[R] Kite diagrams

I teach biology, and would like to show the students how to use R for some statistical assignments. One of those is to make a kite diagram (for example as seen in http://www.medinavalleycentre.org.uk/images/Bembri1.jpg). Is there any way to create one using R? I did a help.search(kite) and looked

Re: [R] LaTeX slide show (Was: Re: Taking code from packages)

I have a few notes on using beamer with Sweave here: https://biostat.ucsd.edu/~cberry/beamer/ Particularly, getting verbatim material to display nicely took a bit of fiddling. On Sat, 14 Jan 2006, Duncan Murdoch wrote: On 1/14/2006 2:39 AM, Henrik Bengtsson wrote: Duncan Murdoch

[R] General partition search algorithm (local search, genetic algorithm, ...)

Dear R users! I was wondering if there exists (in R) any general algorithm for finding optimal partition (optimal allocation of n units into k groups or bins), such as local search, genetic algorithm, tabu search, ... By general I mean such that would find an (approximately) optimal partition

Re: [R] R-help Digest, Vol 35, Issue 14

On Sun, 15 Jan 2006, Werner Wernersen wrote: Dear all, Is anybody aware of a tutorial, introduction, overview or alike for cluster analysis with R? I have been searching for something like that but it seems there are only a few rather specialized articles around. As an overview (rather

Re: [R] Kite diagrams

Par Leijonhufvud wrote: I teach biology, and would like to show the students how to use R for some statistical assignments. One of those is to make a kite diagram (for example as seen in http://www.medinavalleycentre.org.uk/images/Bembri1.jpg). Is there any way to create one using R? I did a

[R] Matrix package download problem

Trying to install the Matrix package with install.packages fails for me on Linux, it is trying to fetch the wrong version 0.99-4, downloading the tgz which is 0.99-6 and using R CMD INSTALL works fine The output from the failed install was install.packages(c(Matrix)) trying URL

Re: [R] Kite diagrams

Barry Rowlingson [EMAIL PROTECTED] [2006.01.16] wrote: The joy of R is that of course there is a way to create these - you just have to write the code! Ok. time to start learning... The data are, I guess, on the X-axis a discrete set of distance points, (identical for each species?),

Re: [R] Matrix package download problem

Ashley Ford wrote: Trying to install the Matrix package with install.packages fails for me on Linux, it is trying to fetch the wrong version 0.99-4, downloading the tgz which is 0.99-6 and using R CMD INSTALL works fine The output from the failed install was

[R] R function for Gap statistic

Dear All, I need to calculate the optimal number of clusters for a classification based on a large number of observations (tens of thousands). Thibshirani et al. proposed the gap statistic for this purpose. Is any R code or fucntion available for this? Any help would be appreciated, including

Re: [R] Matrix package download problem

Try another mirror. This looks like a caching problem between you and the mirror, as the entry in PACKAGES is correct on the mirror. (The code tries to avoid cached copies, but not all caches cooperate.) On Mon, 16 Jan 2006, Ashley Ford wrote: Trying to install the Matrix package with

[R] Problems of data processing

I have two problems for the data processing of my large data base (5 rows). For example, a sample is as follows Num - c(1,2,3,4,4,4,5,5) Date - c(1/1/04 0:48,1/1/04 1:52, 1/1/04 1:55, 1/1/04 2:14, 1/1/04 3:09, 1/1/04 8:02, 1/1/04 9:05, 1/1/04 9:06) Place - c(x1,x1,x3,x4,x4,x4,x5,x5) X -

[R] Snow Rmpi Heterogeneous Cluster

Dear R-users, I am trying to make Snow and Rmpi working on an heterogenous cluster of linux computers. The master computer is built on a 64 bit architecture whereas all nodes are built on a 32 bit architecture. LAM/MPI was installed successfully on all machine. LAM boots correctly on the

Re: [R] Problems of data processing

something wrong in X and Y definitions... but this could work: do.call(rbind, lapply(split(toto, toto$Num), function(x) x[which.min(as.POSIXct(strptime(toto$Date, %d/%m/%y %H:%M))),])) i don't understand the second query; do you want to keep the first line when there are several lines for

[R] How to analysis Y98 chips using RankProd package?

