Re: [R] frequency table?

2011-12-05 Thread Jim Lemon
On 12/04/2011 08:21 PM, set wrote: Hello R-users, I've got a file with individuals as colums and the clusters where they occur in as rows. And I wanted a table which tells me how many times each individual occurs with another. I don't really know how such a table is called...it is not a

[R] Spatstat - problem with which.marks and as.pp

2011-12-05 Thread karajamu
I forgot to change the header, so I guess no one read my mail. That's why I'm trying it again... Hello everbody, I am new to this mailing list and hope to find some help. I'm trying to get into the spatstat package and encountered two problems. First a graphical one: There is an

[R] ANNOUNCEMENT: Call for Proposals for The R Series from Chapman Hall/CRC

2011-12-05 Thread Calver, Rob
Chapman Hall/CRC: The R Series We are delighted to announce that our new series of books on R is up and running, with two books already published and another nine forthcoming (including three set to publish in 2012). We are keen to receive proposals for books covering all aspects of the

Re: [R] [rggobi] ggplot like pdf output

2011-12-05 Thread S Ellison
neither the *DescribeDisplay* package, nor *ggplot* are available in 2.13.2. ggplot's package name is ggplot2. It certainly _was_ available for 2.13.2. S*** This email and any attachments

[R] iterative variable names

2011-12-05 Thread bcdc
Hi, I'm trying to assign iterative names to variable, but all my attempts have failed. I have a loop, and for every iteration, I need to create a variable, and I'd like to name them iteratively, such as: for(i in 1:10) { x_i - c(values) } I need it to return ten variables: x_1, x_2, ...,

Re: [R] iterative variable names

2011-12-05 Thread Uwe Ligges
On 05.12.2011 11:00, bcdc wrote: Hi, I'm trying to assign iterative names to variable, but all my attempts have failed. I have a loop, and for every iteration, I need to create a variable, and I'd like to name them iteratively, such as: for(i in 1:10) { x_i- c(values) } You actually

Re: [R] iterative variable names

2011-12-05 Thread Jim Holtman
?assign for (i in 1:10) assign(paste('x_', i, sep = ''), i) but before you do this, consider using a 'list'; check the archives since this is asked a lot. Sent from my iPad On Dec 5, 2011, at 5:00, bcdc bia@gmail.com wrote: Hi, I'm trying to assign iterative names to variable, but all

Re: [R] problems using the thin plate spline method

2011-12-05 Thread Mintewab Bezabih
Dear Sarah and R users, Sorry again for not being explicit enough. Here is my full problem dat - read.table(E:/thin plate/thin plate.csv, header=T, sep=,) dat names(dat) - c(x1, x2, y) library(fields) plot (dat) #load the fields package (containing Tps) and fit a thin plate spline tpsfit -

Re: [R] Data alignment

2011-12-05 Thread Petr PIKAL
Re: [R] Data alignment Thanks for your suggestions. I will try them. The - in my original post was actually only there to serve as a separator so that it is easier for you to see the data structure but apparently it rather confused you... sorry :) That is why dput is to be used. Try

Re: [R] problem merging data with different shapes

2011-12-05 Thread Petr PIKAL
Hi I have been trying to merge datasets, one of which has a long format (Adata) and one has a (different) long format (Bdata): Adata Bdata subject order bpm subject order trial agegroup gender 1 1 70.21 1

[R] Problem with parsing HTML table

2011-12-05 Thread Philipp Chapkovski
Hello! Can anybody help to convert this table (in fact there are two adjacent tables) into dataset?

Re: [R] nipals in the chemometrics package in R

2011-12-05 Thread zz dd
Hello The solution maybe there but i need to compute it into R if someone can help me : (Previously store score vector t in score matrix T; store loading vector p in loading matrix P) that's done by nipals in chemometrics After use of nipals function you have T and P matrix First : Calculate the

Re: [R] problems using the thin plate spline method

2011-12-05 Thread Jeff Newmiller
Try plot( dat$x1, dat$y ) or plot( x1, y, data=dat ) Note that your example is still not reproducible because you have not supplied the data or a shortened version of your data for us to work with. Also, your problem is not with thin plates but with plot, and reading the help for that

[R] Subsetting a data frame

2011-12-05 Thread natalie.vanzuydam
Hi R users, I really need help with subsetting data frames: I have a large database of medical records and I want to be able to match patterns from a list of search terms . I've used this simplified data frame in a previous example: db - structure(list(ind = c(ind1, ind2, ind3, ind4), test1

Re: [R] nipals in the chemometrics package in R

2011-12-05 Thread Jeff Newmiller
This is not a homework help list. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go...

