Re: [R] Reproducible research

2010-09-09 Thread Peng, C
FYI: If you use LaTex, you can work out on something between R and LaTex. -- View this message in context: http://r.789695.n4.nabble.com/Reproducible-research-tp2532353p2532361.html Sent from the R help mailing list archive at Nabble.com. __

Re: [R] lattice: layout and number of pages

2010-09-09 Thread Deepayan Sarkar
On Wed, Sep 8, 2010 at 5:49 AM, Philipp Pagel p.pa...@wzw.tum.de wrote:        Dear expeRts, ?xyplot says: In general, giving a high value of ‘layout[3]’ is not wasteful because blank pages are never created. But the following example does generate blank pages - well except for the ylab:

[R] plot symbol +, but with variable bar lenghts

2010-09-09 Thread Rainer Machne
Hi, does anybody know of some plotting function or an easy way to generate + symbols with individually settable bar lengths? I tried just combining | and - as pch and setting the size via cex, but that doesn't really work since the two symbols have different default lengths. Is there a

Re: [R] How to project a vector on a subspace?

2010-09-09 Thread James
Hi Peng, Gabor Peter, Thank you very much for replying me so soon. I will try it right now! -- View this message in context: http://r.789695.n4.nabble.com/How-to-project-a-vector-on-a-subspace-tp2530886p2532388.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Reproducible research

2010-09-09 Thread David Hajage
Hello David, You could also have a look to the ascii package : http://eusebe.github.com/ascii/ With asciidoc (http://www.methods.co.nz/asciidoc/), or one of other markup languages supported (restructuredtext, txt2tags, or textile), you can obtain good results. For example, vignettes of the book

[R] See what is inside a matrix

2010-09-09 Thread Alaios
Hello everyone.. Is there any graphical tool to help me see what is inside a matrix? I have 100x100 dimensions matrix and as you already know as it does not fit on my screen R splits it into pieces. I would like to thank you in advance for your help Best Regards Alex

Re: [R] two questions

2010-09-09 Thread Iasonas Lamprianou
This sounds interesting, thank you. I'll have a look. jason Dr. Iasonas Lamprianou Assistant Professor (Educational Research and Evaluation) Department of Education Sciences European University-Cyprus P.O. Box 22006 1516 Nicosia Cyprus Tel.: +357-22-713178 Fax: +357-22-590539 Honorary

Re: [R] plot symbol +, but with variable bar lenghts

2010-09-09 Thread Ted Harding
On 09-Sep-10 06:41:34, Rainer Machne wrote: Hi, does anybody know of some plotting function or an easy way to generate + symbols with individually settable bar lengths? I tried just combining | and - as pch and setting the size via cex, but that doesn't really work since the two symbols have

[R] Help request: highlighting R code on WordPress.com blogs

2010-09-09 Thread Tal Galili
Hello dear R help members (and also Yihui and Romain), There are currently 28 R bloggers (out of the 117 R-bloggershttp://www.r-bloggers.com/I know of) that are using wordpress.com for publishing their R code (and I suspect this number will increase with time). WordPress.com doesn't support R

[R] Emacs function argument hints

2010-09-09 Thread Tim Elwell-Sutton
Hi I've recently started using Emacs as my text editor for writing R script. I am looking for a feature which I have seen on the standard R text editor for Mac OS. In the Mac OS editor when you start typing a function, the possible arguments for that function appear at the bottom of the

Re: [R] Reproducible research

2010-09-09 Thread Rainer M Krug
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/09/10 07:47, David Scott wrote: I am investigating some approaches to reproducible research. I need in the end to produce .html or .doc or .docx. I have used hwriter in the past but have had some problems with verbatim output from R. Tables

Re: [R] optimized value worse than starting Value

2010-09-09 Thread Barry Rowlingson
On Wed, Sep 8, 2010 at 6:26 PM, Michael Bernsteiner dethl...@hotmail.com wrote: @Barry: Yes it is the Rosenbrock Function. I'm trying out some thing I found here: http://math.fullerton.edu/mathews/n2003/PowellMethodMod.html @Ravi: Thanks for your help. I will have a closer look at the BB

Re: [R] plot symbol +, but with variable bar lenghts

2010-09-09 Thread baptiste Auguié
Hi, The TeachingDemos package has a my.symbols() function that you could use with you own glyph. HTH, baptiste On Sep 9, 2010, at 9:36 AM, (Ted Harding) wrote: On 09-Sep-10 06:41:34, Rainer Machne wrote: Hi, does anybody know of some plotting function or an easy way to generate +