Dear R and Bioconductor Helpers, I am using a package called RankProd under Bioconductor to analysis my Y98 (yeast) microarray data. I had no problem following the example in the vignette but got stocked when I tried to analyze my own data. When I tried to run the following command, RP.out -

Re: [R] Problems of data processing

Indeed, X - c(1,Na,2,3,3,3,6,6) Y - c(1,Na,9,7,7,7,8,8) I want to obtain one line for each Num. It's not a problem if there are several lines for the same place, because my identifier is Num. I just want to get X and Y well-informed in an other line for the same place. For example, Num=2 is at

[R] Poisson and negative binomial models with truncation

I am fitting count data models with zero-truncated data. Are there commands in R to adjust the Poisson model (glm(y~x, poisson)) and the negative binomial model (glm.nb(y~x)) for truncated distributions? Thanks in advance! Katrin Bernath

Re: [R] General partition search algorithm (local search, genetic algorithm, ...)

You may be able to use linear programming. Check out this thread: http://tolstoy.newcastle.edu.au/~rking/R/help/05/11/16009.html On 1/16/06, Aleš Žiberna [EMAIL PROTECTED] wrote: Dear R users! I was wondering if there exists (in R) any general algorithm for finding optimal partition

Re: [R] Powell's Metod

I am not aware of an R implementation of that method. However, if you meet the licensing conditions (which for my copy of NR do not allow me to use the code on a Unix machine even if I typed it in) you could interface to the NR C/C++ routines. On Sun, 15 Jan 2006, Tolga Uzuner wrote: Ah, my

Re: [R] Powell's Metod

Tolga, Have you considered an EM algorithm for your factor analysis problem? A reference for this is: Rubin, D. and Thayer, D. (1982). EM algorithms for ML factor analysis. Psychometrika, 47(1):69--76. Hope this is helpful, Ravi. -Original Message- From: [EMAIL PROTECTED]

Re: [R] Powell's Metod

Many thanks, let me look, Tolga Quoting Ravi Varadhan [EMAIL PROTECTED]: Tolga, Have you considered an EM algorithm for your factor analysis problem? A reference for this is: Rubin, D. and Thayer, D. (1982). EM algorithms for ML factor analysis. Psychometrika, 47(1):69--76. Hope this

[R] Standardized beta-coefficients in regression

Hello list, I am used to give a lot of attention to the standardized regression coefficients, which in SPSS are listed automatically. Is there alternative to running the last two lines in the following example to get all the information? ctl -

[R] gplots

Hi I am sure that this question has been asked before ... appologies in advance This - which comes out very nicely - better than the commercial stuff. plotmeans (cdpy~Dodefordpy, Data = Dataset, connect = False, minbar = 1, mean.labels = FALSE, col = blue, barwidth = 1.5, barcol = red,

Re: [R] Standardized beta-coefficients in regression

Try this, possibly with a better name: f - function(formula, ...) { print(summary(lm(formula, ...))) formula - update(formula, scale(.) ~ scale(.)) print(summary(lm(formula, ...))) } f(ctl ~ trt) On 1/16/06, Dr. Walter H. Schreiber [EMAIL PROTECTED] wrote: Hello list,

[R] Homogenous groups building - Randomisation

Dear R-users, We expect to form N homogeneous groups of n features from an experimentation including N*n data. The aim is to prevent group effects. How to do that with R functionalitites ? Does anyone know any way enabling this ? Example : 100 patients are observed. 3 biochemical

[R] lme output

I am trying to extract the solution from a simple lme calculation. For example (the first 4 have a mean 0, sd 1): y-c(-1.118,-.5,.5,1.118,10) gp-factor(c(rep('one',4),'two')) res-lme(y~1,rand=~1|gp) Linear mixed-effects model fit by REML Data: NULL Log-restricted-likelihood: -8.67141

