Re: [R] Recurrence plot in package tseriesChaos

Hello! As far as I know, there is not yet any package for R, which can compute the RQA measures you mentioned. I can only suggest to use the Matlab toolbox CRP Toolbox, which computes almost everything regarding recurrence plots. For those, who don't know what is RQA or even a recurrence plot:

Re: [R] Agnes Help

Vinicius == Vinicius Placco [EMAIL PROTECTED] on Mon, 23 Oct 2006 12:59:33 -0200 writes: Vinicius Hi Vinicius I'm trying to use the cluster package and I'm having some trouble... trouble with e-mail as well? You sent your message twice (to several thousand people)...

Re: [R] [ggplot] trouble with ggabline and log-log-plots

Yes, but for abline (the way it is currently written) to work out where that line should go, uses the equation y = mx + c. In this case, where c = 0, or -infinity on the log scale, y is going to be -infinty for the entire range of x's. I don't see how to interpret the specification in a

[R] loading and quitting R ...

Dear R'Helpers, Below is something which don't prevent me from going ahead but which I think is not a good behavior of my version/installation of R; Each time I open the R software, it gives me the following: R version 2.4.0 (2006-10-03) Copyright (C) 2006 The R Foundation for Statistical

Re: [R] Installing stats4 package

Himanshu == Himanshu Ardawatia [EMAIL PROTECTED] on Tue, 24 Oct 2006 22:17:47 +0200 writes: Himanshu Hi, Himanshu Problem solved (installing stats4 package). Well, for posteriority, you could have mentioned that you NEVER EVER need to install the 'stats4' package, since it has

[R] [R-pkgs] X2R: R-compatible output routines from C, ADMB, Fortran to R

We announce the availability of three related software libraries: C2R, ADMB2R, and For2R (together, X2R). Each contains output routines to simplify transfer of complicated data structures from models written in a compiled language to R. The user's data can be written as a structured ASCII

[R] simplification of code using stamp?

Hi I have the following code which I would like to simplify. Id does linear regressions and returns the r-squares, and the coefficients. It runs slow, as it is doing the regressions for each - is it possible to get the values in a dataframe which looks as follow: expert | xx | seeds |

Re: [R] variables with dynamic names?

Thanks very much for your help. I found the solution. I created a matrix with Strings and within a loop I read the files and processed them wellInfo - matrix(nrow = rows, ncol = cols) for(i in 1:rows) { tempRow - paste(rowString[i], formatC(c(1:cols), flag=0, width=2), sep=)

[R] Semi-competing Risk

Dear All, I am looking, before to do it by myself, for some code to implement the approach by Fine et( Biometrika 2001) 'On semi-competing risk data'. TIA Giovanni -- dr. Giovanni Parrinello Department of Biotecnologies Medical Statistics Unit University of Brescia Viale Europa, 11 25123

Re: [R] simplification of code using stamp?

I think your script is slow because it has to recalculate the same model five times. I've tried to avoid this by rewriting your function(df). function(df){ fit - summary(lm(distance ~ generation, data=df)) result - c(fit$$r.squared, $coefficients[2], $coefficients[4],

[R] Quantile Regression

Hi, how is it possible to retrieve the corresponding tau value for each observed data pair (x(t) y(t), t=1,...,n) when doing a quantile regression like rq.fit - rq(y~x,tau=-1). Thank you for your help. Jaci -- __ R-help@stat.math.ethz.ch mailing

Re: [R] extract certain values from a ts

Gabor Grothendieck escribió: There was still a typo in this so here it is again: # Consider the builtin in nhtemp ts series # Then the runs below above and below the mean are r - rle(as.vector(nhtemp mean(nhtemp))) r # with the first and last indexes of each # runs being given by:

Re: [R] simplification of code using stamp?