Re: [R] problems using the thin plate spline method

2011-12-05 Thread Mintewab Bezabih
Dear Jeff and R users, Thanks Jeff. Your first plot suggestion worked. And when I stick dat$x1, dat$x2,dat$y, tpsfit seems to work as well. But it gives me a new error message tpsfit - Tps(cbind(dat$x1, dat$x2), dat$y, scale.type=unscaled) Warning message: In gcv.Krig(out, nstep.cv =

[R] how to just download file on disk by the link

2011-12-05 Thread Philipp Chapkovski
Sorry for stupid question but is there any way to just download file (excel file) from the url to the disk with a certain name? Now it seems that I should open it (via read.xls) and then write it by write.xls. But I am pretty sure it should be something much easier? [[alternative HTML

[R] extract cov matrix in summary.rq and use as a matrix.

2011-12-05 Thread Julia Lira
Dear all, I need to extract the covariance matrix of my quantile regression estimation to use in a test. My regression is: qf2_1 - summary(rq(wb2 ~ apv2 + vol2, tau = phi2[1]), cov = TRUE) I can extract the covaraince matrix by using: qf2_1 [3]. However, if I try to use it in the test, it

Re: [R] Toggle cASE

2011-12-05 Thread Eik Vettorazzi
Hi Antonio, how about this: txt2 - useRs may fly into JFK or laGuardia chartr(a-zA-Z, A-Za-z, txt2) Cheers. Am 05.12.2011 08:11, schrieb Tonio: Hello R-help list, I am looking for way to toggle the case of the characters like a flip-flop; that is from ''Hello'' to hELLO or vice versa.

Re: [R] how to just download file on disk by the link

2011-12-05 Thread Gabor Grothendieck
On Mon, Dec 5, 2011 at 7:03 AM, Philipp Chapkovski chapkov...@gmail.com wrote: Sorry for stupid question but is there any way to just download file (excel file) from the url to the disk with a certain name? Now it seems that I should open it (via read.xls) and then write it by write.xls. But I

Re: [R] nipals in the chemometrics package in R

2011-12-05 Thread zz dd
Thank you for your brevity you don't have to say more things to show who you are. Else if you don't understand what we are talking about, you shouldn't be rude and insulting. May be you are quite young please take time to read Nonaka and Takeuchi and moreover Takanashi to uderstand the way to go

[R] spatial analysis

2011-12-05 Thread Marianne.ZEYRINGER
Dear all, I am a PhD student in energy modelling. I am completely stuck with the following problem and would be very grateful for any kind of help. I have cells and each cell is assigned a number. I would like to form clusters of cells where the sum of the cell numbers in each cluster must not

Re: [R] extract cov matrix in summary.rq and use as a matrix.

2011-12-05 Thread R. Michael Weylandt michael.weyla...@gmail.com
I'm not at my desk so this is untested, but I'm pretty sure double brackets will do the trick: qf2_1[[3]] M On Dec 5, 2011, at 7:14 AM, Julia Lira julia.l...@hotmail.co.uk wrote: Dear all, I need to extract the covariance matrix of my quantile regression estimation to use in a test.

Re: [R] equating approximate values

2011-12-05 Thread R. Michael Weylandt michael.weyla...@gmail.com
Change which to which.min, but then you won't easily be able to get the corresponding x,y indices. Look at the arrayInd() function to translate the result to a particular x,y. Michael On Dec 4, 2011, at 7:04 PM, vamshi999 vamshi...@gmail.com wrote: this is exactly what i wanted. How to

Re: [R] problems using the thin plate spline method

2011-12-05 Thread R. Michael Weylandt michael.weyla...@gmail.com
Your data was scrubbed by the server. Use dput() to create a plain text representation of dat you can put in the body of the email. Michael On Dec 5, 2011, at 6:54 AM, Mintewab Bezabih mintewab.beza...@economics.gu.se wrote: Dear Jeff and R users, Thanks Jeff. Your first plot

Re: [R] Subsetting a data frame

2011-12-05 Thread jim holtman
does this do what you want: db - structure(list(ind = c(ind1, ind2, ind3, ind4), test1 = c(1, + 2, 1.3, 3), test2 = c(56L, 27L, 58L, 2L), test3 = c(1.1, 28, + 9, 1.2)), .Names = c(ind, test1, test2, test3), class = + data.frame, row.names = c(NA, + -4L)) terms_include - c(1,2,3) terms_exclude

Re: [R] iterative variable names

2011-12-05 Thread bcdc
Thank you very much, assign was exactly what I needed! For my case, it worked better than list! :) Beatriz -- View this message in context: http://r.789695.n4.nabble.com/iterative-variable-names-tp4159888p4160262.html Sent from the R help mailing list archive at Nabble.com.

