Re: [R] invert 160000x160000 matrix

2007-08-14 Thread Patnaik, Tirthankar
A variety of tricks would need to be used to invert a matrix of this size. If there are any other properties of the matrix that you know (symmetric, positive definite, etc, sparse) then they could be useful too. You could partition the matrix first, then use an in-place inverse technique for

[R] cov.unscaled in gls object

2007-08-14 Thread Sven Garbade
Hi list, can I extract the cov.unscaled (the unscaled covariance matrix) from a gls fit (package nlme), like with summary.lm? Background: In a fixed effect meta analysis regression the standard errors of the coefficients can be computed as sqrt(diag(cov.unscaled)) where cov.unscaled is (X'WX). I

Re: [R] invert 160000x160000 matrix

2007-08-14 Thread Prof Brian Ripley
On Tue, 14 Aug 2007, Patnaik, Tirthankar wrote: A variety of tricks would need to be used to invert a matrix of this size. If there are any other properties of the matrix that you know (symmetric, positive definite, etc, sparse) then they could be useful too. You could partition the

[R] LimmaGUI and Design Matrix

2007-08-14 Thread tee` suesean
Hi all, I'm working on microarray and currently analyzing the microrarray data using limmaGUI. Loop design has been applied in this experiment. This is a 2X2 factorial experiment where there are control and treatment at 2 different time points, week 6 and 9. The experimental design is

[R] makeSOCKcluster

2007-08-14 Thread Michael Janis
Hi, I am attempting to implement a mixed (windows/linux) snow sockets parallelism in R, but am running into difficulties similar to a post made Aug 31, 2006 under the same subject heading. I feel like I may be one or two non-obvious steps away from getting it all working, but I'm stuck. If

[R] R 2.5.1 configure problem

2007-08-14 Thread Andreas Hey
Hi, I have follwoing problem: I will install R-2.5.1 on a Linux Maschine (64Bit) and I will use the R-GUI JGR (Jaguar) SO I make following steps: ./configure --with-gnu-ld --enable-R-shlib VAR=fPIC VAR=TCLTK_LIBS make I become following error messages: . Entering

[R] Mixed effects and hierarchical error terms

2007-08-14 Thread Richard Gunton
Please could someone help me understand the difference between the following two models? lme (Y ~ X, random= ~1|G1/G2) aov (Y ~ X + Error (G1/G2)) Since random effects can be considered as additional error terms, I would have thought these two model formulations should amount to the same

Re: [R] binomial simulation

2007-08-14 Thread sigalit mangut-leiba
Thank you, I'm trying to run the joint probabilty: C(N,k)*p^k*(1-p)^(N-k)*C(k,m)*q^m*(1-q)^(k-m) and get the error: Error in C(N, k) : object not interpretable as a factor so I tried the long way: gamma(N+1)/(gamma(k+1)*(gamma(N-k))) and the same with k, and got the error: 1: value out of

Re: [R] R 2.5.1 configure problem

2007-08-14 Thread Peter Dalgaard
Andreas Hey wrote: Hi, I have follwoing problem: I will install R-2.5.1 on a Linux Maschine (64Bit) Which? (CPU and OS, please. There are about four likely possibilities, half a dozen less likely ones...) and I will use the R-GUI JGR (Jaguar) SO I make following steps:

[R] Import of Access data via RODBC changes column name (NO to Expr1014) and the content of the column

2007-08-14 Thread Maciej Hoffman-Wecker
Dear all, I have some problems with importing data from an Access data base via RODBC to R. The data base contains several tables, which all are imported consecutively. One table has a column with column name NO. If I run the code attached on the bottom of the mail I get no complain, but the

Re: [R] cov.unscaled in gls object

2007-08-14 Thread Prof Brian Ripley
This is what the vcov() generic is for. You are asking for internal details from a different class (summary.lm). On Tue, 14 Aug 2007, Sven Garbade wrote: Hi list, can I extract the cov.unscaled (the unscaled covariance matrix) from a gls fit (package nlme), like with summary.lm?

