Re: [R] Error setting rowname if rowname currently NULL

2009-03-03 Thread Wacek Kusnierczyk
snubian wrote: snip I've noticed a behaviour when using rownames() that I think is odd, wondering if I'm doing something wrong. To illustrate, say I create a very simple matrix (called fred): fred-matrix(,4,2) It looks like this: [,1] [,2] [1,] NA NA [2,] NA NA [3,]

[R] [R-pkgs] package ltm -- version 0.9-0

2009-03-03 Thread Dimitris Rizopoulos
Dear R-users, I'd like to announce the release of the new version of package 'ltm' (i.e., ltm_0.9-0 soon available from CRAN) for Item Response Theory analyses. This package provides a flexible framework for analyzing dichotomous and polytomous data under various IRT models. Furthermore,

Re: [R] Goldbach partitions code

2009-03-03 Thread Robin Hankin
Hi interesting blog! not strictly relevant, but there are various number-theoretic functions implemented in the elliptic package which you might find useful. best wishes Robin murali.me...@fortisinvestments.com wrote: Folks, I put up a brief note describing my naive attempts to compute

Re: [R] Help with Wilcoxon Test

2009-03-03 Thread Jim Lemon
Amit Patel wrote: Hi I have 2 sets of data that I want to do a Wilcoxon test on. They are of the same dimension. One has 4 zero values and the other has 5. dim(SampA) [1] 1 10 dim(SampV) [1] 1 10 I get the folowing error Error in wilcox.test.default(SampA, SampV, na.rm

[R] Characters To Matrix

2009-03-03 Thread Bob Roberts
Hi, I have a data set that I read in using readLines, but R classes it as a character string. The data set has multiple columns and rows, but I only want the first 2 columns in the form of a matrix. Thanks for the help. [[alternative HTML version deleted]]

Re: [R] Error loading packages at sprintf()

2009-03-03 Thread Prof Brian Ripley
This is a Mac-specific issue, as you are installing binary packages. The real error message was /bin/sh: line 1: tar: command not found so the problem is that tar is not in your path. I've no idea how that would come to be (all Macs I have used had /usr/bin/tar), so please ask on

Re: [R] regular expression question

2009-03-03 Thread Wacek Kusnierczyk
markle...@verizon.net wrote: can someone show me how to use a regular expression to break the string at the bottom up into its three components : (-0.791,-0.263] (-38,-1.24] (0.96,2.43] I tried to use strplit because of my regexpitis ( it's not curable. i've been to many doctors all over

Re: [R] Characters To Matrix

2009-03-03 Thread Dieter Menne
Bob Roberts quagmire54321 at yahoo.com writes: I have a data set that I read in using readLines, but R classes it as a character string. The data set has multiple columns and rows, but I only want the first 2 columns in the form of a matrix. Thanks for the help. data(CO2) str(CO2) col2 =

Re: [R] RWeka dataset running

2009-03-03 Thread Dieter Menne
ahmet kocyigit kh3l at hotmail.com writes: I'm a newbie to R and will work on it from now. I'm preparing my thesis based on rpart and RWeka. I've managed to run already existing test data but couldn't import a data set from out of R. There is a special Export/Import manual R-data.pdf in

Re: [R] regular expression question

2009-03-03 Thread Romain Francois
Wacek Kusnierczyk wrote: markle...@verizon.net wrote: can someone show me how to use a regular expression to break the string at the bottom up into its three components : (-0.791,-0.263] (-38,-1.24] (0.96,2.43] I tried to use strplit because of my regexpitis ( it's not curable. i've been

[R] New mailing list: R-help-es

2009-03-03 Thread UsuarioR España
Hi all, I am writing to announce the creation of a new R mailing list: R-help-es. It is going to be a list for spanish speakers users of R so I am sorry to write the rest of the email in spanish. Os escribo para anunciaros que hemos creado una nueva lista de correo llamada R-help-es para

Re: [R] Inefficiency of SAS Programming

2009-03-03 Thread Gerard M. Keogh
Ajay, I think this is somewhat unnecessary! For regular SAS users PROC SUMMARY/MEANS is the data manipulation staple. A SAS user interested in R will look at Intro to R and find it recommends tapply for data manipulation jobs. This is a problem - tapply just isn't simple and obvious. A better

Re: [R] Inefficiency of SAS Programming

2009-03-03 Thread Jim Lemon
Ajay ohri wrote: for an inefficient language , it sure has dominated the predictive analytics world for 3 plus decades. I referred once to intellectual jealousy between newton and liebnitz. i am going ahead and creating the R package called Anne. If you want to market this, Ajay, I'd