Re: [R] Reproducible research

2010-09-09 Thread Vijayanpadmanabhan
Dear David I have tried odfWeave and I find it quite useful for the purpose. I would recommend you give it a try. It comes with simple example files along with installation. You might have some difficulty in getting the zip files and path configurations set, which is a pre-requisite, but I am

[R] Maxdiff Analysis in R

2010-09-09 Thread Vijayan Padmanabhan
Dear Group Does anybody have an example data and R Script for analysis of Maxdiff study in R. Thanks Regards Vijayan Padmanabhan What is expressed without proof can be denied without proof - Euclide. Can you avoid printing this? Think of the environment before printing the email.

Re: [R] Correlation question

2010-09-09 Thread Dennis Murphy
Did you try taking out P7, which is text? Moreover, if you get a message saying ' the standard deviation is zero', it means that the entire column is constant. By definition, the covariance of a constant with a random variable is 0, but your data consists of values, so cor() understandably throws

[R] advise on operations speed with Rcpp,Boost::ipc Shared Memory

2010-09-09 Thread raje...@cse.iitm.ac.in
Hi, I have an implementation where I transfer data records via shared memory to an R program. If anyone has prior experience, I'd like to find out which would be faster 1) storing data records in shared memory as they are(in a matrix) and then use the Rcpp::wrap to convert them to R

[R] Help with HB analysis in R for a conjoint study Data

2010-09-09 Thread Vijayan Padmanabhan
Dear Group I was referring to a conjoint analysis scenario using R from the paper referred below: Agricultural Information Research 17(2),2008,86-94 available online at www.jstage.jst.go.jp/ This paper describes the data modelling of a conjoint study design based on conditional logit

Re: [R] Feature selection via glmnet package (LASSO)

2010-09-09 Thread Dennis Murphy
Hi: When you need to search for a function in R, rely on our good friend, the package sos: library(sos) findFn('elastic net') found 23 matches; retrieving 2 pages HTH, Dennis On Wed, Sep 8, 2010 at 6:58 PM, jjenkner jjenk...@web.de wrote: Hello Lai! You can try the elastic net which is a

Re: [R] Calculating with tolerances

2010-09-09 Thread Bernardo Rangel Tura
On Thu, 2010-09-09 at 09:16 +0430, Jan private wrote: Dear list, I am from an engineering background, accustomed to work with tolerances. For example, I have measured Q = 0.15 +- 0.01 m^3/s H = 10 +- 0.1 m and now I want to calculate P = 5 * Q * H and get a value with a

Re: [R] 'par mfrow' and not filling horizontally

2010-09-09 Thread Ivan Calandra
Hi! I think you've got already all useful solutions, but I usually just change mfrow to c(2,2). There is then free space left, but I usually edit my graphs in Illustrator anyway. Ivan Le 9/8/2010 21:01, (Ted Harding) a écrit : Greetings, Folks. I'd appreciate being shown the way out of

Re: [R] See what is inside a matrix

2010-09-09 Thread Dennis Murphy
Hi: One possibility is a heatmap, although there are other approaches. x - matrix(sample(1:100, 1, replace = TRUE), nrow = 100) image(x) xx - apply(x, 1, sort) # sorts the rows of x image(xx) # ggplot2 version: library(ggplot2) ggplot(melt(x), aes(x=X1, y=X2, fill=value)) + geom_tile() +

Re: [R] problem with outer

2010-09-09 Thread tuggi
thank you for your answers, but my problem is that i want plot the function guete for the variables p_11 and p_12 between zero and one. that means that i also want to plot p_11=0.7 and p_12=0.3. but with a=0.4 and b=0.6 and p_11=seq(0,a,0.05*a) and p_12=seq(0,b,0.0*b) i cannot do that. i hope you

[R] Strange output daply with empty strata

2010-09-09 Thread Jan van der Laan
Dear list, I get some strange results with daply from the plyr package. In the example below, the average age per municipality for employed en unemployed is calculated. If I do this using tapply (see code below) I get the following result: no yes A NA 36.94931 B

[R] markov model

2010-09-09 Thread Isaac SAGAON TEYSSIER
Dear all, I would like some help to writing the likelihood function for the continuous-time markov model, even if it can be calculated with the msm package, I need to know how it is calculated Thank you Luis [[alternative HTML version

[R] Which language is faster for numerical computation?