Re: [R] RWeka cross-validation and Weka_control Parametrization

2007-08-14 Thread Kurt Hornik
On Wed, 01 Aug 2007 10:52:02 +0200, Bjoern wrote: Hello, I have two questions concerning the RWeka package: 1.) First question: How can one perform a cross validation, -say 10fold- for a given data set and given model ? 2.) Second question

Re: [R] vertically oriented color key in heatmaps

2007-08-14 Thread Jim Lemon
Rajarshi Guha wrote: Hi, I have some data which I was plotting using image(). I wanted to add a vertical color key to the plot and I found that heatmap.2 in gplots does let me add a color key. However, I was thinking of a vertical bar with the color range rather than the style that

[R] Slack variable in OR

2007-08-14 Thread Amir Safari
Hi dear R users, Is it basically correct that a problem is ( linearly on nonlinearly ) modeled so that the slack variable is bounded by an upper bound ? If so, how it can be handled and coded practically ? for example: x1+ x2 = b so x1 + x2 + s=b

Re: [R] Slack variable in OR

2007-08-14 Thread gyadav
hi Amir please see inline answers Amir Safari [EMAIL PROTECTED] Sent by: [EMAIL PROTECTED] 08/14/2007 02:37 PM To R-help@stat.math.ethz.ch cc Subject [R] Slack variable in OR Hi dear R users, @@@ although i have not understood your problemos clearly whatever i can help, i

Re: [R] Import of Access data via RODBC changes column name (NO to Expr1014) and the content of the column

2007-08-14 Thread Prof Brian Ripley
On Tue, 14 Aug 2007, Maciej Hoffman-Wecker wrote: Dear all, I have some problems with importing data from an Access data base via RODBC to R. The data base contains several tables, which all are imported consecutively. One table has a column with column name NO. If I run the code attached

Re: [R] diffusing GIS data in maps

2007-08-14 Thread Vladimir Eremeev
Hi. You will find some useful information in the http://r-spatial.sourceforge.net/ Particularly, Fig. 07 in the Graph gallery. Package spmaps can be used to extract desired boundaries from the mapdata and convert them to the format suitable for sp and others. Lawrence D. Brenninkmeyer

Re: [R] Help with npmc

2007-08-14 Thread Paul Fenner
I cant't seem to get npmc to make a comparison to a control level summary(npmc(brain), type=BF, control=1) $`Data-structure` group.index class.level nobs c 1 c 30 l 2 l 30 r 3 r 30 $`Results of the multiple Behrens-Fisher-Test`

[R] graph dimensions default

2007-08-14 Thread Simon Pickett
Hi, I would like to (if possible) set the default width and height for graphs at the start of each session and have each new graphic device overwrite the previous one. I only know how to do this using windows(width=,height=...) which opens up a new plotting device every time, so I end up with

Re: [R] Slack variable in OR

2007-08-14 Thread Amir Safari
Hi Thank you very much. So sorry for the badly writing an example. Let assume we are modelling in a quadratic programming framework. So we have min 1/2xHx + fx subject to: Ax=b Here A is a matrix. Therefore the questions are valid here. [EMAIL PROTECTED]

Re: [R] GML with tweedie: AIC=NA

2007-08-14 Thread Catarina Miranda
Thanks for your reply, but I still couldn't solve the problem. I am using the package statmod, and I need the AIC because I want to use the step function (I am modelling many species, so I would prefer to do the step automatically). I can't find the tweedie package in the R packages list and I

[R] pakages

2007-08-14 Thread Safaa Najla
Good Morning i am in doctorate. i want to ask for the packages of R, i tried to install it, but it appears not found. each time i have to delete and install again the programme R. Are there another method for installing the package? thank you __

Re: [R] pakages

2007-08-14 Thread gyadav
please give details of the system, OS, etc which version of R you are using, how you are installing the packages etc etc --- Regards, Gaurav Yadav (mobile: +919821286118) Assistant Manager, CCIL, Mumbai (India) mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Profile:

Re: [R] BDS test - results unclear to me

2007-08-14 Thread Adrian Trapletti
Hi Nicolas Most likely because the higher embedding dimension uses less data points, even when applied to the lower dimension. Therefore, the actual numbers should be similar, but do not exactly match. But it's a very long time ago I last touched this code. So pls read bdstest.c from tseries

Re: [R] pakages

2007-08-14 Thread Uwe Ligges
Safaa Najla wrote: Good Morning i am in doctorate. i want to ask for the packages of R, i tried to install it, What? R or packages? How did you try it, please give us more details as suggested in the posting guide! but it appears not found. Complete error message, please. each time

[R] Linear Regression with slope equals 0

2007-08-14 Thread E . N . D . Grew
Hi there, am trying to run a linear regression with a slope of 0. I have a dataset as follows t d 1 303 2 302 3 304 4 306 5 307 6 303 I would like to test the significance that these points would lie on a horizontal straight line. The standard regression lm(d~t) doesn't seem to

Re: [R] diffusing GIS data in maps

2007-08-14 Thread Felix Andrews
Package akima allows simple 2D interpolation from points to a grid. On 8/14/07, Lawrence D. Brenninkmeyer [EMAIL PROTECTED] wrote: Hi- I am trying to find a way to diffuse GIS data on a European map. I have a dataset consisting of particular locations scattered across Europe, along with