Re: [R] Inefficiency of SAS Programming

2009-03-03 Thread Ajay ohri
Ok. Basically everything that SAS can do, R can do, but vice versa isnt true. using the Anne package just renames the functions into standardized data and proc steps for user comfort. Once SAS user finds that R is productive , and useful and even more powerful for even less money, he can unload

[R] select nls starting values from list was: nls does not accept start values

2009-03-03 Thread Petr PIKAL
Hallo Here is my final solution, but i still wonder if it could not be improved somehow. fit - modely(fol, data.frame(x=x, y=y1) fit or fit - modely(fol, data.frame(x=x, y=y2) fit shows that it arrives to some results. However selection starting values as means of response variable seems to

Re: [R] Inefficiency of SAS Programming

2009-03-03 Thread Ajay ohri
no market for R packages exists in true economic sense as there is demand and supply and utility but no price Ajay Did Tom Sawyer create the first collaborative project ever ( to paint the fence ?) On Tue, Mar 3, 2009 at 4:24 PM, Jim Lemon j...@bitwrit.com.au wrote: Ajay ohri wrote: for

[R] Arbirtrary column names with write.csv

2009-03-03 Thread Rafael Laboissiere
Is there a way to prevent write.csv to transform the column names a la make.names? I mean, if I write the code: x - structure (NULL) x [[a+b]] - c (1,2) write.csv (x, file = foo.csv, row.names = FALSE, quote = FALSE) I get in foo.csv: a.b 1 2 but I want: a+b 1 2 Any suggestions?

Re: [R] monotonic GAM with more than one term

2009-03-03 Thread Simon Wood
There's an example at the end of the pcls help file in version 1.5-0 --- just submitted to CRAN. best, Simon On Wednesday 25 February 2009 18:48, Benjamin Tyner wrote: Hi, Does anyone know how to fit a GAM where one or more smooth terms are constrained to be monotonic, in the presence of by

Re: [R] barplot with specific order of x axis labels

2009-03-03 Thread Paul Hiemstra
sort.df() in the reshape packge. cheers, Paul R User R User wrote: Hi all, I'd appreciate your help with this problem. I need to plot a barplot with the categories in a specific order. My data might be: hours Freq AN 10 MO 14 LU 30 I need the categories to be in the order: MO

[R] R - MATLAB apply like function

2009-03-03 Thread ARDIA David
Dear all, I very often use the R function apply, for speedup purposes. I am now also using MATLAB, and would like to use the same kind of function. I have already asked MATLAB people, and the answer is : vectorize... but of course, this is not always possible. So, instead of using a FOR loop all

[R] Self-Organizing Map analysis

2009-03-03 Thread glaporta
Dear list, I read the SOM package manual but I don't understand how to perform (for example) 1) the SOM analysis on Iris data 2) with a visualization similar to that of figure 7 in http://www.cis.hut.fi/projects/somtoolbox/package/papers/techrep.pdf Any suggestion? Thanks in advance, Gianandrea

Re: [R] survival::survfit,plot.survfit

2009-03-03 Thread Bernhard Reinhardt
You are right. In my case it doesn´t make much difference since the mean of my covariates is about 0. I made some more plots and again I´m confused. I thought when forcing all covariates via the newdata argument to be zero I would get the baseline function since the linear predictor is then

Re: [R] Inefficiency of SAS Programming

2009-03-03 Thread Barry Rowlingson
2009/3/3 Jim Lemon j...@bitwrit.com.au: Ajay ohri wrote: for an inefficient language , it sure has dominated the predictive analytics world for 3 plus decades. I referred once to intellectual jealousy between newton and liebnitz. i am going ahead and creating the R package called Anne.

Re: [R] regular expression question

2009-03-03 Thread Gabor Grothendieck
Here are two solutions using gsubfn package. strapply works by matching the what you want rather than what you don't want which may make it easier in this case. The two solutions are the same except we use \\ escapes in the first and [ ... ] in the second, i.e. \\( has the same effect as [(].