2010-09-09 Thread Christofer Bogaso
Dear all, R offers integration mechanism with different programming languages like C, C++, Fortran, .NET etc. Therefore I am curious on, for heavy numerical computation which language is the fastest? Is there any study? I specially want to know because, if there is some study saying that C is the

[R] Making R lazy

2010-09-09 Thread Lorenzo Isella
Dear All, I hope this is not too off-topic. I am wondering if there is any possibility to make an R code lazy i.e. to prevent it from calculating quantities which are not used in the code. As an example: you are in a rush to modify your code and at the end it ends up with dead branches, let's

Re: [R] Strange output daply with empty strata

2010-09-09 Thread Dennis Murphy
Hi: Here's what I tried: # data frame versions (aggregate, ddply): aggregate(age ~ municipality + employed, data = data.test, FUN = mean) municipality employed age 1B no 55.57407 2C no 44.67463 3A yes 41.58759 4B yes

[R] confidence intervals around p-values

2010-09-09 Thread Fernando Marmolejo Ramos
Dear all I wonder if anyone has heard of confidence intervals around p-values... Any pointer would be highly appreciated. Best Fer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] R-help Digest, Vol 91, Issue 9

2010-09-09 Thread Fernando Marmolejo Ramos
dear all I wonder if anyone has heard of confidence intervals around p-values... Any pointer would be highly appreciated. Best Fer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] Calculating with tolerances (error propagation)

2010-09-09 Thread Jan private
Hello Bernardo, - If I understood your problem this script solve your problem: q-0.15 + c(-.1,0,.1) h-10 + c(-.1,0,.1) 5*q*h [1] 2.475 7.500 12.625 - OK, this solves the simple example. But what if the example is not that simple. E.g. P = 5 * q/h Here, to get the maximum

[R] UseR groups: NewJersey R - LondonR - BaselR

2010-09-09 Thread Sarah Lewis
NewJerseyR Mango Solutions is pleased to announce the inaugural meeting of NewJerseyR a networking and social event for all local and regional R users. Thank you to those of you already registered to attend the first NewJerseyR meeting on Thursday 16th September and to those of you who have

Re: [R] try-error can not be test. Why?

2010-09-09 Thread Duncan Murdoch
On 08/09/2010 11:46 PM, Philippe Grosjean wrote: On 08/09/10 19:25, David Winsemius wrote: On Sep 8, 2010, at 1:18 PM, telm8 wrote: Hi, I am having some strange problem with detecting try-error. From what I have read so far the following statement: try( log(a) ) == try-error should yield

Re: [R] Which language is faster for numerical computation?

2010-09-09 Thread Rainer M Krug
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/09/10 12:26, Christofer Bogaso wrote: Dear all, R offers integration mechanism with different programming languages like C, C++, Fortran, .NET etc. Therefore I am curious on, for heavy numerical computation which language is the fastest? Is

[R] modulo operation

2010-09-09 Thread José M. Blanco Moreno
Dear R-users, May be there is something that I am not understanding, missed or else... Why do these operations yield these results? 25%/%0.2 [1] 124 25%%0.2 [1] 0.2 I would expect (although I know that what I do expect and what is really intended in the code may be different things) 25/0.2

[R] createDataPartition

2010-09-09 Thread Trafim Vanishek
Dear all, does anyone know how to define the structure of the required samples using function createDataPartition, meaning proportions of different types of variable in the partition? Smth like this for iris data: createDataPartition(y = c(setosa = .5, virginica = .3, versicolor = .2), times =

Re: [R] Error in normalizePath(path) : with McAfee

2010-09-09 Thread Duncan Murdoch
On 09/09/2010 12:01 AM, Erin Hodgess wrote: Dear R People: I keep getting the Error in normalizePath(path) : while trying to obtain the necessary packages to use with the Applied Spatial Statistics with R book. I turned off the Firewall (from McAfee) but am still getting the same message.