Resending the function because of a typo in the result vector. function(df){ fit - summary(lm(distance ~ generation, data=df)) result - c(fit$r.squared, fit$coefficients[2], fit$coefficients[4], fit$coefficients[1], fit$coefficients[3]) names(result) - c(rsqs, slope,

Re: [R] Progress Monitor in R / looping

Xiaofan Cao wrote: Hi there, I'm writing a program in R that has a few nested loops. I'd like to monitor the progress when the program is running and be able to estimate the remaining time. A long time ago I started writing some code to give R something like an 'iterator' object. You

Re: [R] simplification of code using stamp?

ONKELINX, Thierry wrote: Resending the function because of a typo in the result vector. function(df){ fit - summary(lm(distance ~ generation, data=df)) result - c(fit$r.squared, fit$coefficients[2], fit$coefficients[4], fit$coefficients[1], fit$coefficients[3])

[R] over- or underdispersion

Has anyone tried to do generalized linear modelling with the Conway-Maxwell-Poisson distribution? There's a recent paper on it in J. Royal Stat. Soc. C (Volume 54 Page 127 - January 2005). It might be useful when underdispersion is really present in the data. All the best, Tom

Re: [R] Progress Monitor in R / looping

This question is regularly asked. Have a look at progress() in svMisc() package (SciViews bundle). Best, Philippe Grosjean Barry Rowlingson wrote: Xiaofan Cao wrote: Hi there, I'm writing a program in R that has a few nested loops. I'd like to monitor the progress when the program is

Re: [R] Error when naming rows of dataset

At 17:30 24/10/2006, yongchuan wrote: I get the following error when I try reading in a table. How are 1.1, 1.2, 1.3 duplicate row names? Thx. R gives you brief details of where it was when it fell over. Have you checked in latestWithNumber.txt' to see whether R is right? table -

Re: [R] Error when naming rows of dataset

I'm pretty new with R, so the only error message I see is the below that I pasted. I'm attaching the first few rows of the file for reference. The layout looks screwy when I attach it here but 'Start' to 'closingCoupon' is the first row in the .txt file. Thx! Start StopPrepayDate

Re: [R] Error when naming rows of dataset

yongchuan [EMAIL PROTECTED] writes: I'm pretty new with R, so the only error message I see is the below that I pasted. I'm attaching the first few rows of the file for reference. The layout looks screwy when I attach it here but 'Start' to 'closingCoupon' is the first row in the .txt file.

Re: [R] Error when naming rows of dataset

At 12:44 25/10/2006, yongchuan wrote: I'm pretty new with R, so the only error message I see is the below that I pasted. I'm attaching the first few rows of the file for reference. You seem to have 2 rows called 2.1 The layout looks screwy when I attach it here but 'Start' to 'closingCoupon' is

Re: [R] Recurrence plot in package tseriesChaos

In terms of non-R software there is a review of software packages in this JSS article: http://www.jstatsoft.org/v07/i09/JSS_055.pdf On 10/25/06, pucicu [EMAIL PROTECTED] wrote: Hello! As far as I know, there is not yet any package for R, which can compute the RQA measures you mentioned. I

Re: [R] Quantile Regression

data(engel) attach(engel) rq(y~x) Call: rq(formula = y ~ x) Coefficients: (Intercept) x 81.4822474 0.5601806 Degrees of freedom: 235 total; 233 residual rq(y~x)-f f$tau [1] 0.5 url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]

Re: [R] How to start R with a file loaded?

Assume you want to execute code in 'mycode.R', the easiest way is: echo source('mycode.R') | R --vanilla --quiet If you do it in a shell script, you can also pass variables to your code like this (list of shell script): #!/bin/sh echo var1=${1};var2=${2};source('mycode.R') | R --vanilla --

Re: [R] Error when naming rows of dataset

On 10/25/2006 7:44 AM, yongchuan wrote: I'm pretty new with R, so the only error message I see is the below that I pasted. What caught you is that R truncates the text when it prints an error. So it only listed the first 3 row names, which are unique, and didn't point out that the real

Re: [R] Recurrence plot in package tseriesChaos

This article is alittle bit outdatet ... Gabor Grothendieck wrote: In terms of non-R software there is a review of software packages in this JSS article: http://www.jstatsoft.org/v07/i09/JSS_055.pdf On 10/25/06, pucicu [EMAIL PROTECTED] wrote: Hello! As far as I know, there is not

Re: [R] variables with dynamic names?

