[R] Measure execution time

Dear list members, I would like to measure how much time one function call makes from the time is call until the time it returns. Could you please tell me if that is possible in R? Best Regards Alex __ R-help@r-project.org mailing list

Re: [R] Boxplot

This should do it: boxplot(log(a[,2:52]),main = list.files()[3],col = c(red, green)) Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il

Re: [R] Please help -- Converting a 2D matrix to 3 columns for graphical representation

There you go: rdata = replicate(100, rnorm(15)) #construct a 2D matrix c1 = cor(rdata) require(reshape) m_c1 - melt(as.matrix(c1)) head(m_c1) Cheers, Tal Contact Details:--- Contact me: tal.gal...@gmail.com |

Re: [R] read.table() versus scan()

Hi Roark, From my experience, this error is because of problem with reading the headers, or problem with the sep parameter in read.table Try something like read.table(... ,sep =\t) (This is for tab delimited files) Others might give more ideas. Cheers, Tal Contact

Re: [R] Warning with mle

Hi Ben, thanks a lot for your answer. There are four reasonable solutions to your problems: 1. ignore the warnings, as long as they are all of the same type (NaNs/NAs being produced by dbinom or dpois), and as long as the final results look sensible. probably fine for me. The fit for my

Re: [R] agnes clustering and NAs

On Fri, 2011-01-28 at 10:00 +1100, Dario Strbenac wrote: Hello, Yes, that's right, it is a values matrix. Not a dissimilarity matrix. i.e. str(iMatrix) num [1:23371, 1:56] -0.407 0.198 NA -0.133 NA ... - attr(*, dimnames)=List of 2 ..$ : NULL ..$ : chr [1:56] -8100 -7900 -7700

[R] asterisk in subscript

hi, i am trying to label a plot axis with the equivalent of the latex $n_*$. i initially tried expression(paste(italic(n)[*])) but this made the * absolutely tiny and centred about midway wrt the n. then expression(paste(italic(n)[textstyle(*)])) made the * about the right size but now it

Re: [R] boxplot - code for labeling outliers - any suggestions for improvements?

On 01/28/2011 07:57 AM, Greg Snow wrote: Try: library(TeachingDemos) plot(Sepal.Length~Sepal.Width, data=iris) tmp.y- iris$Sepal.Length for( i in unique(iris$Sepal.Width) ) { tmp- iris$Sepal.Width == i tmp.y[ tmp ]- spread.labs( tmp.y[tmp], .6*strheight('A'),

Re: [R] asterisk in subscript

On Fri, 28 Jan 2011, Andrew Collier wrote: hi, i am trying to label a plot axis with the equivalent of the latex $n_*$. i initially tried expression(paste(italic(n)[*])) but this made the * absolutely tiny and centred about midway wrt the n. then expression(paste(italic(n)[textstyle(*)]))

Re: [R] identifying when one element of a row has a positive number

Hello, Thanks to everyone for the multiple answers. Josh, thanks for the function. My data 12 datasets have over 500,000 rows so your answer greatly appreciated. Cheers, Daisy On Thu, Jan 27, 2011 at 9:10 PM, Joshua Wiley jwiley.ps...@gmail.com wrote: Hi, This problem seemed deceptively

[R] Letters(V1,V2..) as row col indices instead of numbers

What makes matrix to print V1, V2 as the row and col indices instead of numbers?? cdata = read.table(ramesh.txt) #cdata is read from a file. c1 = cor(cdata) I am printing c1 below. I need only numbers. I dont need V1, V2...what should I do in this case??