Re: [R] modulo operation

2010-09-09 Thread Barry Rowlingson
2010/9/9 José M. Blanco Moreno jmbla...@ub.edu:  Dear R-users, May be there is something that I am not understanding, missed or else... Why do these operations yield these results? 25%/%0.2 [1] 124 25%%0.2 [1] 0.2 I would expect (although I know that what I do expect and what is really

Re: [R] Making R lazy

2010-09-09 Thread Duncan Murdoch
On 09/09/2010 6:27 AM, Lorenzo Isella wrote: Dear All, I hope this is not too off-topic. I am wondering if there is any possibility to make an R code lazy i.e. to prevent it from calculating quantities which are not used in the code. As an example: you are in a rush to modify your code and at

Re: [R] average columns of data frame corresponding to replicates

2010-09-09 Thread jim holtman
try this: myData sample1.id1 sample1.id2 sample2.id1 sample1.id3 sample3.id1 sample1.id4 sample2.id2 11 2 2 1 1 1 1 21 2 2 2 1 2 1 31 2

Re: [R] modulo operation

2010-09-09 Thread Duncan Murdoch
On 09/09/2010 7:56 AM, Barry Rowlingson wrote: 2010/9/9 José M. Blanco Moreno jmbla...@ub.edu: Dear R-users, May be there is something that I am not understanding, missed or else... Why do these operations yield these results? 25%/%0.2 [1] 124 25%%0.2 [1] 0.2 I would expect (although I

Re: [R] Reproducible research

2010-09-09 Thread Erik Iverson
Another vote for org-mode here. In addition the advantages the other posts mentioned, you get multiple export engines (html, latex, ...) all built in. On 09/09/2010 12:47 AM, David Scott wrote: I am investigating some approaches to reproducible research. I need in the end to produce .html or

Re: [R] Failure to aggregate

2010-09-09 Thread Gabor Grothendieck
On Wed, Sep 8, 2010 at 4:48 AM, Dimitri Shvorob dimitri.shvo...@gmail.com wrote: I was able to aggregate (with sqldf, at least), after saving and re-loading the dataframe. My first guess was that h (and/or price?) now being a factor - stringsAsFactors = T by default - made the difference, and

Re: [R] modulo operation

2010-09-09 Thread José M. Blanco Moreno
Did you read the documentation before you read the code? ‘%%’ and ‘x %/% y’ can be used for non-integer ‘y’, e.g. ‘1 %/% 0.2’, but the results are subject to rounding error and so may be platform-dependent. Because the IEC 60059 representation of ‘0.2’ is a binary fraction slightly larger than

Re: [R] Emacs function argument hints

2010-09-09 Thread Ista Zahn
Hi Tim, This works out of the box for me, with ESS 5.11 and Emacs 23.1 -Ista On Thu, Sep 9, 2010 at 4:07 AM, Tim Elwell-Sutton tesut...@hku.hk wrote: Hi I've recently started using Emacs as my text editor for writing R script. I am looking for a feature which I have seen on the standard R

Re: [R] confidence intervals around p-values

2010-09-09 Thread Ben Bolker
Fernando Marmolejo Ramos fernando.marmolejoramos at adelaide.edu.au writes: Dear all I wonder if anyone has heard of confidence intervals around p-values... Any pointer would be highly appreciated. No, and my reflex is that it seems like a bad idea. If you are using p-values as an

Re: [R] confidence intervals around p-values

2010-09-09 Thread Duncan Murdoch
On 09/09/2010 6:44 AM, Fernando Marmolejo Ramos wrote: Dear all I wonder if anyone has heard of confidence intervals around p-values... That doesn't really make sense. p-values are statistics, not parameters. You would compute a confidence interval around a population mean because that's

[R] [R-pkgs] New package for medical image registration: RNiftyReg

2010-09-09 Thread Jon Clayden
The first release of RNiftyReg, an R package for registration (alignment and resampling) of medical images, is now available on CRAN [1]. It may also be useful for other 3D array-like data sets. RNiftyReg is built on top of the NiftyReg library [2], and is written in a mixture of C, C++ and R. It

[R] Invitation to the ICANNGA'11 Conference

2010-09-09 Thread ICANNGA organizing committee
Dear Colleague, The 10th ICANNGA conference, to be held April 14-16 2011 in Ljubljana, Slovenia, is fast approaching and with it the paper submission deadline, which is October 1st, 2010. Let us kindly invite you to visit our web page: www.icannga.com, where all the details on ICANNGA, its

Re: [R] Strange output daply with empty strata

2010-09-09 Thread hadley wickham
daply(data.test, .(municipality, employed), function(d){mean(d$age)} )     employed municipality   no  yes    A 41.58759 44.67463    B 55.57407 43.82545    C 43.59330   NA The .drop argument has a different meaning in daply. Some R functions have

[R] Highlighting a few bars in a barplot

2010-09-09 Thread Daniel Brewer
Hello, I have a bar plot where I am already using colour to distinguish one set of samples from another. I would also like to highlight a few of these bars as ones that should be looked at in detail. I was thinking of using hatching, but I can't work out how or if you can have a background