[R] Dynamic Linear Models for Times Series - Implemented?

2011-12-05 Thread Amsalu Walelign
Dear sir, As far as my understanding goes, the book “dynamic linear models with R” does everything based up on the non innovations form. The problem is that I couldn’t find auxiliary residuals, which can be used to check for the presence of outliers and structural breaks. R packages “dlm” and

Re: [R] Partitioning Around Mediods then rpart to follow

2011-12-05 Thread Terry Therneau
Yes, that seems like a sensible idea to me. Terry Therneau On Sat, 2011-12-03 at 12:00 +0100, r-help-requ...@r-project.org wrote: The problem: There are no a priori groupings to run a classification on My solution: This is a non-R code question, so I appreciate any thoughts. I have

Re: [R] problems using the thin plate spline method

2011-12-05 Thread Mintewab Bezabih
Thanks Michael here is my data structure(list(x1 = c(409.5, 349, 385.5, 273, 543, 746, 198.75, 262.5, 320.5, 259, 399.5, 595.5, 374, 293, 330, 658, 299, 775, 559.75, 251, 402, 395.5, 345.5, 283.5, 452, 816.5, 266.5, 360.25, 386, 160.25, 360, 337, 326, 758, 342.5, 389, 347.5, 819.25, 355.25, 281,

Re: [R] Project local libraries (reproducible research)

2011-12-05 Thread Hadley Wickham
On Sat, Dec 3, 2011 at 11:16 AM, Jim Lemon j...@bitwrit.com.au wrote: On 12/03/2011 06:04 AM, Hadley Wickham wrote: Hi all, I was wondering if any one had scripts that they could share for capturing the current version of R packages used for a project. I'm interested in creating a project

Re: [R] Persp3d freezes when run from within Python

2011-12-05 Thread Duncan Murdoch
On 11-12-04 8:57 PM, wchips wrote: G'day everyone, I've been trying to get an interactive OpenGL plot to work from within Python 2.6 using Rpy2 and the persp3d function. The problem is that the plot seems to freeze upon activation. All interactivity is lost even though it works fine when run

Re: [R] extract cov matrix in summary.rq and use as a matrix.

2011-12-05 Thread R. Michael Weylandt michael.weyla...@gmail.com
No problem, almost all complicated objects that get returned are internally lists so you have to use [[ to get at them as [ will just give you a list again. Take a look at ? '[[' # those should be back ticks for the official documentation. Best, M On Dec 5, 2011, at 8:09 AM, Julia Lira

Re: [R] about interpretation of anova results...

2011-12-05 Thread Roger Koenker
If you were to rtfm you'd see that your anova suggests that the slope coefficients are the same for your tau = .15 and tau = .30 models. url:www.econ.uiuc.edu/~rogerRoger Koenker emailrkoen...@uiuc.eduDepartment of Economics vox: 217-333-4558

[R] finding interpolated values along an empirical parametric curve

2011-12-05 Thread Michael Friendly
Given the following data, I am plotting log.det ~ norm.beta, where the points depend on a parameter, lambda (but there is no functional form). I want to find the (x,y) positions along this curve corresponding to two special values of lambda lambda.HKB - 0.004275357 lambda.LW - 0.03229531 and

Re: [R] iterative variable names

2011-12-05 Thread S Ellison
-Original Message- Thank you very much, assign was exactly what I needed! For my case, it worked better than list! :) If assign(paste('x_', i)) works better for your case than using a list or array , you must surely have a very strange case S

Re: [R] finding interpolated values along an empirical parametric curve

2011-12-05 Thread John Fox
Hi Michael, I can get what appears to be a good interpolation with a regression spline in a multivariate LM, playing around with the tuning parameter to leave 1 residual df. Try this: library(splines) mod - lm(cbind(log.det, norm.beta) ~ bs(lambda, df=4), data=pd) summary(mod) x -

[R] R 2-14.0 locking up

2011-12-05 Thread Erin Hodgess
Dear R People: I'm working with R-2.14.0 created from source on a quad core Windows 7 machine. Starting yesterday, nearly everything I run just sits. When I hit escape or Ctrl C, nothing happens. Has anyone run into this, please? Any suggestions would be much appreciated. Thanks, Erin --

Re: [R] nipals in the chemometrics package in R

2011-12-05 Thread Pedro Mardones
Perhaps you can try the examples given in http://www.jstatsoft.org/v18/i02 for getting a better idea about how the NIPALS algorithm works. BTW, yes,it looks like a homework question specially when your user name is zz dd void1...@gmail.com so you can't be recognized. On Mon, Dec 5, 2011 at 9:27

