02-05 Thread Murray Cooper
Categorical data analysis is definitely the way you want to go. Which test you use depends on how you are going to use the results. For quick and dirty I would suggest using Fisher's exact test on all 2x2 submatricies of counts. In this case, with 4 treatments you have 6 possible 2x2

[R] sqlQuery problem

2009-02-05 Thread stenka1
__ 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 code.

[R] tm Module in R

2009-02-05 Thread ryan
__ 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 code.

Re: [R] optimal control, maximization with several variables?

2009-02-05 Thread Ravi Varadhan
I assume that you are looking to solve, in R, the constrained optimization problem: H (u1, u2) = a*u1+b*u2+c*f1(u2)+lambda*(x') with constraints: 0u1x, 0u2f2(x,u2) where a, b, x, and x' are known. Am I right? If so, you can use the package Rdonlp2. I have written an extension

Re: [R] A way to lock down the order of bars for ggplot dodgedhistogram

2009-02-05 Thread Jason Rupert
Thierry,   Thank you for such a quick response.   I changed the code, but I seem to get the same response.  Ugh.  Maybe I am missing a step.  Thank you again for any feedback.   Me_df-data.frame(Data = c(1:15), Person = Me) You_df-data.frame(Data = c(10:20), Person = You)

[R] Suppressing output in Garch estimation

2009-02-05 Thread Shimrit Abraham
HI, I'm calling the garch() function several times within a for-loop and I would like to suppress the output that the function generates. Setting garch.control(trace = F) does not seem to help. Any suggestions on how to solve this problem? Thanks, S.A. [[alternative HTML version

Re: [R] R-help Digest, Vol 72, Issue 3

2009-02-05 Thread Charles Geyer
Date: Mon, 2 Feb 2009 12:56:15 +0100 From: friedrich.lei...@stat.uni-muenchen.de Subject: Re: [R] Problems in Recommending R To: thomas.petzo...@tu-dresden.de Cc: r-help@r-project.org r-help@r-project.org, user-2...@r-project.org,p...@stat.auckland.ac.nz Message-ID:

Re: [R] Sweave and \Sexpr{}

2009-02-05 Thread Felipe Carrillo
Thaks Eric and Dieter: It is working now although I still have to specify the path to Sweave.sty \usepackage{C:/R/R-2.8.1/share/texmf/Sweave} and it doesn't evaluate \Sexpr{} when I simply use \usepackage{Sweave}. I placed Sweave.sty in the same folder where my rnw and tex file reside. --- On

[R] See source code for survplot function in Design package

2009-02-05 Thread Eleni Rapsomaniki
Dear R users, I know one way to see the code for a hidden function, say function_x, is using default.function_x (e.g. summary.default). But how can I see the code for imported packages that have no namespace (in this case Design)? Many Thanks Eleni

[R] Does the labpt object in the Polygons-class represent the centroid of the polygon

2009-02-05 Thread Rizzo . Michael
Hello, I need to calculate the centroids of some spatial polygons that I have placed into a Polygons-class object. Is the labeling point in the Polygons-class the centroid of the polygon? Thank you for your help. __ R-help@r-project.org mailing list

Re: [R] How do I get my IT department to bless R?

2009-02-05 Thread Christian Langkamp
I know on the website there are some pretty reputable sponsors of the software who at some stage donated some (presumably significant) amount of money out of thankfulness because some project worked and the software helped in some way. In order to push however the use of that software, might it

Re: [R] Sweave and \Sexpr{}

2009-02-05 Thread Dieter Menne
Felipe Carrillo mazatlanmexico at yahoo.com writes: It is working now although I still have to specify the path to Sweave.sty \usepackage{C:/R/R-2.8.1/share/texmf/Sweave} and it doesn't evaluate \Sexpr{} when I simply use \usepackage{Sweave}. I placed Sweave.sty in the same folder where my rnw

Re: [R] Numeric class and sasxport.get

2009-02-05 Thread Frank E Harrell Jr
Sebastien Bihorel wrote: Ok, just so as I get that straight, is the 'labelled' class something that you created in your package or a readily available class in base R? It's something we added for the Hmisc package. Signing off, Frank *Sebastien Bihorel, PharmD, PhD* PKPD Scientist Cognigen

[R] ThinkCell type waterfall charts in R?