Re: [R] Standardized beta-coefficients in regression

On Mon, 16 Jan 2006, Dr. Walter H. Schreiber wrote: Hello list, I am used to give a lot of attention to the standardized regression coefficients, which in SPSS are listed automatically. I do wonder why? Most people I have encountered who do that are interpreting them in invalid ways. Is

[R] [R-pkgs] New package lspls

Dear R useRs, A new package `lspls' is now available on CRAN. It implements the LS-PLS (least squares--partial least squares) regression method, described in for instance Jørgensen, K., Segtnan, V. H., Thyholt, K., Næs, T. (2004) A Comparison of Methods for Analysing Regression Models with Both

[R] label of second y-axis in xyplot (lattice)

Dear group, First I provide you with an example, I found in the newsgroup. Then I'd like to explain my problem to you by means of the output. enviro - data.frame(Year = rep(2001:2002, each = 365), Day = rep(1:365, 2), Precip = pmax(0, rnorm(365 * 2)),

[R] Problem with plot()

Dear R useRs, I have a problem to add title to the following graphics; Tukey=TukeyHSD(aov(CA~C), C,ordered=TRUE)) plot (Tukey, main=My first graph) actually, it draw a graph, but it also display: parameter main could not be set in high-level plot() function. If I execute:

[R] run-time of an R function

I have noticed dramatic differences in the run-time for the execution of one of my functions depending on whether or not R was restarted. Immediately after restart of R GUI, exec time = 2.8 min. If I then repeat the execution of the function in the same R session, exec time = 7.1 min. Removing

Re: [R] Problem with plot()

Andrej Kastrin wrote: Dear R useRs, I have a problem to add title to the following graphics; Tukey=TukeyHSD(aov(CA~C), C,ordered=TRUE)) plot (Tukey, main=My first graph) actually, it draw a graph, but it also display: parameter main could not be set in high-level plot() function.

Re: [R] run-time of an R function

Rossi, Peter E. wrote: I have noticed dramatic differences in the run-time for the execution of one of my functions depending on whether or not R was restarted. Immediately after restart of R GUI, exec time = 2.8 min. If I then repeat the execution of the function in the same R session,

Re: [R] run-time of an R function

Em Seg 16 Jan 2006 16:02, Rossi, Peter E. escreveu: of the function in the same R session, exec time = 7.1 min. Removing all objects via rm(list=(all=TRUE)) and initiating gc (gc(reset=TRUE)) helps, but only slightly (exec time = 5.0 min). Hi, I am currently using extensively a script with

Re: [R] Poisson and negative binomial models with truncation

Did you try RSiteSearch(zero-inflated)? Francisco From: Katrin Bernath [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Subject: [R] Poisson and negative binomial models with truncation Date: Mon, 16 Jan 2006 14:15:14 +0100 I am fitting count data models with zero-truncated data. Are there

[R] rsq.rpart not found ...

Hi to all I tried help.search(rsq) and found Help files with alias or concept or title matching 'rsq.rpart' using regular expression matching: rsq.rpart(rpart)Plots the Approximate R-Square for the Different Splits then I tried to use the function but I got

Re: [R] problem solved

library(rpart) Regards Knut __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

[R] rsq.rpart is there any R-Square value like in SPSS?

I found in the fullrefman only the function rsq.rpart with the search tearm r-square or rsquare. SPSS returnes the R Square an i am not albe to found the value in R Maybe there is another name for it Model Summary(d) ModelR R SquareAdjusted R SquareStd. Error of the

Re: [R] run-time of an R function

On Mon, 16 Jan 2006, Alexandre Santos Aguiar wrote: Em Seg 16 Jan 2006 16:02, Rossi, Peter E. escreveu: of the function in the same R session, exec time = 7.1 min. Removing all objects via rm(list=(all=TRUE)) and initiating gc (gc(reset=TRUE)) helps, but only slightly (exec time = 5.0 min).

Re: [R] rsq.rpart is there any R-Square value like in SPSS?