With the style of whole objects encouraged for R that code looks like this: rowString - LETTERS[1:3]; cols - 3 # test data mat - outer(rowString, formatC(1:cols, flag = 0, width = 2), paste, sep = ) mat - paste(mat, csv, sep = .) sapply(mat, function(el) { if (exists(el)) { DF - read.table(el,

Re: [R] Unable to load foreign after upgrade on ubuntu

| | But since foreign is part of R, installing a new version of R will | update the standard and recommended packages including foreign. So | this suggests that what is being picked up is another copy of foreign | from another library. Good point. As I recall, Christian always

[R] Incorrect 'n' returned by survfit()

I've a data set with 6 rows of data representing 6000+ distinct loans. I did a coxph() regression on it (see call below), but a subsequent survfit() call on the coxph object is almost certainly wrong. It gives n=6 when it should be more like 6000+ (I think) survfit(resultag) Call:

Re: [R] ...... looping

BaRow == Barry Rowlingson [EMAIL PROTECTED] on Wed, 25 Oct 2006 11:06:06 +0100 writes: BaRow Xiaofan Cao wrote: Hi there, I'm writing a program in R that has a few nested loops. I'd like to monitor the progress when the program is running and be able to estimate

Re: [R] Key colour problem with lattice plot

On 23 Oct 2006, at 23:52, Deepayan Sarkar wrote: On 10/23/06, Alex Brown [EMAIL PROTECTED] wrote: Can anyone explain why the key is inverted versus the bar order? Because the key goes from top to bottom, while cartesian coordinates go from bottom to top. Neither can

[R] ns() (pkg splines) vs rcs() (pkg Design)

Dear R-helpers, Why the following calls result in a different output: library(splines) library(Design) x - rnorm(10) ns(x, knots = 0, Boundary.knots = c(-1, 1)) rcs(x, c(-1, 0, 1)) Thanks in advance for any hints. Kind Regards, Moko Kosta __

[R] Help with random effects and smoothing splines in GAMM

Try to fit a longitudinal dataset using generalized mixed effects models via the R function gamm() as follows: library(mgcv) gamm0.fit- gamm(y ~ x+s(z,bs=cr), random=list( x=~1, s(z,bs=cr)=~1

Re: [R] Help with understanding [[]] [] array, list, matrix referencing

I want to thank everyone for their comments and suggestions. P. Burns' S Poetry I think will be a lot of help and I thought it was really poetry:). So will the other references that were provided by I believe Mr Kane. The other replies provided me some great insights. If I understand R uses

Re: [R] Trellis Conditional contourplot

OK! # The R codes to generate the Trellis plot are from the R help archive by Karl Ove Hufthammer panel.estcontplot - function(x, y, ..., pretty=TRUE, region=FALSE) { cest.gr=kde2d(x, y) cest.gr.lat=con2tr(cest.gr) panel.contourplot(cest.gr.lat$x, cest.gr.lat$y, cest.gr.lat$z,

[R] how to improve the efficiency of the following lapply codes

Hi, I have a series of lda analysis using the following lapply function: n - dim(intersect.matrix)[1] net1.lda - lapply(1:(n), function(k) i.lda(data.list, intersect.matrix, i=k, w)) i.lda is function to do the real lda analysis. intersect.matrix is a nx1026 matrix, n can be a really huge