Re: [R] Warning with mle

Hi Ben, thanks a lot for your answer. There are four reasonable solutions to your problems: 1. ignore the warnings, as long as they are all of the same type (NaNs/NAs being produced by dbinom or dpois), and as long as the final results look sensible. probably fine for me. The fit for my

[R] how to test pawer law distribution

Can somebody me helfen? I am confused how to use R to test the data wether it is pawer law distribution or not . power.law.fit in R can be used to calculate alpha,but with my knowledge firstly xmin should be confirmed before testing the data.Aber how? And the data has some zero values, that

Re: [R] Installing rgl

Hi Kevin, I have the same problem that you encountered , how did you resolved it? could you help me please?!!! Mohammad -- View this message in context: http://r.789695.n4.nabble.com/Installing-rgl-tp865867p3243992.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Adding image to plotting area

On 01/28/2011 11:00 AM, Dario Strbenac wrote: Hello, I've drawn a black rectangle over the plotting area, and when I add an image() heatmap, it doesn't take up all the area, but is set inward from the black rectangle. Can anyone suggest how to make it stretch out to the entire area ? Minimal

Re: [R] asterisk in subscript

thanks for the rapid response. yes, in x11 your suggestion works perfectly. i have never thought of the asterisk as being a superscript... to me it has always been the mulitply sign which is centred. thanks for the education! however, my plot is being sent to postscript, which i guess does not

[R] Problem with R Installation - .RData

Dear All, I have Windows Vista and I want to install R. However, when I tried to start it after the installation, I received the following message: 'Fatal error. I cannot retrieve the saved data from .RData'. So, in the moment R does not work. Do you have any idea how to cope with this

Re: [R] optim function multi variables -newbie

I tried to modify the code,thanks for noticing...now i get that the function cannot be evaluated at initial parameters.However I do not know what does that mean..Should I try to modify parameters. I am still not sure of syntax of function. I cannot get that optimize work correctly. I am trying to

[R] Linear mixed model: question about t-values

Dear all, I have a question about the output of linear mixed model fitted in R using nlme package. In particular, what are the t-values that are given in an output, how are they calculated and based on what test? I guess it cannot be a simple Student t-test, otherwise how can the simple

Re: [R] help for a loop procedure

On Thu, Jan 27, 2011 at 05:30:15PM +0100, Petr Savicky wrote: On Thu, Jan 27, 2011 at 11:30:37AM +0100, Serena Corezzola wrote: Hello everybody! I?m trying to define the optimal number of surveys to detect the highest number of species within a monitoring season/session. [...]

Re: [R] HLM Model

Hi Belle, try this: SAS: proc mixed data=test noclprint noinfo covtest noitprint method=reml; class pair grade team school; model score = trt pair grade school / solution ddfm=bw notest; random int / sub=team solution type=un r; run; R: require(nlme) unstruct -

Re: [R] Quasi-poisson glm and calculating a qAIC and qAICc...trying to modilfy Bolker et al. 2009 function to work for a glm model

On Thu, 2011-01-27 at 08:20 -0500, Jason Nelson wrote: Sorry about re-posting this, it never went out to the mailing list when I posted this to r-help forum on Nabble and was pending for a few days, now that I am subscribe to the mailing list I hope that this goes out: I've been a viewer of

Re: [R] asterisk in subscript

On 28-Jan-11 10:24:23, Andrew Collier wrote: thanks for the rapid response. yes, in x11 your suggestion works perfectly. i have never thought of the asterisk as being a superscript... to me it has always been the mulitply sign which is centred. thanks for the education! however, my plot

Re: [R] adding text to y-axis per row of panels (lattice)

On Thu, Jan 20, 2011 at 2:04 PM, E Hofstadler e.hofstad...@gmail.com wrote: Dear all, Being a newbie to R, I've trawled through many old posts on this list looking for a solution to my problem, but unfortunately couldn't quite figure it out myself. I'd be very grateful if someone here on this

Re: [R] Help needed

On Thu, 2011-01-27 at 09:50 -0500, Thomas Stewart wrote: For question 2, TTT - rt(1000,3) mean(TTT[rank(TTT) = 975 rank(TTT) 25]) mean(TTT, trim = 0.05) What you are doing is only removing 5% of observations in total, whilst the question asks for 5% removed off *each* end. G On Thu,

[R] survreg 3-way interaction

Dear All, I was wondering why survreg (in survival package) can not handle three-way interactions. I have an AFT (accelerated failure time) model with a frailty term. If the model is restricted to two-way interactions, survreg and gamlss.cens (with random() term) give very similar results,