Re: [R] plot symbol +, but with variable bar lenghts

2010-09-09 Thread Greg Snow
Look at my.symbols in the TeachingDemos package. -Original Message- From: Rainer Machne r...@tbi.univie.ac.at Sent: Thursday, September 09, 2010 12:42 AM To: R-help@r-project.org R-help@r-project.org Subject: [R] plot symbol +, but with variable bar lenghts Hi, does anybody know of

Re: [R] Saving/loading custom R scripts

2010-09-09 Thread Bos, Roger
Josh, I liked your idea of setting the repo in the .Rprofile file, so I tried it: r - getOption(repos) r[CRAN] - http://cran.stat.ucla.edu; options(repos = r) rm(r) And now when I open R I get an error: Error in r[CRAN] - http://cran.stat.ucla.edu; : cannot do complex assignments in base

[R] multi-class for BRT

2010-09-09 Thread azam jaafari
Hi   I want to do boosted regression(classification) tree for categorical response (with 7 levels). Can I do this by GBM package?   please help me?   Thanks alot   [[alternative HTML version deleted]] __ R-help@r-project.org mailing

[R] Determine Bounds of Current Graph

2010-09-09 Thread Isamoor
I'm having trouble determining the bounds of my current graph. I know how to set the bounds up front (ylim xlim in most cases), but I would rather be able to dynamically see what was chosen to use in later code. Example: library(maps) map('state','Indiana') map.axes() ??Something that lets me

Re: [R] Newbie cross tabulation issue

2010-09-09 Thread John Kane
It would help if you included a bit of sample data. See ?dput as a way of doing this. Also a good place to start is by looking at the package reshape. Have a look at http://had.co.nz/reshape/ for some information on the package. --- On Wed, 9/8/10, Jonathan Finlay jmfinl...@gmail.com wrote:

Re: [R] Which language is faster for numerical computation?

2010-09-09 Thread Matt Shotwell
For the compiled languages, it depends heavily on the compiler. This sort of comparison is rendered moot by the huge variety of compiler and hardware specific optimizations. My suggestion is to use C, or possibly C++ in conjunction with Rcpp, as these are most compatible with R. Also, C and C++

Re: [R] Which language is faster for numerical computation?

2010-09-09 Thread Dirk Eddelbuettel
On 9 September 2010 at 13:26, Rainer M Krug wrote: | -BEGIN PGP SIGNED MESSAGE- | Hash: SHA1 | | On 09/09/10 12:26, Christofer Bogaso wrote: | Dear all, R offers integration mechanism with different programming | languages like C, C++, Fortran, .NET etc. Therefore I am curious on, |

Re: [R] Determine Bounds of Current Graph

2010-09-09 Thread David Winsemius
On Sep 9, 2010, at 10:07 AM, Isamoor wrote: I'm having trouble determining the bounds of my current graph. I know how to set the bounds up front (ylim xlim in most cases), but I would rather be able to dynamically see what was chosen to use in later code. Example: library(maps)

Re: [R] confidence intervals around p-values

2010-09-09 Thread Ted Harding
On 09-Sep-10 13:21:07, Duncan Murdoch wrote: On 09/09/2010 6:44 AM, Fernando Marmolejo Ramos wrote: Dear all I wonder if anyone has heard of confidence intervals around p-values... That doesn't really make sense. p-values are statistics, not parameters. You would compute a confidence

Re: [R] optimized value worse than starting Value

2010-09-09 Thread Ravi Varadhan
Yes, Barry, we are aware of this issue. It is caused by printing to console from FORTRAN in one of the optimization codes, ucminf. If we set trace=FALSE in optimx, this problem goes away. Ravi. Ravi Varadhan, Ph.D.

Re: [R] Calculating with tolerances (error propagation)

2010-09-09 Thread David Winsemius
On Sep 9, 2010, at 6:50 AM, Jan private wrote: Hello Bernardo, - If I understood your problem this script solve your problem: q-0.15 + c(-.1,0,.1) h-10 + c(-.1,0,.1) 5*q*h [1] 2.475 7.500 12.625 - OK, this solves the simple example. But what if the example is not that

Re: [R] Calculating with tolerances (error propagation)

2010-09-09 Thread Peng, C
q-0.15 + c(-.1,0,.1) h-10 + c(-.1,0,.1) 5*q/h[3:1] [1] 0.02475248 0.0750 0.12626263 -- View this message in context: http://r.789695.n4.nabble.com/Re-Calculating-with-tolerances-error-propagation-tp2532640p2532991.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Correlation question

2010-09-09 Thread Stephane Vaucher
Thank you Dennis, You identified a factor (text column) that I was concerned with. I simplified my example to try and factor out possible causes. I eliminated the recurring values in columns (which were not the columns that caused problems). I produced three examples with simple data sets.