Re: [R] Error when naming rows of dataset

On Wed, 25 Oct 2006, yongchuan wrote: I'm pretty new with R, so the only error message I see is the below that I pasted. Which you misread: did you not notice it ended with a comma? I'm attaching the first few rows of the file for reference. The layout looks screwy when I attach it here

Re: [R] how to improve the efficiency of the following lapply codes

object.size(intersect.matrix) 41314204 but my machine has 4 G memory, so it should be ok since after 12 hours, it finishes 16k out of 60k but still slow non-linearly. I am thinking to chop 60k into multiple 5k data.frames to run the program. but just wondering is there a way around it? version

[R] write a help file for my own function

Hi, I am wondering how I can write a help page for my own function so when I type ?myOwnfunc, then the help page will show up? thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III

[R] update index in for statement during calculation

Hello, I have a time series of data as a data.frame. Occasionally there is one or more days missing (e.g. data available for days 2, 3, 4, 8, 9, 10 -- missing days between 4 and 8). The experimental time information can be found in the 2nd column of data. I would like to have a continuous

[R] Drawing a reference line for a qqplot with reference to Weibull distribution

Hi, I'm trying to create a qqplot with reference to a Weibull distribution including a reference line. This is my current code: lights.data - scan(lights.dat) #Generate Weibull quantiles prob.grid - ppoints(length(lights.data)) prob.quant - qweibull(prob.grid , 1.5,4) #Draw QQ plot

Re: [R] Error when naming rows of dataset

Try 'row.names=NULL' on the read.table function. On 10/25/06, yongchuan [EMAIL PROTECTED] wrote: I'm pretty new with R, so the only error message I see is the below that I pasted. I'm attaching the first few rows of the file for reference. The layout looks screwy when I attach it here but

[R] gtools(read.xls) error in perl installation?

My installation is R version 2.4.0 on Mac OS X version 10.4.8 (the latest release in both cases). I've recently had to restore my hard drive after a crash, and fear that this may have screwed up my Perl installation slightly. Whenever I run the read.xls function from library(gtools) I get

Re: [R] update index in for statement during calculation

try using a 'while': i - 1 while (i nrow(data) - 1) { diff.time- round(data[i+1,2], 0) - round(data[i,2], 0)-1 old.row - nrow(data) if (diff.time 0) { fill- c(data[i,1], (round(data[i,2], 0)+1), rep(0,classnumber))

[R] any good way to convert sp class objects to splancs object

Greetings: are there any simple ways to convert an sp class object to a splancs ppp class object, outside of reading the coordinates and computing a bounding box? cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341

Re: [R] write a help file for my own function

On 25 October 2006 at 14:16, Weiwei Shi wrote: | I am wondering how I can write a help page for my own function so when | I type ?myOwnfunc, then the help page will show up? There is an entire manual devoted to 'extending R', which includes sections on writing manual pages. The key insight

Re: [R] Trellis Conditional contourplot

On 10/25/06, Marco LO [EMAIL PROTECTED] wrote: OK! # The R codes to generate the Trellis plot are from the R help archive by Karl Ove Hufthammer panel.estcontplot - function(x, y, ..., pretty=TRUE, region=FALSE) { cest.gr=kde2d(x, y) cest.gr.lat=con2tr(cest.gr)

Re: [R] any good way to convert sp class objects to splancs object

On Wed, 25 Oct 2006, Dylan Beaudette wrote: Greetings: are there any simple ways to convert an sp class object to a splancs ppp class object, outside of reading the coordinates and computing a bounding box? Aren't ppp class objects from the spatstat package? Have you tried the spspatstat

Re: [R] update index in

Kim Milferstedt milferst at uiuc.edu writes: Hello, I have a time series of data as a data.frame. Occasionally there is one or more days missing (e.g. data available for days 2, 3, 4, 8, 9, 10 -- missing days between 4 and 8). The experimental time information can be found in the 2nd