[R] Question about multiple plots of zoo objects

2009-03-03 Thread Sergey Goriatchev
Hello, everyone I have a zoo object containing several time series of daily frequency. One of these timeseries is an indicator function with value (-1) at certain times, and (+1) at the other. I do a plot of several of the timeseries in one go (a multiple plot). I wonder if I can automatically in

[R] calculating standard deviation and variance

2009-03-03 Thread johnhj
Hiii, I have some problems to plot standard deviation and variance from a texfile. Ich have the following code so far: x -read.table(file=new.txt) x$gruppe - 100*rep(1:36, each=20) png(filename = D:/Uni/new.png, width = 640, height = 480,pointsize = 12, bg = white) boxplot(V3 ~ gruppe,

Re: [R] xlsReadWrite package repository for Ubuntu

2009-03-03 Thread Ben Bolker
reverend33 wrote: I'm sorry, maybe i didn't explain clearly: i'm trying to install xlsReadWrite on a Linux-type OS (Ubuntu)... I think you didn't understand the answers: the package is only available under Windows. cheers Ben Bolker -- View this message in context:

Re: [R] Characters To Matrix

2009-03-03 Thread jim holtman
Why aren't you using 'read.table'? On Tue, Mar 3, 2009 at 3:47 AM, Bob Roberts quagmire54...@yahoo.com wrote: Hi,   I have a data set that I read in using readLines, but R classes it as a character string. The data set has multiple columns and rows, but I only want the first 2 columns in

Re: [R] Question about multiple plots of zoo objects

2009-03-03 Thread Gabor Grothendieck
Are you trying to color the points themselves? This plots the first two series in frame 1 (they are the same but one is plotted as points and the other as a line) and the third series is shown in frame 2 and for the series of points it colors them green or red. The lines are all colored black:

Re: [R] xlsReadWrite package repository for Ubuntu

2009-03-03 Thread Gabor Grothendieck
If your purpose is to read Excel spreadsheets on Linux read.xls in the gdata packages can do that. It uses perl software underneath which is portable across systems. On Tue, Mar 3, 2009 at 7:38 AM, reverend33 periac_r...@hotmail.com wrote: I'm sorry, maybe i didn't explain clearly: i'm trying

Re: [R] Question about multiple plots of zoo objects

2009-03-03 Thread Sergey Goriatchev
Hi, Gabor No, what I am trying to do is similar to: abline(v=time(spread)[spread[,Indicator]==(-1)], col=yellow), where spread is the multivariate zoo object (say, 5 timeseries). That is, I want to color parts of the plots where indicator==(-1), but do the coloring without using layout() and

Re: [R] xlsReadWrite package repository for Ubuntu

2009-03-03 Thread Marc Schwartz
You perhaps missed the key point in Uwe's response, which is that the package is only available under Windows, as it depends upon Windows specific functionality (MS Office API via a third party library which is available for Windows only) to natively read and write Excel files. Thus, there is no

Re: [R] R - need more memory, or rejection sampling algorithm doesn't work?

2009-03-03 Thread Ben Bolker
ekwaters wrote: b12=log(.4/.6) b13=log(.85/.15) Can you point out the syntax errors in the first one? You have a double caret (^^). f(k) should be f[k] Watch out for raising numbers to such large powers (although to my surprise things didn't over/underflow when I tried your

Re: [R] Inefficiency of SAS Programming

2009-03-03 Thread Frank E Harrell Jr
Ajay ohri wrote: for an inefficient language , it sure has dominated the predictive analytics world for 3 plus decades. I referred once to intellectual jealousy between newton and liebnitz. i am going ahead and creating the R package called Anne. It basically is meant only for SAS users who

Re: [R] Question about multiple plots of zoo objects

2009-03-03 Thread Gabor Grothendieck
Do you mean you want to shade a portion of the plot? There are two examples of that in the examples section of ?plot.zoo and a further example using xyplot.zoo in the examples section of ?xyplot.zoo On Tue, Mar 3, 2009 at 8:37 AM, Sergey Goriatchev serg...@gmail.com wrote: Hi, Gabor No, what

Re: [R] SPSS data import: problems work arounds for GSS surveys

2009-03-03 Thread John Fox
Dear Paul, I encountered this problem the other day, and it went away when I updated the foreign package from version 0.8-32 to 0.8-33. I hope this helps, John -- John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada web:

Re: [R] FW: partial residual plots

2009-03-03 Thread John Fox
Dear Dwayne, I didn't see your post until now, because our email system was down all day yesterday. Mark Difford has already pointed your towards the cr.plots() and ceres.plots() functions in the car package. In your description of what you want to do, you mention the adjusted explanatory

[R] RES: xlsReadWrite package repository for Ubuntu

2009-03-03 Thread Leandro Marino
I think in this case its better use the write.csv. Microsoft Excel reads csv files normally. Atenciosamente, Leandro Lins Marino Centro de Avaliação Fundação CESGRANRIO Rua Santa Alexandrina, 1011 - 2º andar Rio de Janeiro, RJ - CEP: 20261-903 R (21) 2103-9600 R.:236 ( (21) 8777-7907 (