Re: [R] Highlighting a few bars in a barplot

2010-09-09 Thread RINNER Heinrich
Hello Daniel, something like that might work: x - runif(6) marker1 - rep(c(red, blue), 3) marker2 - c(rep(0,5), 10) barplot(x, col = marker1) barplot(x, density = marker2, add=T) But I'd be interested if you learn about other solutions... -Heinrich. -Ursprüngliche Nachricht- Von:

Re: [R] Calculating with tolerances (error propagation)

2010-09-09 Thread David Winsemius
On Sep 9, 2010, at 6:50 AM, Jan private wrote: Hello Bernardo, - If I understood your problem this script solve your problem: q-0.15 + c(-.1,0,.1) h-10 + c(-.1,0,.1) 5*q*h [1] 2.475 7.500 12.625 - OK, this solves the simple example. But what if the example is not that

Re: [R] Reproducible research

2010-09-09 Thread Matt Shotwell
I have a little package I've been using to write template blog posts (in HTML) with embedded R code. It's quite small but very flexible and extensible, and aims to do something similar to Sweave and brew. In fact, the package is heavily influenced by the brew package, though implemented quite

Re: [R] Failure to aggregate

2010-09-09 Thread Petr PIKAL
Hi you has to provide some more info about x e.g. str(x) x-data.frame(price=1, h=Sys.time()) r-help-boun...@r-project.org napsal dne 08.09.2010 10:18:52: Mnay thanks fr suggestions. I am afraid this is one tough daatframe... t = sqldf(select h, count(*) from x group by h) Error in

Re: [R] Calculating with tolerances (error propagation)

2010-09-09 Thread Keith Jewell
Jan private jrheinlaen...@gmx.de wrote in message news:1284029454.2740.361.ca...@localhost.localdomain... Hello Bernardo, - If I understood your problem this script solve your problem: q-0.15 + c(-.1,0,.1) h-10 + c(-.1,0,.1) 5*q*h [1] 2.475 7.500 12.625 - OK, this

Re: [R] Newbie cross tabulation issue

2010-09-09 Thread Jonathan Finlay
2010/9/8 David Winsemius dwinsem...@comcast.net I hope you mean only two factors and an n x m table. Yes David I like say factor, but am new here. -- Jonathan. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] Error in normalizePath(path) : with McAfee

2010-09-09 Thread peter dalgaard
On Sep 9, 2010, at 13:52 , Duncan Murdoch wrote: On 09/09/2010 12:01 AM, Erin Hodgess wrote: Dear R People: I keep getting the Error in normalizePath(path) : while trying to obtain the necessary packages to use with the Applied Spatial Statistics with R book. I turned off the Firewall

Re: [R] problem with outer

2010-09-09 Thread Peng, C
Can you set the multinomial prob. to zero for p1+p2+p3 != 1 if you have to use the multinomial distribution in guete(). Otherwise, I would say the problem/guete() itself is problematic. -- View this message in context: http://r.789695.n4.nabble.com/problem-with-outer-tp2532074p2533050.html Sent

Re: [R] Newbie cross tabulation issue

2010-09-09 Thread David Winsemius
On Sep 8, 2010, at 7:32 PM, Jonathan Finlay wrote: Thanks David, gmodels::Crosstable partially work because can show only 1 x 1 tablen CrossTable(x,y,...) I need something how can process at less 1 variable in X an 10 in Y. A further thought (despite a lack of clarification on what your

Re: [R] Prediction confidence intervals for a Poisson GLM

2010-09-09 Thread stephenb
I am following up on an old post. Please, comment: it appears that predict(glm.model,type=response,se.fit=T) will do all the conversions and give se on the scale of the response. This only takes into account the error in parameter estimation. what a prediction interval is meant to be usually