Re: [R] write a help file for my own function

Note the R command, prompt, which will generate an outline of the help page for you. Also you might want to look through the existing help files for many examples. On 10/25/06, Weiwei Shi [EMAIL PROTECTED] wrote: Hi, I am wondering how I can write a help page for my own function so when I

[R] Excel files

Hi every one, I am very very new to R and solicit your kind help I am trying to use my excel files in R. I used the Xlread/write package and able to load the a sample file into console. Then I tried to find the mean of a column vector for example. But I could not proceed Here is the problem

Re: [R] Excel files

ramelan thiagarajah [EMAIL PROTECTED] writes: Hi every one, I am very very new to R and solicit your kind help I am trying to use my excel files in R. I used the Xlread/write package and able to load the a sample file into console. Then I tried to find the mean of a column vector for

[R] How to specify a constant in gnls{nlme}

Hi All, I have question about speficifying a constant in gnls() from package nlme. Here is a testing code: # library(nlme) x = exp( rnorm(100)) y = 1/(1+x) + rnorm(100)/10 plot( y ~ x) fm1 = gnls( y ~ 1/(1+(x/v)^w), start=list( v=1, w=1)) a =1; b=1; fm2 = gnls( y ~

Re: [R] Drawing a reference line for a qqplot with reference to Weibull distribution

The reference line needs to know the distribution. The qqline function has the normal built in. You need to write something similar. qqline puts a line through the quartiles. I extended that to the t-distribution in the qqline.t function appended here. You need to do something similar to get

Re: [R] How to start R with a file loaded?

Thanks to all you numerous r-helpers, the problem is solved! It's so much easier when someone explains. I was going crazy trying to understand the manual on my own! Thanks again to everyone! GF On 10/25/06, Pierce, Ken [EMAIL PROTECTED] wrote: You can edit the below file which runs during R

Re: [R] any good way to convert sp class objects to splancs object

On Wednesday 25 October 2006 12:02, Roger Bivand wrote: On Wed, 25 Oct 2006, Dylan Beaudette wrote: Greetings: are there any simple ways to convert an sp class object to a splancs ppp class object, outside of reading the coordinates and computing a bounding box? Aren't ppp class

[R] Coding style query (braces)

Re: placement of braces and else clauses. At the R prompt, I believe their placement must avoid causing a syntactically complete statement at the wrong place. This can results in what might be considered rather awkward looking code. IF it is known that code will be used via sourcing a script

Re: [R] Mixed conditional logit model

Ryuichi Tamura ry.tamura at gmail.com writes: I wrote a collection of R functions for estimating discrete choice models by simulated maximum likelihood. It includes: ... My R functions is based on GAUSS program listed in this site. Have you considered to wrap all funcs in a package? Gregor

Re: [R] Coding style query (braces)

On Wed, 2006-10-25 at 16:44 -0400, Mike Prager wrote: Re: placement of braces and else clauses. At the R prompt, I believe their placement must avoid causing a syntactically complete statement at the wrong place. This can results in what might be considered rather awkward looking code.

[R] cloud() works but wireframe() is blank

Per the message from Alexander Nervedi, 29 April 2006: I have to be making a riddiculously silly ommission. when I run the fillowing i get the cloud plot ok. But I cant figure out what I am missing out when I call wireframe. Any help would be appreciated. x-runif(100) y-rnorm(100)

Re: [R] cloud() works but wireframe() is blank

On 10/25/06, Larry Layne [EMAIL PROTECTED] wrote: Per the message from Alexander Nervedi, 29 April 2006: I have to be making a riddiculously silly ommission. when I run the fillowing i get the cloud plot ok. But I cant figure out what I am missing out when I call wireframe. Any help

[R] density plot text

Is there any way of adding text to a density plot? I have had a go using the text() function but I think the error is because this function doesn't work with densityplot(). Alternatively, I understand I can achieve pretty much the same result if I plot a density kernel estimate using plot()

Re: [R] Coding style query (braces)