[R] Reshape

2009-03-03 Thread Usuario R
Hi all, I would like to transform to long format a matrix which has only information about individuals and a value for each individual. I would like to have it in ling format with more information related to groups, so ell values and individuals are repeated for each group. Let me show the

Re: [R] RES: xlsReadWrite package repository for Ubuntu

2009-03-03 Thread Marc Schwartz
That is fine if you only have one or two R objects to write out to CSV files and then read them into Excel. It becomes rapidly tedious as the number of objects increases. If you go back and read my original post, the incentive for me to write the Perl routine was that I had to create an Excel

Re: [R] Question about multiple plots of zoo objects

2009-03-03 Thread Sergey Goriatchev
Gabor, yes, I want to color portions of EACH plot of the MULTIPLE plot done with plot.zoo() I tried to do: plot(multivariate zoo object) abline(v=...) but that does not work. I will check your suggestions of the examples. Thank you for your help, as always! Best, Sergey On Tue, Mar 3, 2009 at

Re: [R] Reshape

2009-03-03 Thread stephen sefick
check out the melt function in the reshape package. On Tue, Mar 3, 2009 at 8:53 AM, Usuario R r.user.sp...@gmail.com wrote: Hi all, I would like to transform to long format a matrix  which has only information about individuals and a value for each individual. I would like to have it in ling

Re: [R] RES: xlsReadWrite package repository for Ubuntu

2009-03-03 Thread Gabor Grothendieck
There is a recently updated review of the alternatives on the R Wiki: http://wiki.r-project.org/rwiki/doku.php?id=tips:data-io:ms_windows On Tue, Mar 3, 2009 at 9:00 AM, Marc Schwartz marc_schwa...@comcast.net wrote: That is fine if you only have one or two R objects to write out to CSV files

Re: [R] xlsReadWrite package repository for Ubuntu

2009-03-03 Thread Dirk Eddelbuettel
On 3 March 2009 at 07:38, Marc Schwartz wrote: | You perhaps missed the key point in Uwe's response, which is that the | package is only available under Windows, as it depends upon Windows | specific functionality (MS Office API via a third party library which is | available for Windows only) to

Re: [R] Inefficiency of SAS Programming

2009-03-03 Thread Girish A.R.
On Mar 3, 9:58 am, Ajay ohri ohri2...@gmail.com wrote: for an inefficient language , it sure has dominated the predictive analytics world for 3 plus decades. I referred once to intellectual jealousy between newton and liebnitz. i am going ahead and creating the R package called Anne. It

Re: [R] Arbirtrary column names with write.csv

2009-03-03 Thread Rafael Laboissiere
* Uwe Ligges lig...@statistik.tu-dortmund.de [2009-03-03 15:27]: Rafael Laboissiere wrote: Is there a way to prevent write.csv to transform the column names a la make.names? I mean, if I write the code: x - structure (NULL) x [[a+b]] - c (1,2) write.csv (x, file = foo.csv,

Re: [R] Reshape

2009-03-03 Thread baptiste auguie
If you have many such repetitions it can be annoying to type the rbind(cbind ... sequence. Perhaps this would help, m - read.table(textConnection( IndividualsValue A3 B4 C5 D2), head=T) data.frame(groups= rep(c(group1, group2, group3), each=nrow(m)), Ind=m[, 1],

Re: [R] Question about multiple plots of zoo objects

2009-03-03 Thread Sergey Goriatchev
Supreme! Thanks Gabor! On Tue, Mar 3, 2009 at 15:20, Gabor Grothendieck ggrothendi...@gmail.com wrote: If you want to use abline on a multivariate plot it must be issued within a panel function like this: # same set up as in prior email p - function(x, y, ...) { points(x, y); lines(x, y);

[R] REMINDER: DSC 2009 abstract submission before March 15

2009-03-03 Thread Peter Dalgaard
Just a friendly reminder that the closing date for abstract submissions for the DSC conference in Copenhagen is next Sunday. See http://www.r-project.org/dsc-2009 Notice that the website has been revised since we decided to engage a professional convention bureau. The good news is that payment

[R] New R mailing list: R-SIG-insurance

2009-03-03 Thread Vincent Goulet
Dear useRs, Over the last few years R has gained a significant momentum in the insurance industry. Dedicated packages have been written, numerous presentations given, courses held, businesses set up, and IT departments convinced. ;-) Therefore, together with Markus Gesmann of Lloyd's of

Re: [R] Inefficiency of SAS Programming

2009-03-03 Thread Ajay ohri
why didnt you call it procunivariate if that was exactly what you wanted to do . On Tue, Mar 3, 2009 at 7:11 PM, Frank E Harrell Jr f.harr...@vanderbilt.edu wrote: Ajay ohri wrote: for an inefficient language , it sure has dominated the predictive analytics world for 3 plus decades.