I guess you want the Multiple R-Squared for a linear model. You can get that by using summary() on a linear model. For example: ctl - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) trt - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) group - gl(2,10,20, labels=c(Ctl,Trt)) weight -

[R] new comer's question

I am new to R. I try to search the web but could not find the answer so I post it here asking for help. I have a csv file looks like this: (between two lines) === Machine Name,Resource, Type,Resource, Sub-type,Resource, Instance,Date,,Data -,,

Re: [R] rsq.rpart is there any R-Square value like in SPSS?

Chuck Cleland schrieb: I guess you want the Multiple R-Squared for a linear model. You can get that by using summary() on a linear model. For example: ctl - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) trt - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) group -

Re: [R] new comer's question

Chang Shen schrieb: I have a csv file looks like this: (between two lines) === First I load it by read.table call: myArray - read.table(c:/mydata.csv,sep=,); did you try read.csv(c:/mydata.csv,sep=,) Regards Knut

[R] importing from Stata

Hi, I have a new job, and everyone here uses Stata. I won't give up on R, but I must learn better how to exchange data between the two softwares. I am now focusing on importing data from Stata to R, and I must confess that I am a bit disappointed with the read.dta function from the foreign

[R] fitted values from lmer (lme4 0.98)

-- R-List Can someone tell me how to get fitted values etc. after fitting lmer? for example, from lme, I can fit mod.1 - lme() and get fitted values, coefficients, etc. in this way mod.1$fitted[,1] or mod.1$fitted[,2] etc. It seems lmer uses slots that are unfamiliar to me. Thanks. Dan

[R] singular convergence(7)?

Hi all, I just wonder what singular convergence means. Thanks. Yen Lin Error in lme.formula(Data ~ 1, random = ~1 | Wafer/fie/loc, subset = Wafer == : singular convergence (7) [[alternative HTML version deleted]] __

[R] Current state of support for BUGS access for Linux users?

Greetings: I'm going to encourage some students to try Bayesian ideas for hierarchical models. I want to run the WinBUGS and R examples in Tony Lancaster's An Introduction to Modern Bayesian Econometrics. That features MS Windows and bugs from R2WinBUGS. Today, I want to ask how people are

[R] princomp() with missing values in panel data?

dear R wizards: the good news is that I know how to omit missing observations and run a principal components analysis. p= princomp( na.omit( dataset ) ) p$scores[ ,1] # the first factor (where dataset contains missing values; incidentally, princomp(retailsmall, na.action=na.omit) does not

[R] Legends in xyplot

Hi, How can I add legends in the xyplot function, in the lattice library? Here is a simulation example: x - runif(90) z - sample(1:3, 90, rep=T) y - rnorm(90, mean = x^2 + z, sd=1) library(lattice) trellis.par.set(col.whitebg()) xyplot(y ~x, groups=as.factor(z), type = c('p',

Re: [R] [BioC] How to analysis Y98 chips using RankProd package?

Dear R and Bioconductor Helpers, I am using a package called RankProd under Bioconductor to analysis my Y98 (yeast) microarray data. I had no problem following the example in the vignette but got stocked when I tried to analyze my own data. When I tried to run the following command,

[R] looking for ENAR partner

Please forgive my abuse of this list. One of my friend is going to ENAR spring meeting and has booked air tickets. As a student with only limited support, he is looking for a partner to share the hotel costs. If you happen to know any information, could you please contact me at this email?

[R] off topic: how is xlispstat used in the industry?

I am sorry for this off-topic question. Just curious how xlispstat is used in the industry and what's it strengthen compared with other computing languages such as R or matlab? Thanks a lot. [[alternative HTML version deleted]] __

Re: [R] Standardized beta-coefficients in regression

On Mon, 16 Jan 2006, Dr. Walter H. Schreiber wrote: Hello list, I am used to give a lot of attention to the standardized regression coefficients, which in SPSS are listed automatically. Prof Brian Ripley [EMAIL PROTECTED] replied I do wonder why? Most people I have encountered who do

Re: [R] off topic: how is xlispstat used in the industry?