Re: [R] circular reference lines in splom

On Thu, Jan 20, 2011 at 9:45 AM, Max Kuhn mxk...@gmail.com wrote: Hello everyone, I'm stumped. I'd like to create a scatterplot matrix with circular reference lines. Here is an example in 2d: library(ellipse) set.seed(1) dat - matrix(rnorm(300), ncol = 3) colnames(dat) - c(X1, X2, X3)

[R] axis name editing

Dear All, I'm generating a heatmap, is there a way to make Y axis name display horizontally, X axis name display vertically? I tried using horiz=TRUE: axis(1,at=1:dim(cor.meta.m)[1],labels=gsub(module,,pw.names),horiz=T RUE) but got warning message and the name is not displayed as I wish:

Re: [R] asterisk in subscript

magic! this does the trick: expression(paste(italic(n)[symbol(\052)])) thanks for the hint, ted! -- Andrew B. Collier Physicist Waves and Space Plasmas Group Hermanus Magnetic Observatory Honorary Senior Lecturer tel: +27 31 2601157 Space Physics Research

Re: [R] Help for lattice. par(new=TRUE)

On Fri, Jan 21, 2011 at 8:22 PM, Fabrice Tourre fabrice.c...@gmail.com wrote: Hi list, I want to plot two plot in the same figure. I set par(new=TRUE). But it does not work. library(lattice) myPanel - function(x,...) {       panel.histogram(x,alpha=0.4,...)      

Re: [R] agnes clustering and NAs

Gavin Simpson gavin.simp...@ucl.ac.uk on Fri, 28 Jan 2011 09:23:05 + writes: On Fri, 2011-01-28 at 10:00 +1100, Dario Strbenac wrote: Hello, Yes, that's right, it is a values matrix. Not a dissimilarity matrix. i.e. str(iMatrix) num

Re: [R] Problem with R Installation - .RData

On 11-01-28 5:15 AM, Iva wrote: Dear All, I have Windows Vista and I want to install R. However, when I tried to start it after the installation, I received the following message: 'Fatal error. I cannot retrieve the saved data from .RData'. So, in the moment R does not work. Do you have any

Re: [R] Problem with R Installation - .RData

On Fri, 28 Jan 2011, Duncan Murdoch wrote: On 11-01-28 5:15 AM, Iva wrote: Dear All, I have Windows Vista and I want to install R. However, when I tried to start it after the installation, I received the following message: 'Fatal error. I cannot retrieve the saved data from .RData'. So,

Re: [R] read.table() versus scan()

On Thu, Jan 27, 2011 at 11:23 PM, H Roark hrbuil...@hotmail.com wrote: I need to import a large number of simple, space-delimited text files with a few columns of data each. The one quirk is that some rows are missing data and some contain junk text at the end of each line. A typical file

Re: [R] adding text to y-axis per row of panels (lattice)

Hello Deepayan, many thanks for your reply and help. Does this solution with ylab.right require a newer version of lattice (somewhere in the archives I noted ylab.right being mentioned in the context of a development version of lattice)? I currently use R version 2.11.1 (2010-05-31) via Emacs

Re: [R] Quasi-poisson glm and calculating a qAIC and qAICc...trying to modilfy Bolker et al. 2009 function to work for a glm model

Gavin, Thanks for your help, but I did find in Booker et al. 2009 supplemental material where they did use logLik for quasi- distributed data. Even though it was for mixed models effect. In section 6 in the supplemental material, this is the model: mp1 - lmer(total.fruits ~ nutrient * amd +

[R] Error using write.xlsx library(xlsx)

Dear Adrian, I would like to export a quite large matrix from R to Excel (40 columns, 257 597 rows). After 10 minutes of work, I get the following error message: Error in .jcall(row[[ir]], Lorg/apache/poi/ss/usermodel/Cell;, createCell, : Java Exception no description because toString()