[R] SAS Macros for R Users Only

2009-03-03 Thread Ajay ohri
I think SAS Macros has capability to call R, and execute it without it being in the picture anywhere. So you can use SAS Macros in a file called R.sas In this you can create a macro called %Describe that can call R , load Hmisc ,run the describe function Note you will need repeated use of

[R] spatial markov chain methods

2009-03-03 Thread Torsten Lange
Hello, can any one point me to R-packages (if available) which include spatial Markov Chain methods? My second question is more general but hopefully not OT: Currently we are using the software TPROGS, which let people simulate property distributions in space by some Markov Chain approaches.

Re: [R] xlsReadWrite package repository for Ubuntu

2009-03-03 Thread reverend33
Thanks a lot for all your answers. Indeed, i hadn't understood the previous answers. I just downloaded the gdata package and it works perfectly now. Thanks again. Gabor Grothendieck wrote: If your purpose is to read Excel spreadsheets on Linux read.xls in the gdata packages can do

[R] PLS regression on near infrared (NIR) spectra data

2009-03-03 Thread Paulo Ricardo Gherardi Hein
Dear collegues, I´ ve worked with near infrared (NIR) spectroscopy to assess chemical, physical, mechanical and anatomical properties of wood. I use The Unscrambler software to correlate the matrix of dependent variables (Y) with the matrix of spectral data (X) and I would like to migrate to R.

[R] behavior of squishplot in TeachingDemos

2009-03-03 Thread Stephen Tucker
Hi list, I wonder if anyone has had this experience with squishplot() in the TeachingDemos package. Taking the example from the ?image help page, library(TeachingDemos) x - 10*(1:nrow(volcano)) y - 10*(1:ncol(volcano)) layout(matrix(c(1,2,3,4),ncol=2,byrow=TRUE),height=c(2,1)) ## 1st plot op

[R] Mantel test!

2009-03-03 Thread Jason Sexton
Dear Gavin, What is the interpretation of a simulated p-value of 1 in a mantel test and how is the p-value derived? When we run two highly negatively correlated matrices we get this result: r: -1, simulated p value: 1 I would expect the high p-value of 1 to mean not significant. Could

[R] Comparing two matrices

2009-03-03 Thread Koen Hufkens
Hi List, I would like to compare two (confusion) matrices. I ended up with the ade4 mantel.rtest function as my best option. However it seems that my data is non-euclidean in nature (is.euclid gives a FALSE). I attached both matrices at the end of the document. Are there any tools to

Re: [R] Mantel test!

2009-03-03 Thread Sarah Goslee
I'm not Gavin, but since you posted this to the R-help list I assume you are open to other respondents. Since you are asking Gavin, I assume you are using mantel() from the vegan package (it's a good idea to specify, as there are other possibilities). The help for that function explains the

Re: [R] Comparing two matrices

2009-03-03 Thread Sarah Goslee
Hi, For the Mantel test, your matrices do not need to be Euclidean, but they do need to be symmetric. You could write a similar test that does not require a symmetric matrix, though. Sarah On Tue, Mar 3, 2009 at 11:40 AM, Koen Hufkens koen.hufk...@ua.ac.be wrote: Hi List, I would like to

[R] modifying a built in function from the stats package (fixing arima)

2009-03-03 Thread Marc Vinyes
Dear members of the list, I'm a beginner in R and I'm having some trouble with: Error in optim(init[mask], armafn, method = BFGS, hessian = TRUE, control = optim.control, : non-finite finite-difference value [8] when running arima. I've seen that some people have come accross the same

Re: [R] Inefficiency of SAS Programming

2009-03-03 Thread Frank E Harrell Jr
Ajay ohri wrote: why didnt you call it procunivariate if that was exactly what you wanted to do . Why would I ever do that? describe is a improvement on univariate, saving an estimated 87 +/- 87 trees per year in paper by printing what you need in much less space and concentrating on

Re: [R] locfit smoothing question (package maintainer not reachable)