On 1/16/06, Wensui Liu [EMAIL PROTECTED] wrote: I am sorry for this off-topic question. Just curious how xlispstat is used in the industry and what's it strengthen compared with other computing languages such as R or matlab? Thanks a lot. [[alternative HTML version deleted]]

[R] Installing a package yet it will not work.

I want R to read my Microsoft Access database or maybe even a Sybase database. I installed RODBC or at least thought I did. Then I issued the following command: library(RODBC) And got Error in lazyLoadDBfetch(key, datafile, compressed, envhook) : ReadItem: unknown type 241 In

Re: [R] importing from Stata

Dear Dimitri, I don't have a solution for your problem, but your comment about factor levels isn't the source of the problem. Factors are stored as integer vector with a levels attribute (try, e.g., unclassing the factor), so the level names are not repeated. Regards, John

Re: [R] Installing a package yet it will not work.

Several people have reported problem with installed packages recently, and several turned out to be caused by the use of the StatLib mirror site. Please try installing from a different mirror site and see if that solves the problem for you. Andy From: Farrel Buchinsky I want R to read my

Re: [R] first derivative of a time series

First, I have to say that R is great. I'd never heard of cyclone before I read your post, but in only a couple of minutes, I was able to install it, try it out, and form a (perhaps erroneous) opinion thereof. The function coefFit fits a polynomial of degree N-1 to a

[R] Dynamic load

Hi, I am trying to load a FORTRAN program which I have downloaded from netlib. Counting the number of dependencies, there are about 10 programs which have to be loaded. This is under SunOS 5.9 and R 2.2.1. I have compiled the files with R221 CMD SHLIB *.f. If I load these object files one by

[R] Calculation of daily max

Good day everyone. I have a large dataset of 1 min wind speeds covering 5 years. How can I make an array of maximum daily values? The vectors I have are: 'VDATE' with dates in format '%Y-%m-%d' (like '1992-10-28') and 'WS' with wind speed data (same number of elements as VDATE). I want an

Re: [R] Problems of data processing

OK ! so try this: merge(toto[1:3], unique(na.omit(toto[3:5])),by=Place,all.x=T) Florent Bonneu a écrit : Indeed, X - c(1,Na,2,3,3,3,6,6) Y - c(1,Na,9,7,7,7,8,8) I want to obtain one line for each Num. It's not a problem if there are several lines for the same place, because my identifier

Re: [R] Calculation of daily max

Assuming VDATE is a character vector this produces a zoo time series object. library(zoo) z - aggregate(zoo(WS), as.Date(VDATE), max) coredata(z) and time(z) are the data vector of maximums and corresponding times, respectively. The R command: vignette(zoo)

Re: [R] princomp() with missing values in panel data?

See ?na.exclude (on the same page as na.omit) On Mon, 16 Jan 2006, ivo welch wrote: dear R wizards: the good news is that I know how to omit missing observations and run a principal components analysis. p= princomp( na.omit( dataset ) ) p$scores[ ,1] # the first factor (where dataset

Re: [R] Standardized beta-coefficients in regression

I had intended not to answer since I had a question regarding R and not about justification of a specific statistic. But nonetheless: (a) standardized betas are liberated of the original scale and facilitates reading off the relative influcence of a variable on the hyperplane. I find it easy

Re: [R] Current state of support for BUGS access for Linux users?

Paul Johnson wrote: Greetings: I'm going to encourage some students to try Bayesian ideas for hierarchical models. I want to run the WinBUGS and R examples in Tony Lancaster's An Introduction to Modern Bayesian Econometrics. That features MS Windows and bugs from R2WinBUGS. Today, I

Re: [R] Dynamic load

Mikael Anderson wrote: Hi, I am trying to load a FORTRAN program which I have downloaded from netlib. Counting the number of dependencies, there are about 10 programs which have to be loaded. This is under SunOS 5.9 and R 2.2.1. I have compiled the files with R221 CMD SHLIB *.f. If I