Re: [R] Failure to aggregate

2010-09-09 Thread Dimitri Shvorob
g = head(x) dput(g) structure(list(price = c(500L, 500L, 501L, 501L, 500L, 501L), size = c(221000L, 2000L, 1000L, 13000L, 3000L, 3000L), src = c(R, R, R, R, R, R), t = structure(list(sec = c(24.133, 47.096, 12.139, 18.142, 10.721, 28.713), min = c(0L, 0L, 1L, 1L, 2L, 2L),

Re: [R] regression function for categorical predictor data

2010-09-09 Thread karena
Hi, thank you very much for the help. one more quick question: is that, my predictor variable should be coded as 'factor' when using either 'lm' or 'glm'? sincerely, karena -- View this message in context:

Re: [R] a question about replacing the value in the data.frame

2010-09-09 Thread karena
Thanks a lot! -- View this message in context: http://r.789695.n4.nabble.com/a-question-about-replacing-the-value-in-the-data-frame-tp2532010p2533036.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list

Re: [R] Reproducible research

2010-09-09 Thread Matt Shotwell
Well, the attachment was a dud. Try this: http://biostatmatt.com/R/markup_0.0.tar.gz -Matt On Thu, 2010-09-09 at 10:54 -0400, Matt Shotwell wrote: I have a little package I've been using to write template blog posts (in HTML) with embedded R code. It's quite small but very flexible and

[R] Alignment of lines within barplot bars

2010-09-09 Thread Steve Murray
Dear all, I have a barplot upon which I hope to superimpose horizontal lines extending across the width of each bar. I am able to partly achieve this through the following set of commands: positions - barplot(bar_values, col=grey) par(new=TRUE) plot(positions, horiz_values, col=red, pch=_,

[R] Axis break with gap.plot()

2010-09-09 Thread Filoche
Hi everyone. I'm trying to break the y axis on a plot. For instance, I have 2 series (points and a loess). Since the loess is a continuous set of points, it passes in the break section. However, with gap.plot I cant plot the loess because of this (I got the message some values of y will not be

[R] scalable delimiters in plotmath

2010-09-09 Thread baptiste auguie
Dear list, I read in ?plotmath that I can use bgroup to draw scalable delimiters such as [ ] and ( ). The same technique fails with however, and I cannot find a workaround, grid.text(expression(bgroup(,atop(x,y),))) Error in bgroup(, atop(x, y), ) : invalid group delimiter Regards, baptiste

Re: [R] See what is inside a matrix

2010-09-09 Thread Greg Snow
The image function will create a plot with the values transformed to colors. Or the View function (note the capitol V) will let you look at it in a spreadsheet like window with scrollbars. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org

Re: [R] Failure to aggregate

2010-09-09 Thread jim holtman
I think your main problem is that you have your time as POSIXlt which is a multiple valued vector. I converted the 't' to POSIXct, removed the other POSIXlt value and created a 'h' as the character for the hour and it works fine: str(g) 'data.frame': 6 obs. of 5 variables: $ price: int 500

[R] Bug on chron

2010-09-09 Thread skan
hello I think I've found a bug I don't know if it's a chron bug or a R one. (05/12/05 23:00:00) +1/24 gives (05/12/05 24:00:00) instead of (05/13/05 00:00:00) it looks like the same but it's not because when you get the date of this datetime it says day 12 instead of 13. Please, forward it

[R] rgl and lighting

2010-09-09 Thread james.foadi
Dear R community (and Duncan more specifically), I can't work out how to make additional light sources work in rgl. Here is the example. First I create a cube and visualize it: cubo - cube3d(col=black) shade3d(cubo) Next I position the viewpoint at theta=0 and phi=30: view3d(theta=0,phi=30)

Re: [R] coxph and ordinal variables?

2010-09-09 Thread Thomas Lumley
On Wed, 8 Sep 2010, Paul Johnson wrote: run it with factor() instead of ordered(). You don't want the orthogonal polynomial contrasts that result from ordered if you need to compare against Stata. If you don't want polynomial contrasts for ordered factors, you can just tell R not to use

Re: [R] Saving/loading custom R scripts

2010-09-09 Thread Joshua Wiley
On Thu, Sep 9, 2010 at 7:05 AM, Bos, Roger roger@rothschild.com wrote: Josh, I liked your idea of setting the repo in the .Rprofile file, so I tried it: r - getOption(repos) r[CRAN] - http://cran.stat.ucla.edu; options(repos = r) rm(r) And now when I open R I get an error:  Error