2009-03-03 Thread Suresh Krishna
Dear all, I just realized that using family=qgauss restores normal-looking confidence bands... I read that using family=gaussian rather than family=qgauss fixes the dispersion parameter at 1, but without knowing the theory behind the code, I dont understand why there is such a

[R] preparing data for barplot()

2009-03-03 Thread Andrew Ziem
What is the best way to produce a barplot from my data? I would like the barplot to show each person with the values stacked val1+val2+val3, so there is one bar for each person When I use barplot(data.matrix(realdata)), it shows one bar for each value instead. To post here, I created an

[R] ggplot2: annotated horizontal lines

2009-03-03 Thread Dave Murray-Rust
Hello, I'm using geom_hline to add a minimum line to my plot (representing the best solution found so far by a search algorithm). I'd like to annotate this line with it's numerical value to save trying to read it off the graph, but I can't see a clear way to do this - any ideas?

Re: [R] Fit indexes in SEM with categorical data + ML estimation

2009-03-03 Thread jebyrnes
Hey, Dorothee. SEM does not use the S-B chi squared index. If you want to use it, however, I have some methods written for the Satorra-Bentler Chi Square test in the sem.additions package over at r-forge. To install it directly within R type

Re: [R] ggplot2: annotated horizontal lines

2009-03-03 Thread baptiste auguie
What's wrong with geom_text? my.value = 0.65 qplot(1,1)+geom_hline(v=0)+ geom_text(mapping=aes(x=1,y=0),label=paste(my.value),vjust=-1) baptiste On 3 Mar 2009, at 18:10, Dave Murray-Rust wrote: Hello, I'm using geom_hline to add a minimum line to my plot (representing the best

[R] nlme: problem with fitting logistic function

2009-03-03 Thread jakub kreisinger
Dear colegues I am trying to analyze growth data on mice. To do this I attempted to fit logistic curve using nlme package. However, the dataset I use is large (in total ca 20 000 measures on ca 3 000 individuals) with relatively complicated structure (several explanatory variables with

Re: [R] locfit smoothing question (package maintainer not reachable)

2009-03-03 Thread David Winsemius
I think you should read (or re-read) the locfit help page and *also* the links from that page to the help pages for locfit.raw and rv. I would have thought that since family= is not an argument to locfit per se, but rather is documented in locfit.raw that you have yet done so, but perhaps

[R] scatter plot question

2009-03-03 Thread Dipankar Basu
Hi R Users, I have a dataframe like this: id x rho A 1 0.1 B 20 0.5 C 2 0.9 ... I want to do a scatter plot of x versus rho but for each point on the scatter plot I want the corresponding entry for id instead of points. In STATA I can do so by twoway (scatter x rho, mlabel(id)) How

Re: [R] locfit smoothing question (package maintainer not reachable)

2009-03-03 Thread Liaw, Andy
From: Suresh Krishna [...] ps. The package maintainer, Catherine Loader, is no longer reachable at her Auckland address. For the record, I'm the package maintainer for locfit, and I have not exactly vanished (yet). Please see the package description. That said, it doesn't mean I know all

[R] save the layout using igraph

2009-03-03 Thread kevinchang
Hi R users, I am using built-in functions in igraph package to draw networks . I need to compare several network with exactly the same structure but with edge hightlighted differently. I am wondering if there is a way to save the layout so that every graph will look the same as each other

Re: [R] rgl persp3d bounding box color problem.

2009-03-03 Thread chaogai
rgl_0.83-3 did not help Duncan Murdoch wrote: On 3/2/2009 2:48 PM, chaogai wrote: Oops, sorry R version 2.8.1 (2008-12-22) i686-pc-linux-gnu locale:

Re: [R] Inefficiency of SAS Programming

2009-03-03 Thread Rolf Turner
On 3/03/2009, at 5:58 PM, Ajay ohri wrote: for an inefficient language , it sure has dominated the predictive analytics world for 3 plus decades. I referred once to intellectual jealousy between newton and liebnitz. i am going ahead and creating the R package called Anne. It basically is

Re: [R] save the layout using igraph

2009-03-03 Thread Gábor Csárdi
Shukai, the layout functions return a matrix that you can supply as the 'layout' argument of the plotting functions, e.g. g1 - erdos.renyi.game(50,2/50) lay - layout.fruchterman.reingold(g1) g2 - delete.edges(g1, sample(ecount(g1), 30)-1) plot(g1, layout=lay, vertex.size=10) plot(g2, layout=lay,