Re: [R] R 2-14.0 locking up

2011-12-05 Thread Steve Lianoglou
Hi, On Mon, Dec 5, 2011 at 10:03 AM, Erin Hodgess erinm.hodg...@gmail.com wrote: Dear R People: I'm working with R-2.14.0 created from source on a quad core Windows 7 machine. Starting yesterday, nearly everything I run just sits.  When I hit escape or Ctrl C, nothing happens. Has

Re: [R] similarity matrix

2011-12-05 Thread B77S
That really all depends on what you need; and I can't tell you what you need. set wrote I'm sorry, I made a mistake in my example. you're right. I don't really know how a similarity alogrithm worksbut I'm willing to try that...are there any good examples available? Thank you --

Re: [R] equating approximate values

2011-12-05 Thread David Winsemius
On Dec 5, 2011, at 8:02 AM, R. Michael Weylandt wrote: Change which to which.min, but then you won't easily be able to get the corresponding x,y indices. Look at the arrayInd() function to translate the result to a particular x,y. The arrayInd help page is shared by the which help and

[R] using StatEt IDE for Eclipse

2011-12-05 Thread Matteo Richiardi
Hi, I'm trying to use StatEt IDE for Eclipse as my R editor, but I'm completely lost. I've read all I could find online, made apparently all I had to do (installing rj, configuraing StatEt, etc.) but still cannot make R running. Below is the error log file. Thank you so much for assistance. Matteo

[R] barplot ignoring col parameter

2011-12-05 Thread Federico Calboli
Hi All, I'm having a problem with barplot: mydata [1,] 2 108 0 0 0 1 3 0 0 0 0 0 7 18 3 4 8 20 26 20 19 7 1 1 mycol = c(rep('yellow', 2), rep('white', 3), rep('orange',2), rep('white', 5), rep('orange',3), rep('red',9)) barplot(mydata, col = mycol) gives me an uniformly

Re: [R] nipals in the chemometrics package in R

2011-12-05 Thread zz dd
Thank's Pedro Madrones, you're right that i have removed my name of the email (because of Spam, and datas that i can't remove on the net). Ok, i explain a bit more : X is a centred matrix. PCA summarise all variation of X into a few new variables called scores T.These new variables are linearly

Re: [R] barplot ignoring col parameter

2011-12-05 Thread David Winsemius
On Dec 5, 2011, at 10:44 AM, Federico Calboli wrote: Hi All, I'm having a problem with barplot: mydata [1,] 2 108 0 0 0 1 3 0 0 0 0 0 7 18 3 4 8 20 26 20 19 7 1 1 mycol = c(rep('yellow', 2), rep('white', 3), rep('orange',2), rep('white', 5), rep('orange',3),

Re: [R] barplot ignoring col parameter

2011-12-05 Thread R. Michael Weylandt
x - c(2L, 108L, 0L, 0L, 0L, 1L, 3L, 0L, 0L, 0L, 0L, 0L, 7L, 18L, 3L, 4L, 8L, 20L, 26L, 20L, 19L, 7L, 1L, 1L) mycol = c(rep('yellow', 2), rep('white', 3), rep('orange',2), rep('white', 5), rep('orange',3), rep('red',9)) barplot(x, col = mycol) Produces a multi-colored barplot on my machine so I

Re: [R] finding interpolated values along an empirical parametric curve

2011-12-05 Thread Michael Friendly
Thanks, John That's very clever. I didn't realize that the splines package supports multivariate regression splines and that works well enough for my purposes; plus this solution is very transparent. best, -Michael On 12/5/2011 9:50 AM, John Fox wrote: Hi Michael, I can get what appears

Re: [R] extract cov matrix in summary.rq and use as a matrix.

2011-12-05 Thread Julia Lira
Dear Michael, Thank you very much for your suggestion. It indeed worked! All the best, Julia CC: r-help@r-project.org From: michael.weyla...@gmail.com Subject: Re: [R] extract cov matrix in summary.rq and use as a matrix. Date: Mon, 5 Dec 2011 07:55:45 -0500 To:

[R] Weighting and recodification

2011-12-05 Thread SilvaForever
I have a question that is more statistical than r-specific I have to recode a variable into quartiles, and I have weighted individuals. To calculate the quartiles that will serve me to recode the variable, should I use the weight or not? -- View this message in context:

[R] Flexclust package: kcca object's methods and properties?