Re: [R] Bug on chron

2010-09-09 Thread Gabor Grothendieck
On Thu, Sep 9, 2010 at 11:59 AM, skan juanp...@gmail.com wrote: hello I think I've found a bug I don't know if it's a chron bug or a R one. (05/12/05 23:00:00) +1/24  gives (05/12/05 24:00:00) instead of (05/13/05 00:00:00) it looks like the same but it's not because when you get the

Re: [R] regression function for categorical predictor data

2010-09-09 Thread Joshua Wiley
Hi, If your predictor variable is categorical than it should be converted to a factor. If it is continuous or being treated as such, you do not need to. It is generally quite easy to do: varname - factor(varname) or if it is in a data frame yourdf$varname - factor(yourdf$varname) Cheers,

[R] Uncertainty analysis

2010-09-09 Thread Lathouri, Maria
Dear all I would like to run in R an uncertainty/sensitivity analysis. I know that these two are performed together. I have a geochemical model where I have the inputs, the water variables (e.g. pH, temperature, oxygen ect) and as well an output of different variables. What I would like to do

Re: [R] Saving/loading custom R scripts

2010-09-09 Thread Jakson A. Aquino
On Thu, Sep 9, 2010 at 1:14 PM, Joshua Wiley jwiley.ps...@gmail.com wrote: On Thu, Sep 9, 2010 at 7:05 AM, Bos, Roger roger@rothschild.com wrote: Josh, I liked your idea of setting the repo in the .Rprofile file, so I tried it: r - getOption(repos) r[CRAN] - http://cran.stat.ucla.edu;

Re: [R] confidence intervals around p-values

2010-09-09 Thread Greg Snow
One other case where a confidence interval on a p-value may make sense is permutation (or other resampling) tests. The population parameter p-value would be the p-value that would be obtained from the distribution of all possible permutations, but in practice we just sample from that

Re: [R] Bug on chron

2010-09-09 Thread skan
Something strange. Your example work but... I have a zoo object. I extract its element 21 index(test[21]) [1] (05/12/05 23:00:00) index(test[21])+1/24 [1] (05/12/05 24:00:00) Why 24:00 ? packageDescription(chron)$Version [1] 2.3-35 R.version.string [1] R version 2.11.1

Re: [R] Correlation question

2010-09-09 Thread Joshua Wiley
Hi Stephane, When I use your sample data (e.g., test, test.number), cor() throws an error that x must be numeric (because of the factor or character data). Are you not getting any errors when trying to calculate the correlation on these data? If you are not, I wonder what version of R are you

Re: [R] Saving/loading custom R scripts

2010-09-09 Thread Joshua Wiley
On Thu, Sep 9, 2010 at 9:28 AM, Jakson A. Aquino jaksonaqu...@gmail.com wrote: On Thu, Sep 9, 2010 at 1:14 PM, Joshua Wiley jwiley.ps...@gmail.com wrote: On Thu, Sep 9, 2010 at 7:05 AM, Bos, Roger roger@rothschild.com wrote: Josh, I liked your idea of setting the repo in the .Rprofile

Re: [R] Bug on chron

2010-09-09 Thread Greg Snow
Could this be a case of faq 7.31? where rounding error means that you are seeing a time that is slightly before midnight (but printing shows it at midnight). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original

Re: [R] Bug on chron

2010-09-09 Thread skan
I don't know. You can look at the file, is very short. http://r.789695.n4.nabble.com/file/n2533223/test test -- View this message in context: http://r.789695.n4.nabble.com/Bug-on-chron-tp2533135p2533223.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] optimized value worse than starting Value

2010-09-09 Thread Hans W Borchers
Barry Rowlingson b.rowlingson at lancaster.ac.uk writes: On Wed, Sep 8, 2010 at 1:35 PM, Michael Bernsteiner dethlef1 at hotmail.com wrote: Dear all, I'm optimizing a relatively simple function. Using optimize the optimized parameter value is worse than the starting. why? I would

Re: [R] confidence intervals around p-values

2010-09-09 Thread JLucke
A confidence interval around the p-value makes no sense because there is no parameter being estimated, but the sampling distribution of the p-value makes a lot of sense. The pre-observational P-value is a random variable that is a function of the underlying random variable being tested. That

Re: [R] rgl and lighting

2010-09-09 Thread Duncan Murdoch
On 09/09/2010 12:02 PM, james.fo...@diamond.ac.uk wrote: Dear R community (and Duncan more specifically), I can't work out how to make additional light sources work in rgl. Here is the example. First I create a cube and visualize it: cubo- cube3d(col=black) shade3d(cubo) Next I position

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