Re: [R] ggplot2: annotated horizontal lines

2009-03-03 Thread Dave Murray-Rust
On 3 Mar 2009, at 18:41, baptiste auguie wrote: What's wrong with geom_text? my.value = 0.65 qplot(1,1)+geom_hline(v=0)+ geom_text(mapping=aes(x=1,y=0),label=paste(my.value),vjust=-1) Well, firstly I hadn't thought to use it. Ooops. Secondly, I can't make it just do a single

[R] par and a substitute for mtext to write one time a title per page

2009-03-03 Thread Aldi Kraja
RE: par and a substitute for mtext to write one time a title per page Hi, Q1. Is there way I can set mfg =c(2,1) which for me could have meant 2 pages and no split on the columns per page; and mfrow =c(4,1) which for me it means 4 graphs per page in

[R] repeated measures anova, sphericity, epsilon, etc

2009-03-03 Thread Paul Gribble
I have 3 questions (below). Background: I am teaching an introductory statistics course in which we are covering (among other things) repeated measures anova. This time around teaching it, we are using R for all of our computations. We are starting by covering the univariate approach to repeated

Re: [R] locfit smoothing question (package maintainer not reachable)

2009-03-03 Thread Suresh Krishna
David Winsemis wrote: I think you should read (or re-read) the locfit help page and *also* the links from that page to the help pages for locfit.raw and rv. I would have thought that since family= is not an argument to locfit per se, but rather is documented in locfit.raw that you have

Re: [R] modifying a built in function from the stats package (fixing arima)

2009-03-03 Thread Carlos J. Gil Bellosta
Hello, I do not think that is the way to go. If you believe that your algorithm is better than the existing one, talk to the author of the package and discuss the improvement. The whole community will benefit. If you want to tune the existing function and tailor it to your needs, you have

Re: [R] spatial markov chain methods

2009-03-03 Thread Rolf Turner
On 4/03/2009, at 4:36 AM, Torsten Lange wrote: Hello, can any one point me to R-packages (if available) which include spatial Markov Chain methods? My second question is more general but hopefully not OT: Currently we are using the software TPROGS, which let people simulate property

Re: [R] xlsReadWrite package repository for Ubuntu

2009-03-03 Thread Hans-Peter Suter
2009/3/2 Prof Brian Ripley rip...@stats.ox.ac.uk: The CRAN Windows ones. It is a windows-only package, see http://cran.r-project.org/web/packages/xlsReadWrite/index.html (incidentally to you: it seems no longer maintained and does not build under R-devel on Windows, see

Re: [R] xlsReadWrite package repository for Ubuntu

2009-03-03 Thread Rolf Turner
On 4/03/2009, at 2:38 AM, Marc Schwartz wrote: You perhaps missed the key point in Uwe's response, which is that the package is only available under Windows, as it depends upon Windows specific functionality (MS Office API via a third party library which is available for Windows only) to

Re: [R] ggplot2: annotated horizontal lines

2009-03-03 Thread baptiste auguie
I see your problem (although label should be outside the mapping in your case, i think). A possible workaround is to provide some dummy data, as the default NULL doesn't seem to work, qplot( wt, mpg, data=mtcars ) + geom_text(data=data.frame(x=0,y=0),mapping=aes(x=1,y=0),label=test) I'm

Re: [R] repeated measures anova, sphericity, epsilon, etc

2009-03-03 Thread Peter Dalgaard
Paul Gribble wrote: I have 3 questions (below). Background: I am teaching an introductory statistics course in which we are covering (among other things) repeated measures anova. This time around teaching it, we are using R for all of our computations. We are starting by covering the univariate

Re: [R] locfit smoothing question (package maintainer not reachable)

2009-03-03 Thread David Winsemius
That is what I thought to be the critical paragraph. The variance is assumed to be = 1 when you use family=gaussian rather than the default of family=qgauss. You give it a vector, 1000*rnorm(100), that ranges widely and a small (relative) variance is assumed and so the confidence intervals

[R] sm.density.compare

2009-03-03 Thread James Lenihan
I am running the sm.density.compare function amd I am getting the following error:   my code is  sm.density.compare(LBSTRESN,COHORT,xlab=Units = umol/Lsubset = LBTEST==Creatinine)   Error in if (from == to) rep.int(from, length.out) else as.vector(c(from,  :   missing value where TRUE/FALSE