2009-02-05 Thread Millo Giovanni
Hello Kerstin, I had done something like this in the past but can't find it any more, so I've put up a very raw example you might want to sophisticate upon. The idea is that of drawing an empty high-level plot and then putting some low-level elements (mainly bars and connecting lines) into it

[R] liknage analysis

2009-02-05 Thread Federico Calboli
Dear All, is there a package in R that implements parametric and non parametric genetic linkage analysis (with both case/control or quantitative phenos)? I tried using Merlin, which could not deal with pedigrees the size I have, and SimWalk2 does not look like the answer either --for

[R] Non-linear optimisation

2009-02-05 Thread ehxpieterse
Hi there, I have a piece of Matlab code I use to optimise a trding strategy. If there are any Matlab/R specialists out there, I would appreciate your help in doing the exact same optimisation in R. I suspect I would use nlm() in R but am not sure where to define my constraints. I have attached

[R] Reading images

2009-02-05 Thread gabo
Hi Can anyone tell me how to convert an image file (a jpg file for instance) into a matrix file? The command image(blabla) transforms a matrix into an image file, I am searching exactly the inverse. Thanks... [[alternative HTML version deleted]]

Re: [R] See source code for survplot function in Design package

2009-02-05 Thread Dieter Menne
Eleni Rapsomaniki e.rapsomaniki at mail.cryst.bbk.ac.uk writes: I know one way to see the code for a hidden function, say function_x, is using default.function_x (e.g. summary.default). But how can I see the code for imported packages that have no namespace (in this case Design)? Just

Re: [R] See source code for survplot function in Design package

2009-02-05 Thread Frank E Harrell Jr
Eleni Rapsomaniki wrote: Dear R users, I know one way to see the code for a hidden function, say function_x, is using default.function_x (e.g. summary.default). But how can I see the code for imported packages that have no namespace (in this case Design)? Many Thanks Eleni

Re: [R] See source code for survplot function in Design package

2009-02-05 Thread Marc Schwartz
on 02/05/2009 10:54 AM Eleni Rapsomaniki wrote: Dear R users, I know one way to see the code for a hidden function, say function_x, is using default.function_x (e.g. summary.default). But how can I see the code for imported packages that have no namespace (in this case Design)? Many

Re: [R] Target Plot?

2009-02-05 Thread Jason Rupert
I had a bit of problems with my email, so if any one responded to this I may have not received it.    Is there any chance you can repost any ideas you might have?   Right now I am looking at the plotrix package, but I have not been able to put together what I'm looking for.   Thank you again

Re: [R] See source code for survplot function in Design package

2009-02-05 Thread David M Smith
Uwe Ligges actually had a nice write-up on finding source code for functions like this in R-news a couple of years ago. You can find it here: http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf (see p44) There are some other tips for finding R source code here:

Re: [R] Non-linear optimisation

2009-02-05 Thread Ravi Varadhan
Hi, I don't understand your Matlab code. However, let me say this: - you could use L-BFGS-B algorithm in optim() or nlminb(), if you only have box constraints - you could use ConstrOptim(), if you only have linear inequality constraints - you could use Rdonlp2 if you have more general

[R] seq(along= surprise

2009-02-05 Thread Kjetil Halvorsen
This surprised me: reps - 100 sims - list(length=reps) sims $length [1] 100 for(i in seq(along=sims))print(i) [1] 1 This is R 2.8.1. Kjetil [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] Unexpected mfrow, layout behavior (pdf still has multiple pages)

2009-02-05 Thread Paul Johnston
You are correct, thank you. I added a new subsection 'Graphics Devices' in http://wiki.r-project.org/rwiki/doku.php?id=tips:surprises:traps to document this behavior. Paul On Thu, Feb 5, 2009 at 4:58 AM, Peter Dalgaard p.dalga...@biostat.ku.dk wrote: Paul Johnston wrote: My goal is to create a

Re: [R] lattice key inside panel

2009-02-05 Thread Dieter Menne
Deepayan Sarkar deepayan.sarkar at gmail.com writes: One other thing that has so far eluded me is how to specify two different kinds of symbols on a single column. The key above shows text line text rectangle but I would really like to get text line text rectangle but this

Re: [R] Reading images

2009-02-05 Thread Sarah Goslee
There's lots of info in the mailing list archives on this topic - 2 minutes with google would have gotten you to read.jpeg and saved you some time. Sarah On Thu, Feb 5, 2009 at 1:01 PM, gabo gabriel.31...@gmail.com wrote: Hi Can anyone tell me how to convert an image file (a jpg file for

Re: [R] maptools: Test if point is in polygon

2009-02-05 Thread Renaud Lancelot
See function pip (point in polygon) in package splancs. Renaud 2009/2/5 Rainer M Krug r.m.k...@gmail.com On Thu, Feb 5, 2009 at 3:21 PM, Aleksandr Andreev aleksandr.andr...@gmail.com wrote: In R's maptools package, is there a built-in function to test if a given point is inside a given