On 10/25/06, Mike Prager [EMAIL PROTECTED] wrote: Re: placement of braces and else clauses. At the R prompt, I believe their placement must avoid causing a syntactically complete statement at the wrong place. This can results in what might be considered rather awkward looking code. IF it

Re: [R] density plot text

On 10/25/06, Murray Pung [EMAIL PROTECTED] wrote: Is there any way of adding text to a density plot? I have had a go using the text() function but I think the error is because this function doesn't work with densityplot(). Alternatively, I understand I can achieve pretty much the same result

[R] Recoding categorical variables

I want to recode an integer-valued variable y so that its values become 1:length(y). I can do this using a loop but maybe someone can suggest code without a loop. My code is this: y - round(20*runif(25)) table(y) suy - sort(unique(y)) m - length(suy) z - y + max(suy) for(i in 1:m) z[y==suy[i]]

Re: [R] set.seed() and .Random.number

Taka Matzmoto wrote: Hi R-users I have two conditions. For each condition, 100 sets of 10 random numbers from N(0,1) need to be generated. Here is my question. At the begining I specify a seed number. I want to make the 100th set of the first condition and 1st set of the second conditon

[R] Read.csv

Are there ways to load a csv file without row.names by read.csv? Thanks. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] simplification of code using stamp?

I get the following, which is not what I am looking for. test[1:10,] expertxx seeds runvalue 1 BW x001025 1 rsqs, slope, d.slope, intercept, d.intercept 2 BW x001025 2 rsqs, slope, d.slope, intercept, d.intercept 3

Re: [R] Recoding categorical variables

Dear Murray, How about as.numeric(factor(y)) ? I hope this helps, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original

Re: [R] Recoding categorical variables

Thanks John! Deepayan Sarkar also suggested this. I don't really expect to see any better solution. Murray John Fox wrote: Dear Murray, How about as.numeric(factor(y)) ? I hope this helps, John John Fox Department of Sociology McMaster University

Re: [R] Progress Monitor in R / looping

This is easy to do with the proto package. Here is a basic version: library(proto) ml - proto(start = 1, end = 5, val = NULL, it = function(.) { if (is.null(.$val)) return(.$val - .$start) else .$val - .$val + 1 if (.$val .$end) return(FALSE) else .$val }) # test 1 while(ml$it())

Re: [R] Read.csv

Try: read.csv(name.csv, header = F) On 26/10/06, Wang, Joshua (EQS) [EMAIL PROTECTED] wrote: Are there ways to load a csv file without row.names by read.csv? Thanks. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch

Re: [R] Read.csv

Mr. Pung, Thank you. It works in terms of loading the data. Except that there is a header in the file that I would like to load it to be the names in the data.frame. Regards, Josh From: Murray Pung [mailto:[EMAIL PROTECTED] Sent: Thursday,

[R] Get the names of the columns in a tserie

Hello everybody, I'm a beginner in R, and I'm currently working on Tseries (analysis of a portfolio) I imported the data like this (library tseries) : X-read.ts(X.dat, start=c(1995,1), frequency=261, header=T, sep=;) There is a header which contains the names of each column (codes of shares)

[R] help fo finding R package utils

Sir I have a problem that from which country i can assess R package utils for data entry for loading it in R Please help me in this regard. -- AMINA SHAHZADI Department of Statistics GC University Lahore, Pakistan. Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED]

Re: [R] help fo finding R package utils

Amina, utils is a base package and should be already installed in a functional R system. You can try sessionInfo() to verify that it is loaded. -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of amna khan Sent: Thursday, October 26, 2006

[R] Library

Hi, I am a new to R, but I used S+ before. Now I am trying to estimate t-copula based BEKK GARCH model. I am using window version. I have downloaded R-2.4.0 and added some libraries. I visited the site http://www.vsthost.com/vstDocs/mgarchBEKK/release/ and downloaded mgarchBEKK_0.07-6.zip