Re: [R] spatial markov chain methods

2009-03-03 Thread Torsten Lange
Rolf Turner schrieb: On 4/03/2009, at 4:36 AM, Torsten Lange wrote: Hello, can any one point me to R-packages (if available) which include spatial Markov Chain methods? My second question is more general but hopefully not OT: Currently we are using the software TPROGS, which let people

Re: [R] repeated measures anova, sphericity, epsilon, etc

2009-03-03 Thread Paul Gribble
Have a look at http://cran.r-project.org/doc/Rnews/Rnews_2007-2.pdf Wow. I think my students would keel over. Anova() from the car package looks promising - I will check it out. Thanks On Tue, Mar 3, 2009 at 4:00 PM, Peter Dalgaard p.dalga...@biostat.ku.dkwrote: Paul Gribble wrote: I

Re: [R] par and a substitute for mtext to write one time a title per page

2009-03-03 Thread Aldi Kraja
Hmm, Reading some responses in the archives on mfg, the first one was simple the mfg does not control the pages. After removing mfg=c(2,1), and leaving in the program only mfrow=(4,1) although I am printing one after the other in a loop, pages are printed and do not overwrite the same page.

Re: [R] scatter plot question

2009-03-03 Thread Mark Lyman
Dipankar Basu basu.15 at gmail.com writes: Hi R Users, I have a dataframe like this: id x rho A 1 0.1 B 20 0.5 C 2 0.9 ... I want to do a scatter plot of x versus rho but for each point on the scatter plot I want the corresponding entry for id instead of points. test

Re: [R] portable R editor

2009-03-03 Thread Erich Neuwirth
EditPad Pro is commercial, which makes it a nonchoice for recommending it to my students. I recently switched from tinn-R to Notepad++ with NppToR and am quite happy with it. tinn-R is quite good, but possibly the project is getting too ambitous now. It needs quite some fiddling with Rprofile.site

[R] detect outliers and high levarage points

2009-03-03 Thread choonhong ang
Hi friends, How to detect outliers and high leverage points for GLM ? Could I use plot(model) (i) Residuals vs Fitted graph to detect the outliers ? (ii) Residuals vs Leverage graph to detect the high leverage points ? And then remove those points from the data and re-run the model ?

[R] clust with hclustWard

2009-03-03 Thread Anirudh Kondaveeti
Hello everyone I tried to use clust function using hclustWard clustering method The distance mesaured I have used is rf The data used is in the form of data frame (it is not a distance matrix) - sd.df The piece of code I have used is: c1 - clust(sd.df,k=6,method=hclustWard,distMethod=rf) But I

Re: [R] Inference for R Spam

2009-03-03 Thread Michael A. Miller
Dieter == Dieter Menne dieter.me...@menne-biomed.de writes: And, since my son asked me and I am basketball ignorant: Why are basketball scores mostly much too close to equality? The arguments (loose power when leading) might suggest that 2:0 might not be significant, but

[R] reading scanned graphs

2009-03-03 Thread Aad Termorshuizen
I have a graph (a curve with a x- and y-axis) on paper. (The device from which I receive this is not able to output the data digitally unfortunately.) Is there a procedure by which I can scan the graph, save it into, e.g., a bitmap file and make it R to read this file into x

Re: [R] reading scanned graphs

2009-03-03 Thread Remko Duursma
Check out http://www.datathief.org/ Remko - Remko Duursma Post-Doctoral Fellow Centre for Plant and Food Science University of Western Sydney Hawkesbury Campus Richmond NSW 2753 Dept of Biological Science Macquarie University North Ryde NSW

[R] periodogram smoothing question

2009-03-03 Thread otunno
Hello - I am currently simulating bivariate AR(1) time series data and have the following line in my code: Px=spec.pgram(ts.union(X,XX),spans=c(?,?)) The spans option is where I enter in the vector containing the Daniell smoother numbers, but I don't know what a Daniell smoother is (hence the

Re: [R] reading scanned graphs

2009-03-03 Thread Frank E Harrell Jr
Remko Duursma wrote: Check out http://www.datathief.org/ Remko For Linux I recommend the engauge-digitizer package. Frank - Remko Duursma Post-Doctoral Fellow Centre for Plant and Food Science University of Western Sydney Hawkesbury Campus

[R] score test statistic in logistic regression

2009-03-03 Thread Greg Dropkin
re post from bkelcey at umich.edu bkelcey at umich.edu Wed Feb 27 15:09:48 CET 2008 If the response y is given as the proportion of successes out of n trials, and y, n, p, x, and z are vectors of length M, and the model is logit(p) = b0 + b1*x + b2*z then for the score test for the null

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