Re: [R] Linear mixed model: question about t-values

Kostenko, Olga O.Kostenko at nioo.knaw.nl writes: I have a question about the output of linear mixed model fitted in R using nlme package. In particular, what are the t-values that are given in an output, how are they calculated and based on what test? I guess it cannot be a simple Student

[R] boxplot - how to supress groups with low counts

In a boxplot - how can I prevent groups where the number of cases is less than a set threshold from being plotted. set.seed(42) DF - data.frame(type=sample(LETTERS[1:5], 100, replace=TRUE), cost=rnorm(100)) count - boxplot(cost ~ type, data=DF, plot = 0) count$n ## how to only include

Re: [R] adding text to y-axis per row of panels (lattice)

On Fri, Jan 28, 2011 at 5:21 PM, E Hofstadler e.hofstad...@gmail.com wrote: Hello Deepayan, many thanks for your reply and help. Does this solution with ylab.right require a newer version of lattice (somewhere in the archives I noted ylab.right being mentioned in the context of a development

[R] plot not generic

Hello list. I was trying to see some of the code for plot.glmnet in package glmnet (this function name is in the documentation). After loading the library, I tried the obvious typing in the name, but I received a message telling me it could not be found. So I fiddled around a little, and

Re: [R] Saving log file in R and display run time

On 27.01.2011 19:33, Raquel Rangel de Meireles Guimarães wrote: Hi all, I have two basic questions, hope you should help me: 1. How do I save a log file in R with the results? For example, in Stata it can be done by using log using c:\...\test.txt See ?sink. 2. How do I display the

[R] Free R Course Chile / Curso Gratis R (Universidad Andres Bello)

(English version below) Queridos R-usuarios!   Con mis colegas estamos creando un curso básico de nuestra espectacular herramienta R. Nos hemos dado cuenta que muchas personas usan software comercial y pensamos que sería una buena oportunidad para dar un curso gratis acerca de R. Por otro

Re: [R] plot not generic

dear Nick, getAnywhere(plot.glmnet) Note the message you get when you type methods(plot) ... Non-visible functions are asterisked Il 28/01/2011 14.26, Nick Sabbe ha scritto: Hello list. I was trying to see some of the code for plot.glmnet in package glmnet (this function name is in

Re: [R] read.table() versus scan()

On 2011-01-27 20:23, H Roark wrote: I need to import a large number of simple, space-delimited text files with a few columns of data each. The one quirk is that some rows are missing data and some contain junk text at the end of each line. A typical file might look like: a b c d 1 2 3 x 4 5

[R] get type functions (was: RE: plot not generic)

Thanks for that, Vito. Somehow, I often get lost in the whole slew of similar methods: * get * getMethod * showMethods * getAnywhere * methods Does anybody have a simple list of when to use which one? And maybe I'm even missing some variants? Thx. Nick. -Original Message- From: Vito

[R] Odp: Letters(V1,V2..) as row col indices instead of numbers

Hi r-help-boun...@r-project.org napsal dne 28.01.2011 09:52:05: What makes matrix to print V1, V2 as the row and col indices instead of numbers?? cdata = read.table(ramesh.txt) #cdata is read from a file. c1 = cor(cdata) I am printing c1 below. I need only numbers. I dont need V1,

Re: [R] help for a loop procedure

Hello Petr. First of all, thank you for your help! If i understand you correctly, your real table U has 32 rows and you want to consider all subsets of at most 10 rows. Sorry, I wasn’t clear: I have more datasets to analyse, some of them of just 10 samples, and others of 32. So:

[R] Injecting code in a package?

Dear list, I've had this a few times now, and wonder if this is possible: I'm using a package, often for plotting something, but I want to tune the way the plotting goes, in a way that was not foreseen by the maker of the package. Now, most of the time, these kinds of R functions (say

Re: [R] boxplot - how to supress groups with low counts

On 28.01.2011 14:21, pdb wrote: In a boxplot - how can I prevent groups where the number of cases is less than a set threshold from being plotted. set.seed(42) DF- data.frame(type=sample(LETTERS[1:5], 100, replace=TRUE), cost=rnorm(100)) count- boxplot(cost ~ type, data=DF, plot = 0)

Re: [R] Measure execution time

On 28.01.2011 09:07, Alaios wrote: Dear list members, I would like to measure how much time one function call makes from the time is call until the time it returns. Could you please tell me if that is possible in R? ?system.time Uwe Ligges Best Regards Alex

Re: [R] Injecting code in a package?