2011-12-05 Thread Pundurs, Mark
What are all the methods and properties for the flexclust package's kcca object? Neither http://cran.r-project.org/web/packages/flexclust/flexclust.pdf nor http://www.stat.uni-muenchen.de/~leisch/papers/Leisch-2006.pdf appear to include a comprehensive centralized list. Mark Pundurs Data Analyst

Re: [R] barplot ignoring col parameter

2011-12-05 Thread Federico Calboli
On 5 Dec 2011, at 15:58, R. Michael Weylandt wrote: x - c(2L, 108L, 0L, 0L, 0L, 1L, 3L, 0L, 0L, 0L, 0L, 0L, 7L, 18L, 3L, 4L, 8L, 20L, 26L, 20L, 19L, 7L, 1L, 1L) mycol = c(rep('yellow', 2), rep('white', 3), rep('orange',2), rep('white', 5), rep('orange',3), rep('red',9)) barplot(x, col =

Re: [R] Weighting and recodification

2011-12-05 Thread David Winsemius
On Dec 5, 2011, at 10:19 AM, SilvaForever wrote: I have a question that is more statistical than r-specific I have to recode a variable into quartiles, and I have weighted individuals. To calculate the quartiles that will serve me to recode the variable, should I use the weight or not?

Re: [R] barplot ignoring col parameter

2011-12-05 Thread R. Michael Weylandt
barplot() defaults to stacked bars for matrices and uses the colors fresh for each bar: e.g., layout(1:2) barplot(matrix(1:6, 2), col = c(red, blue,green)) barplot(matrix(1:6, 3), col = c(red, blue,green)) To get what you are looking for, try something like this: x = matrix(1:6,1); colnames(x)

[R] adding hyperlinked text to pdf plot

2011-12-05 Thread Justin Fincher
Howdy, I have read that if you put a URL in the text of a plot being saved into pdf, the result is a functional hyperlink. I am interested in having text in a plot that is linked to a URL, but I would like the text to be something other than the URL. Is this possible? Thank you. - Fincher

[R] explanation why RandomForest don't require a transformations (e.g. logarithmic) of variables

2011-12-05 Thread gianni lavaredo
Dear Researches, sorry for the easy and common question. I am trying to justify the idea of RandomForest don't require a transformations (e.g. logarithmic) of variables, comparing this non parametrics method with e.g. the linear regressions. In leteruature to study my phenomena i need to apply a

Re: [R] adding hyperlinked text to pdf plot

2011-12-05 Thread Ted Harding
On 05-Dec-11 18:39:21, Justin Fincher wrote: Howdy, I have read that if you put a URL in the text of a plot being saved into pdf, the result is a functional hyperlink. I am interested in having text in a plot that is linked to a URL, but I would like the text to be something other than

Re: [R] explanation why RandomForest don't require a transformations (e.g. logarithmic) of variables

2011-12-05 Thread Liaw, Andy
Tree based models (such as RF) are invriant to monotonic transformations in the predictor (x) variables, because they only use the ranks of the variables, not their actual values. More specifically, they look for splits that are at the mid-points of unique values. Thus the resulting trees are

Re: [R] adding hyperlinked text to pdf plot

2011-12-05 Thread David Winsemius
On Dec 5, 2011, at 1:39 PM, Justin Fincher wrote: Howdy, I have read that if you put a URL in the text of a plot being saved into pdf, the result is a functional hyperlink. Don't believe everything you read. pdf(test.pdf) plot(1,1,main=http://test.gov/some.htm;) dev.off()

Re: [R] adding hyperlinked text to pdf plot

2011-12-05 Thread Yihui Xie
It seems I missed the context of this post -- who is you, and what is something other than the URL? I feel the tikzDevice package should be an option for the task. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State

Re: [R] explanation why RandomForest don't require a transformations (e.g. logarithmic) of variables

2011-12-05 Thread gianni lavaredo
about the because they only use the ranks of the variables. Using a leave-one-out, in each interaction the the predictor variable ranks change slightly every time RF builds the model, especially for the variables with low importance. Is It correct to justify this because there are random

[R] lists everywhere

2011-12-05 Thread Kehl Dániel
Dear list members, I have a really simple problem. I connected to a DB and have the following query adat - dbGetQuery(con, paste(select * from kmdata where SzeAZ=', szeazok[i], ' order by datum, sep=)) now I have the data in the adat variable which is a list. In fact the elements of the

Re: [R] explanation why RandomForest don't require a transformations (e.g. logarithmic) of variables

2011-12-05 Thread Liaw, Andy
You should see no differences beyond what you'd get by running RF a second time with a different random number seed. Best, Andy From: gianni lavaredo [mailto:gianni.lavar...@gmail.com] Sent: Monday, December 05, 2011 2:19 PM To: Liaw, Andy Cc:

[R] SOLVED, Re: lists everywhere

2011-12-05 Thread Kehl Dániel
nevermind, typo (and some gray hair) sorry 12/5/2011 8:21 PM keltezéssel, Kehl Dániel írta: Dear list members, I have a really simple problem. I connected to a DB and have the following query adat - dbGetQuery(con, paste(select * from kmdata where SzeAZ=', szeazok[i], ' order by datum,

[R] installing several versions of R (2.14 and 2.12.2) on the same system on Ubuntu

2011-12-05 Thread Jannis
Dear R users, besides the current R 2.14 I would like to install a second version of R (2.12.2) on my Ubuntu system. The current version is easily installed as a precompiled package from Cran but I am heavily fighting with the older version. I tried to follow the instructions here:

Re: [R] lists everywhere

2011-12-05 Thread William Dunlap
First, some general suggestions: To see the structure of an object I would recommend the str() function or, for a more concise output, the class() function. I don't think most ordinary users should be using is.list() and, especially, is.vector(). Now for the particulars. dbGetQuery

Re: [R] adding hyperlinked text to pdf plot

2011-12-05 Thread Justin Fincher
For example, say I am plotting some data that is genomic and therefore maps to a specific locus on the human genome, like a gene. I was hoping to have the title of the plot display the gene name, but have it be a link so that clicking on it would take you to those coordinates on a public browser,

Re: [R] adding hyperlinked text to pdf plot

2011-12-05 Thread Duncan Murdoch
On 05/12/2011 3:10 PM, Justin Fincher wrote: For example, say I am plotting some data that is genomic and therefore maps to a specific locus on the human genome, like a gene. I was hoping to have the title of the plot display the gene name, but have it be a link so that clicking on it would

Re: [R] adding hyperlinked text to pdf plot

2011-12-05 Thread Yihui Xie
Sorry I experimented with tikzDevice using \href{}{} but failed. You can probably try the old image hotspot technique in HTML. I remember someone did this before in R, but I cannot find the link to the work now. The key is your need to use the two functions grconvertX and grconvertY. Regards,

Re: [R] adding hyperlinked text to pdf plot

2011-12-05 Thread Paul Murrell
Hi On 6/12/2011 9:10 a.m., Justin Fincher wrote: For example, say I am plotting some data that is genomic and therefore maps to a specific locus on the human genome, like a gene. I was hoping to have the title of the plot display the gene name, but have it be a link so that clicking on it

[R] Binning the data based on a value

2011-12-05 Thread Diviya Smith
Hello there, I have a matrix with some data and I want to split this matrix based on the values in one column. Is there a quick way of doing this? I have looked at cut but I am not sure how to exactly use it? for example: I would like to split the matrix a based on the spending such that the

Re: [R] Binning the data based on a value

2011-12-05 Thread R. Michael Weylandt
I'd so something like split(a, a$spending) and you can include a round(a$spending, -2) or something similar if you want to group by the 100's. Michael On Mon, Dec 5, 2011 at 3:37 PM, Diviya Smith diviya.sm...@gmail.com wrote: Hello there, I have a matrix with some data and I want to split

Re: [R] Binning the data based on a value

2011-12-05 Thread R. Michael Weylandt
Just a clarification: I can't get round to work as I first expected so if you want to do bins by 100's you'd probably want: split(a, cut(a$spending, breaks = (0:5)*100)) Michael On Mon, Dec 5, 2011 at 3:41 PM, R. Michael Weylandt michael.weyla...@gmail.com wrote: I'd so something like

[R] Problem in while loop

2011-12-05 Thread Gyanendra Pokharel
Hi all, I have the following code, When I run the code, it never terminate this is because of the while loop i am using. In general, if you need a loop for which you don't know in advance how many iterations there will be, you can use the `while' statement so here too i don't know the number how

Re: [R] Problem in while loop

2011-12-05 Thread Gyanendra Pokharel
I forgot to upload the R-code in last email, so heare is one epiann - function(T0 = 1, N=1000, ainit=1, binit=1,rho = 0.99, amean = 3, bmean=1.6, avar =.1, bvar=.1, f){ moving - 1 count - 0 Temp - T0 aout - ainit bout - binit while(moving 0){

[R] args() function does not list function prototype for locally-produced/installed R package

2011-12-05 Thread Rick Reeves
Greetings: I have check the 'Building R Extensions' manual and can find no advice on this issue, so I am asking -- I have created an R package consisting entirely of R source code, and created an installer using the R CMD build / R CMD check commands. The package installs correctly, using R