Re: [R] seq(along= surprise

2009-02-05 Thread Uwe Ligges
Kjetil Halvorsen wrote: This surprised me: reps - 100 sims - list(length=reps) sims $length [1] 100 for(i in seq(along=sims))print(i) [1] 1 This is R 2.8.1. What is surprising? sims is now a list that contains 1 element called length with a numeric value of 100. Then

Re: [R] Reading images

2009-02-05 Thread Jorge Ivan Velez
Hi there, Take a look at this: http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/rimage/html/read.jpeg.html HTH, Jorge On Thu, Feb 5, 2009 at 1:01 PM, gabo gabriel.31...@gmail.com wrote: Hi Can anyone tell me how to convert an image file (a jpg file for instance) into a matrix file? The

[R] Legend for radial.plot?

2009-02-05 Thread Jason Rupert
Using plotrix, is it possible to create a legend for the following and attach it to the radial.plot?   posmat-matrix(sample(2:9,30,TRUE),nrow=3) radial.plot(posmat,labels=paste(X,1:10,sep=),rp.type=p,   main=Spiderweb plot,line.col=2:4,show.grid=FALSE,lwd=1:3,   radial.lim=c(0,10))   Thanks.

Re: [R] seq(along= surprise

2009-02-05 Thread Uwe Ligges
Uwe Ligges wrote: Kjetil Halvorsen wrote: This surprised me: reps - 100 sims - list(length=reps) sims $length [1] 100 for(i in seq(along=sims))print(i) [1] 1 This is R 2.8.1. What is surprising? sims is now a list that contains 1 element called length with a numeric value of

[R] pdata.frame for panel data

2009-02-05 Thread ele . fanti
Hi there, as a newbie in R I have a question on the plm package for panel data: How do I actually manage to get data into the pdata.frame format? i.e. how do I declare id and time? I already tried various things and got even more error messages. for example country -

Re: [R] seq(along= surprise

2009-02-05 Thread baptiste auguie
Perhaps this is what was intended? sims - list(length=100) do.call(seq, sims) seq by itself does not expect a list, but do.call() can create the appropriate call if a list is what you want to pass to the function. Hope this helps, baptiste On 5 Feb 2009, at 19:46, Uwe Ligges wrote:

[R] Incorrect p value for binom.test?

2009-02-05 Thread Michael Grant
I believe the binom.test procedure is producing one tailed p values rather than the two tailed value implied by the alternative hypothesis language. A textbook and SAS both show 2*9.94e-07 = 1.988e-06 as the two tailed value. As does the R summation syntax from R below. It looks to me like the

[R] pdata.frame for panel data

2009-02-05 Thread ele . fanti
Hi there, as a newbie in R I have a question on the plm package for panel data: How do I actually manage to get data into the pdata.frame format? i.e. how do I declare id and time? I already tried various things and got even more error messages. for example country -

[R] R system command on windows

2009-02-05 Thread Aurelie Labbe, Dr.
Hi, I am trying to use the R command system under windows (XP). If I try the simple command system(mkdir toto) to create a directory toto, it tells me that it cannot find the command mkdir... Does anybody knows how it works ? Is it a path problem ? Maybe the answer is simple: I am a R user

[R] R command system under Windows

2009-02-05 Thread Aurelie Labbe, Dr.
Hi, I am trying to use the R command system under windows (XP). If I try the simple command system(mkdir toto) to create a directory toto, it tells me that it cannot find the command mkdir... Does anybody knows how it works ? Is it a path problem ? Maybe the answer is simple: I am a R user

Re: [R] R system command on windows

2009-02-05 Thread Uwe Ligges
Aurelie Labbe, Dr. wrote: Hi, I am trying to use the R command system under windows (XP). If I try the simple command system(mkdir toto) to create a directory toto, it tells me that it cannot find the command mkdir... Does anybody knows how it works ? Is it a path problem ? Maybe the

Re: [R] R system command on windows

2009-02-05 Thread Stephan Kolassa
?shell HTH, Stephan Aurelie Labbe, Dr. schrieb: Hi, I am trying to use the R command system under windows (XP). If I try the simple command system(mkdir toto) to create a directory toto, it tells me that it cannot find the command mkdir... Does anybody knows how it works ? Is it a path

Re: [R] lattice key inside panel

2009-02-05 Thread Deepayan Sarkar
On Thu, Feb 5, 2009 at 11:28 AM, Dieter Menne dieter.me...@menne-biomed.de wrote: Deepayan Sarkar deepayan.sarkar at gmail.com writes: One other thing that has so far eluded me is how to specify two different kinds of symbols on a single column. The key above shows text line text

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