On 28.01.2011 14:57, Nick Sabbe wrote: Dear list, I've had this a few times now, and wonder if this is possible: I'm using a package, often for plotting something, but I want to tune the way the plotting goes, in a way that was not foreseen by the maker of the package. Now, most of the

Re: [R] axis name editing

Use the argument las as explained in ?par. Uwe Ligges On 28.01.2011 11:56, Yan Jiao wrote: Dear All, I'm generating a heatmap, is there a way to make Y axis name display horizontally, X axis name display vertically? I tried using horiz=TRUE:

Re: [R] boxplot - how to supress groups with low counts

On 2011-01-28 06:09, Uwe Ligges wrote: On 28.01.2011 14:21, pdb wrote: In a boxplot - how can I prevent groups where the number of cases is less than a set threshold from being plotted. set.seed(42) DF- data.frame(type=sample(LETTERS[1:5], 100, replace=TRUE), cost=rnorm(100)) count-

Re: [R] Injecting code in a package?

On Fri, Jan 28, 2011 at 8:57 AM, Nick Sabbe nick.sa...@ugent.be wrote: Dear list, I've had this a few times now, and wonder if this is possible: I'm using a package, often for plotting something, but I want to tune the way the plotting goes, in a way that was not foreseen by the maker of

[R] (no subject)

Hello, I have a data set with each column containing data like this: row column1 1 1.2 2 NA 3 NA 4 3 5 5 6 NA 7 1.5 8 NA 9 NA 10 NA 11 3 12 NA 13 3 14 NA 15 NA 16 NA 17 NA 18 3 19 1.2 20 NA From this I would like to extract the sequence containing at least three rows of 3 in

Re: [R] survreg 3-way interaction

I was wondering why survreg (in survival package) can not handle three-way interactions. I have an AFT . You have given us no data to diagnose your problem. What do you mean by cannot handle -- does the package print a message no 3 way interactions, gives wrong answers, your laptop

[R] Fwd: mvoutlier

Begin forwarded message: From: stephen sefick ssef...@gmail.com Date: January 28, 2011 9:11:07 AM CST To: Claudia Paladini claudiapalad...@web.de Subject: Re: [R] mvoutlier Try this. #your code library(mvoutlier) library(robustbase) data(bsstop) x=bsstop[1:100,5:14]

[R] Odp: (no subject)

Hi r-help-boun...@r-project.org napsal dne 28.01.2011 15:37:07: Hello, I have a data set with each column containing data like this: row column1 1 1.2 2 NA 3 NA 4 3 5 5 6 NA 7 1.5 8 NA 9 NA 10 NA 11 3 12 NA 13 3 14 NA 15 NA 16 NA 17 NA 18 3 19 1.2 20

Re: [R] (no subject)

This looks like homework. We don't do homework. Certainly not when you obviously haven't a) read the posting guide, b) asked your professor/tutor, c) googled to see if you find something online, d) at least made an effort to try, and e) read the posting guide. Do all the points above and

[R] ReferenceClasses examples {method}

Dear help, dear John Chambers, I'm trying to learn OOP-possibilities in R and I was going through the documentation 'ReferenceClasses {methods}'. (great work, by the way...) Reading associated Examples, something bothers me : it seems to me that there are errors in 'edit' and 'undo' methods. I

Re: [R] Odp: Letters(V1, V2..) as row col indices instead of numbers

Hi KumaraGuru kumaragur...@gmail.com napsal dne 28.01.2011 17:03:50: I want to melt the cor matrix and form a 3 col matrix with row# col# and cor. Well, in that case it will be probably better to transform it to data frame and use melt. Or you can drop dimensions of this matrix and generate

[R] read ODS (OOorg spreadsheet) files?