Re: [R] a question on autocorrelation acf

2011-12-05 Thread Bazman76
Hi there, I am wondering how R calculates the acf too? I have a data set of approx 1500 returns when I calculate the lag 1 autocorrelation in excel I get a value of -0.4 but in R its approximately -0.18? I have cross checked with PC give and PC give agrees with excel? I'm sure its just some

[R] Summary coefficients give NA values because of singularities

2011-12-05 Thread Gathurst
Hello, I have a data set which I am using to find a model with the most significant parameters included and most importantly, the p-values. The full model is of the form: sad[,1]~b_1 sad[,2]+b_2 sad[,3]+b_3 sad[,4]+b_4 sad[,5]+b_5 sad[,6]+b_6 sad[,7]+b_7 sad[,8]+b_8 sad[,9]+b_9 sad[,10], where

Re: [R] installing several versions of R (2.14 and 2.12.2) on the same system on Ubuntu

2011-12-05 Thread Peter Langfelder
On Mon, Dec 5, 2011 at 11:47 AM, Jannis bt_jan...@yahoo.de wrote: Dear R users, besides the current R 2.14 I would like to install a second version of R (2.12.2) on my Ubuntu system. The current version is easily installed as a precompiled package from Cran but I am heavily fighting with

Re: [R] Binning the data based on a value

2011-12-05 Thread Diviya Smith
Thank you very much Michael. This is very helpful. However, if there is any way to exclude zero length bins. Lets imagine that the matrix was as follows - a - data.frame(patient=1:7, charges=c(100,500,200,90,400,500,600), age=c(0,3,5,7,10,16,19), spending=c(10, 60, 110, 200, 400, 450, 500))

Re: [R] Binning the data based on a value

2011-12-05 Thread R. Michael Weylandt
Add the drop = TRUE command to split ?split split(a, cut(a$spending, breaks = (0:5)*100), drop = TRUE) Michael On Mon, Dec 5, 2011 at 4:06 PM, Diviya Smith diviya.sm...@gmail.com wrote: Thank you very much Michael. This is very helpful. However, if there is any way to exclude zero length

Re: [R] a question on autocorrelation acf

2011-12-05 Thread R. Michael Weylandt
Did you check the MASS reference given above in the thread? If you want to see the source, it's here: http://svn.r-project.org/R/trunk/src/library/stats/src/filter.c (best I can tell) Michael On Mon, Dec 5, 2011 at 2:24 PM, Bazman76 h_a_patie...@hotmail.com wrote: Hi there, I am wondering how

Re: [R] nipals in the chemometrics package in R

2011-12-05 Thread zz dd
That's solved. Just a cor between X and ti values. Thank you all. 2011/12/5 zz dd void1...@gmail.com Thank's Pedro Madrones, you're right that i have removed my name of the email (because of Spam, and datas that i can't remove on the net). Ok, i explain a bit more : X is a centred matrix.

Re: [R] Toggle cASE

2011-12-05 Thread Tonio
Thanks a lot Eik!   That is exactly what I was looking for.   Best Antonio Fra: Eik Vettorazzi e.vettora...@uke.de Cc: r-help@R-project.org r-help@r-project.org Sendt: 23:21 mandag den 5. december 2011 Emne: Re: [R] Toggle cASE Hi Antonio, how about this:

Re: [R] problems using the thin plate spline method

2011-12-05 Thread Mintewab Bezabih
Dear Michael and R users, I generated a more orderly looking data again and below are the data and the codes I am trying to run. many thanks mintewab dat - read.table(E:/thin plate/thin plate.csv, header=T, sep=,) names(dat) - c(x1, x2, y) library(fidelds) plot (dat) plot (dat$x1, dat$x2)

Re: [R] Shading the plot

2011-12-05 Thread R. Michael Weylandt
As David said, your minimal working example is neither minimal nor working...consider this (admittedly quite clunky) example though: time - seq(10, 20, length.out = 100) S1 - 10*exp( cumsum(rnorm(100))/20) S2 - 10*exp( cumsum(rnorm(100))/20) plot(time, S1, ylim = range(c(S1,S2)), type = n)

Re: [R] Problem in while loop

2011-12-05 Thread R. Michael Weylandt
Your code is not reproducible nor minimal, but why don't you put a command print(acceptprob) in and see if you are getting reasonable values. If these values are extremely low it shouldn't surprise you that your loop takes a long time to run. More generally, read up on the use of print() and

Re: [R] Problem in while loop

2011-12-05 Thread Gyanendra Pokharel
Yes, I checked the acceptprob, it is very high but in my view, the while loop is not stopping, so there is some thing wrong in the use of while loop. When I removed the while loop, it returned some thing but not the result what I want. When i run the while loop separately, it never stops. On