I am wondering if there's any news about reading ODS files directly. ODS files are the spreadsheet files produced by OpenOffice.org. Currently, I export sheets in these files to csv files, one for each sheet. However, it would be much more convenient to read them directly. Thanks for hints and

Re: [R] ReferenceClasses examples {method}

On Jan 28, 2011, at 11:05 AM, Marc Carpentier wrote: Dear help, dear John Chambers, I'm trying to learn OOP-possibilities in R and I was going through the documentation 'ReferenceClasses {methods}'. (great work, by the way...) Reading associated Examples, something bothers me : it seems to

Re: [R] read ODS (OOorg spreadsheet) files?

On 11-01-28 17:37, Sascha Vieweg wrote: I am wondering if there's any news about reading ODS files directly. ODS files are the spreadsheet files produced by OpenOffice.org. Currently, I export sheets in these files to csv files, one for each sheet. However, it would be much more convenient to

Re: [R] Odp: Letters(V1, V2..) as row col indices instead of numbers

I want to melt the cor matrix and form a 3 col matrix with row# col# and cor. This I m using to draw a graph. Regards, Kumaraguru On Jan 28, 2011, at 6:47 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi r-help-boun...@r-project.org napsal dne 28.01.2011 09:52:05: What makes matrix

[R] Plot 1:1 relationship

Dear list, I am looking to plot a line on a graph to show the 1:1 relationship, in order to demonstrate the pattern i have observed is off the line, however i am unsure. I have tried abline but i can not see a function to plot the 1:1? Any help would be greatly appreciated #generate data y -

Re: [R] Odp: Letters(V1, V2..) as row col indices instead of numbers

While listing it like that is it possible to remove the rows that has same row and col numbers? Like.. 1 1 x 2 2 x2 Regards, Kumaraguru On Jan 28, 2011, at 9:23 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi KumaraGuru kumaragur...@gmail.com napsal dne 28.01.2011 17:03:50: I

Re: [R] Odp: Letters(V1, V2..) as row col indices instead of numbers

Suppose your correlation matrix is called cc. One way to do what you want is result = cbind(as.vector(row(cc)),as.vector(col(cc)),as.vector(cc)) result = result[result[,1] != result[,2],] - Phil Spector

Re: [R] boxplot - code for labeling outliers - any suggestions for improvements?

Hello Greg, Kevin, Jim and other R-help members, Regarding text spacing: Drew Conway published today a fascinating post about Building a Better Word Cloud. I don't know if his function can help you (or if either of you might help him with his code). But either way, I think it's worth reading his

[R] Problems making subsets with [] or subset

Hi, I'm trying to make a model in order to know wich factors got´s influence in the intensity of a infection, but just in the individuals who's got this infection. In my data I've got a variable called prevalence with 2 levels: 1.- Infected individual 0.- Non infected So what i'm trying to do is

[R] Problems replacing empty cells with NA values

Hi, I am preparing a quite huge database in Excel, I replaced the empty cells with NA, I formatted it like text, and saved the file like a *.txt. After, in R: data-read.table(myfile.txt,header=T,sep=\t) edit(data) When doing this I can see that some columns are OK and they have NA cells, but

[R] Re : ReferenceClasses examples {method}

Right. Shame on me : Friday's tiredness ; I don't know why I stuck on that. Please just consider the main topic of my message, regarding the example of ReferenceClasses (supposing it's appropriate) and sorry for the subsequent question... - Message d'origine De : David Winsemius

Re: [R] Plot 1:1 relationship

abline() takes the intercept and slope, which for a 1:1 relationship are 0 and 1, respectively. So: abline(0, 1) Sarah On Fri, Jan 28, 2011 at 10:42 AM, Peter Francis peterfran...@me.com wrote: Dear list, I am looking to plot a line on a graph to show the 1:1 relationship, in order to

Re: [R] Re : ReferenceClasses examples {method}

On Jan 28, 2011, at 12:35 PM, Marc Carpentier wrote: Right. Shame on me : Friday's tiredness ; I don't know why I stuck on that. Please just consider the main topic of my message, regarding the example of ReferenceClasses (supposing it's appropriate) and sorry for the subsequent

Re: [R] Problems making subsets with [] or subset

Hi Mario, On Fri, Jan 28, 2011 at 12:27 PM, gaiarrido gaiarr...@usal.es wrote: Hi, I'm trying to make a model in order to know wich factors got´s influence in the intensity of a infection, but just in the individuals who's got this infection. In my data I've got a variable called prevalence

[R] R-/Text-editor for Windows?

Tinn-R (http://www.sciviews.org/Tinn-R/) is one of the topmost suggestions when googling an R-(text-)editor for Windows. However, to me it appears dissappointing that Tinn-R does not handle utf-8 (mac-roman, or any other) encoded R-scripts or, in general, text files. Besides Emacs and the R

[R] Re : Re : ReferenceClasses examples {method}

I hadn't found any message on this subject. Nevertheless you're right again : I've posted this report on r-devel-list where it obviously belongs... Marc - Message d'origine De : David Winsemius dwinsem...@comcast.net À : Marc Carpentier marc.carpent...@ymail.com Cc :

[R] how to get coefficient and scores of Principal component analysis in R?

Dear All, It might be a simple question. But I could not find the answer from function “prcomp” or “princomp”. Does anyone know what are the codes to get coefficient and scores of Principal component analysis in R? Your reply will be appreciated! Best Zunqiu [[alternative

[R] mysterious error from foreach

On my first foray into foreach I am getting this error: Error in function (handle) : no function to return from, jumping to top level I get one of these for each worker. I am using the doMC/multicore back end. At first I thought this was caused by the text progress bars that the

Re: [R] how to get coefficient and scores of Principal component analysis in R?

By coefficients do you mean loadings? Anyway, if you read the help for princomp -- ?princomp -- will get that, you'll see that it says, in part: ‘princomp’ returns a list with class ‘princomp’ containing the following components: sdev: the standard deviations of the principal

Re: [R] R-/Text-editor for Windows?

I strongly suggest reconsidering your rejection of Emacs + ESS. However, if you cannot be persuaded of this, I hear WinEdit is pretty good. In case you haven't already found them, the following resources may be helpful: http://www.sciviews.org/_rgui/projects/Editors.html

Re: [R] how to get coefficient and scores of Principal component analysis in R?

Hello On Fri, Jan 28, 2011 at 8:16 PM, Zunqiu Chen che...@ohsu.edu wrote: It might be a simple question. But I could not find the answer from function “prcomp” or “princomp”. Does anyone know what are the codes to get coefficient and scores of Principal component analysis in R? Try these:

[R] Plotting accumulated data

Hello all I have the data frame with this: ID DATETIME TRN TRN_S 1 1192756 2010-06-23 15:39:07 13.420 0.2236667 2 1192757 2010-06-23 15:40:07 13.805 0.2300833 3 1192758 2010-06-23 15:41:07 13.860 0.231 4 1192759 2010-06-23 15:42:07 13.750 0.2291667 5

[R] Paired data survival analysis, part 2

I'm curious. I've used the paired-prentice Wilcoxon test for the analysis of parried survival data. I haven't run into use of the coxph for that previously, but I have seen it referenced a couple of times in recent web searches. I have a data set of subjects like this: SubjectT1 R1 T2

Re: [R] R-/Text-editor for Windows?