[R] plot mixed variables

2011-12-05 Thread Juliet Ndukum
My data consists of a numeric (yy) variable and a categorical (xx) variable, as shown below. xx = c(rep(C, 5), rep(D,5)) yy = rnorm(10, 0, 4) xx1 = as.integer(as.factor(xx))   plot(xx1, yy, ylim = c(-13.5, 4), col=blue)   I wish to generate a scatter plot of the data such

Re: [R] args() function does not list function prototype for locally-produced/installed R package

2011-12-05 Thread Duncan Murdoch
On 11-12-05 3:04 PM, Rick Reeves wrote: Greetings: I have check the 'Building R Extensions' manual and can find no advice on this issue, so I am asking -- I have created an R package consisting entirely of R source code, and created an installer using the R CMD build / R CMD check

Re: [R] installing several versions of R (2.14 and 2.12.2) on the same system on Ubuntu

2011-12-05 Thread Duncan Murdoch
On 11-12-05 4:03 PM, Peter Langfelder wrote: On Mon, Dec 5, 2011 at 11:47 AM, Jannisbt_jan...@yahoo.de wrote: Dear R users, besides the current R 2.14 I would like to install a second version of R (2.12.2) on my Ubuntu system. The current version is easily installed as a precompiled

Re: [R] plot mixed variables

2011-12-05 Thread Sarah Goslee
plot(xx1, yy, ylim = c(-13.5, 4), col=blue, xaxt=n) axis(1, at=c(1, 2), labels=c(C, D)) Defining your own axes with axis() offers a great deal of flexibility. And thank you for providing a small reproducible example. Sarah On Mon, Dec 5, 2011 at 5:43 PM, Juliet Ndukum jpnts...@yahoo.com wrote:

Re: [R] Problem in while loop

2011-12-05 Thread R. Michael Weylandt
If you run out- epiann(f = function(a,b) log(dnorm(a)*dnorm(b))), N = 10) It takes less than 0.5 seconds so there's no problem I can see: perhaps you want to look elsewhere to get better speed (like Rcpp or general vectorization), or maybe your loglikihood is not what's desired, but there's no

[R] Plot numeric and categorical variable

2011-12-05 Thread Juliet Ndukum
My data consists of numeric (yy) and categorical (xx) variables, as shown below.  xx = c(rep(C, 5), rep(D,5)) xx [1] C C C C C D D D D D yy = rnorm(10, 0, 4) yy [1]  2.7219346 -3.7142481  6.8716534 -0.9352463  0.4901249  3.8113247 [7] -2.6602041  1.7714471  4.7298233  0.8848188 xx1 =

[R] Plotting Time Series Data by Month

2011-12-05 Thread crazedruff
Hi, I have a dataset which includes monthly data for 17 years. I want to be able to see the monthly data behavior for the period of all 17 years. What my data looks like: http://r.789695.n4.nabble.com/file/n4162534/data.jpg I would like to represent the data in a graph such as the one below:

Re: [R] Persp3d freezes when run from within Python

2011-12-05 Thread wchips
Thanks Duncan. The thing is, if you want to display a static R graph using Rpy2 you need to bring your Python program to a halt immediately after printing the graph to screen using something like: raw_input(Press any key to continue ...) , otherwise it flashes up on the screen for a fraction of

[R] Why can't I figure this out? :S

2011-12-05 Thread Jasmine007
Hi, so I don't speak computer and I have no idea what this code is telling the program to do, but I apparently need to be able to find and isolate influencial observations. Problem, I have no idea what the error means and where it may be from in the code. error I get is below the code { ## OLS

[R] how to view/edit large matrix/array in R?

2011-12-05 Thread Michael
head, tail and fix commands don't really work well if I have large matrix/array for which I would like to be able to scroll up and dow, left and right ... Could anybody please help me? Thanks [[alternative HTML version deleted]] __

Re: [R] how to view/edit large matrix/array in R?

2011-12-05 Thread Michael
For example, fix does have scrolling, but could we have a grid based or cell based viewer/editor just like Excel sheet or like Matlab's object editor? For some weird reason, fix can only show numbers a weird format... On Mon, Dec 5, 2011 at 7:01 PM, Michael comtech@gmail.com wrote: head,

Re: [R] how to view/edit large matrix/array in R?

2011-12-05 Thread Michael
And fix doesn't show the full content... On Mon, Dec 5, 2011 at 7:07 PM, Michael comtech@gmail.com wrote: For example, fix does have scrolling, but could we have a grid based or cell based viewer/editor just like Excel sheet or like Matlab's object editor? For some weird reason, fix can

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