Notepad ++ handles just about anything and has an accompanying program NppToR to make passing scripts easier. Geany also handles a ton of filetypes, but lacks a direct interface to R in the windows version - I wrote an AutoHotKey script that did this for me in about 5 minutes. On the other

Re: [R] Plotting accumulated data

On Jan 28, 2011, at 3:07 PM, Ottar Kvindesland wrote: Hello all I have the data frame with this: ID DATETIME TRN TRN_S 1 1192756 2010-06-23 15:39:07 13.420 0.2236667 2 1192757 2010-06-23 15:40:07 13.805 0.2300833 3 1192758 2010-06-23 15:41:07 13.860

Re: [R] optim function multi variables -newbie

michalseneca michalseneca at gmail.com writes: I tried to modify the code,thanks for noticing... now i get that the function cannot be evaluated at initial parameters. However I do not know what does that mean.. Should I try to modify parameters. I am still not sure of syntax of function. I

Re: [R] Help with ape - read.GenBank()

James Meadow jfmeadow at gmail.com writes: Hi, I am trying to work with the ape package, and there is one thing I am struggling with. When calling the *read.GenBank()* function, I can get it to work with an object created like this: *x - c(AY395554,AY611035, ...)* *read.GenBank(x)*

Re: [R] R-/Text-editor for Windows?

Hi Sascha, On 01/28/2011 07:55 PM, Sascha Vieweg wrote: Tinn-R (http://www.sciviews.org/Tinn-R/) is one of the topmost suggestions when googling an R-(text-)editor for Windows. However, to me it appears dissappointing that Tinn-R does not handle utf-8 (mac-roman, or any other) encoded R-scripts

Re: [R] Meaning of pterms in survreg object?

Johannes Huesing johan...@huesing.name [Mon, Jan 10, 2011 at 09:26:37PM CET]: I am trying to model survival data with a Weibull distribution using survreg. Units are clustered two apiece, sometimes receiving

Re: [R] survreg 3-way interaction

The fire devoured my laptop, but the PC is still working... :) Sorry for the lazyness, you are totally right. Here goes a reproducible example, which resembles the main features of our dataset: # three experimental factors, 30 subjects expgrid - expand.grid(F1=0:1,F2=0:1,F3=0:1,id=1:30) # set

[R] User error in calling predict/model.frame

I want to predict values from an existing lm (linear model, e.g. lm.obj) result in R using a new set of predictor variables (e.g. newdata). However, it seems that because my linear models was made by calling scale() on the target predictor that predict exits with an error, Error in scale(xxA,

[R] Months in alphabetical order rather than chronological order in graph

Greetings Though I have months in chronological order in my data table, the data were sampled every other month (i.e., February, April, June, August, October, December), every time I try to plot them (on the x-axis) they are plotted in alphabetical order. What am I missing? Cheers Kurt

Re: [R] Months in alphabetical order rather than chronological order in graph

Kurt You need to give us more information if you want good advice. For example, what sort of plot are you trying to make? A barplot? A time series? A reproducible example is always best. Please see the R-news posting guide for hints on a successful query. On Jan 28, 2011, at 1:53 PM,

Re: [R] Months in alphabetical order rather than chronological order in graph

On Jan 28, 2011, at 4:53 PM, kurt_h...@nps.gov wrote: Greetings Though I have months in chronological order in my data table, the data were sampled every other month (i.e., February, April, June, August, October, December), every time I try to plot them (on the x-axis) they are

Re: [R] Months in alphabetical order rather than chronological order in graph

You need to make your variable into a factor and specify the order. mymonths - c(December, March) factor(mymonths) [1] December March Levels: December March factor(mymonths, levels=month.name) [1] December March 12 Levels: January February March April May June July August September October ...

Re: [R] Plot 1:1 relationship

In addition you may want to include asp=1 and pty='s' to the plot command. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org]

Re: [R] Months in alphabetical order rather than chronological order in graph

This would be easier if you showed us a sample of your data and what commands you are using. Without we need to guess. Probably your month variable is being turned into a factor somewhere and the default for factors is alphabetical. The best solution depends on how/where/when your months are

Re: [R] User error in calling predict/model.frame

Hi Russell, There may be some subtleties that I'm not picking up on, but the obvious problem is that the names of the predictors in newdata do not match the names of the predictors in dat. names(newdata) - names(dat)[1:2] newdata$Y - predict(lm.obj,newdata) does work on my machine. Best,

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