Re: [R] makeSOCKcluster

2007-08-14 Thread Luke Tierney
Try using the option homogenoeus=FALSE and make sure the appropriate environment variables are set on the worker nodes. Best, luke On Tue, 14 Aug 2007, Michael Janis wrote: Hi, I am attempting to implement a mixed (windows/linux) snow sockets parallelism in R, but am running into

Re: [R] graph dimensions default

2007-08-14 Thread Prof Brian Ripley
On Tue, 14 Aug 2007, Simon Pickett wrote: Hi, I would like to (if possible) set the default width and height for graphs at the start of each session and have each new graphic device overwrite the previous one. Hmm. It is graphics devices that have dimensions, and plots that overwrite

Re: [R] Linear Regression with slope equals 0

2007-08-14 Thread Prof Brian Ripley
On Tue, 14 Aug 2007, [EMAIL PROTECTED] wrote: Hi there, am trying to run a linear regression with a slope of 0. I have a dataset as follows t d 1 303 2 302 3 304 4 306 5 307 6 303 I would like to test the significance that these points would lie on a horizontal straight line. The

Re: [R] Import of Access data via RODBC changes column name (NO to Expr1014) and the content of the column

2007-08-14 Thread Maciej Hoffman-Wecker
Dear Professor Ripley, Thank you very much for your response. I send the problem, as I didn't have any more ideas were to search for the reason. I didn't say this is a R bug, knowing the responses on such mails.-) But I succeeded in developing a tiny example, that reproduces the bug (wherever

[R] Odp: Linear Regression with slope equals 0

2007-08-14 Thread Petr PIKAL
Hi Not being a trained statistician regression with slope = 0 seems odd to me. If you do fit-lm(d~t) summary(fit) Call: lm(formula = d ~ t) Residuals: 123456 0.04762 -1.43810 0.07619 1.59048 2.10476 -2.38095 Coefficients:

Re: [R] graph dimensions default

2007-08-14 Thread Simon Pickett
Yes, Thankyou, that does the trick nicely. I thought that kind of thing could be specified using par() but I guess not. Thanks again. On Tue, 14 Aug 2007, Simon Pickett wrote: Hi, I would like to (if possible) set the default width and height for graphs at the start of each session and

Re: [R] vertically oriented color key in heatmaps

2007-08-14 Thread Rajarshi Guha
On Aug 14, 2007, at 5:11 AM, Jim Lemon wrote: Rajarshi Guha wrote: Hi, I have some data which I was plotting using image(). I wanted to add a vertical color key to the plot and I found that heatmap. 2 in gplots does let me add a color key. However, I was thinking of a vertical bar

Re: [R] Linear Regression with slope equals 0

2007-08-14 Thread Ted Harding
On 14-Aug-07 11:36:37, [EMAIL PROTECTED] wrote: Hi there, am trying to run a linear regression with a slope of 0. I have a dataset as follows t d 1 303 2 302 3 304 4 306 5 307 6 303 I would like to test the significance that these points would lie on a horizontal

Re: [R] graph dimensions default

2007-08-14 Thread Prof Brian Ripley
On Tue, 14 Aug 2007, Simon Pickett wrote: Yes, Thankyou, that does the trick nicely. I thought that kind of thing could be specified using par() but I guess not. As I said, size is not a property of the plot. And par() applies to the current device, not future ones. Thanks again. On

[R] papply, reuse of data

2007-08-14 Thread Markus Schmidberger
Hello, we are doing some computations with MPI and Rmpi. Therefore papply is a very comfortable function. Is it possible to reuse calculated data on slaves? We do some calculation with papply, then we have to do some overall calculation at the master then we want to do some calculation on the

[R] Problem with by: does not work with ttest (but with lme)

2007-08-14 Thread Daniel Stahl
Hello, I would like to do a large number of e.g. 1000 paired ttest using the by-function. But instead of using only the data within the 1000 groups, R caclulates 1000 times the ttest for the full data set(The same happens with Wilcoxon test). However, the by-function works fine with the lme

[R] Odp: Problem with by: does not work with ttest (but with lme)

2007-08-14 Thread Petr PIKAL
Hi [EMAIL PROTECTED] napsal dne 14.08.2007 15:11:11: Hello, I would like to do a large number of e.g. 1000 paired ttest using the by- function. But instead of using only the data within the 1000 groups, R caclulates 1000 times the ttest for the full data set(The same happens with

Re: [R] Error message when using zero-inflated count regression model in package zicounts

2007-08-14 Thread Hank Stevens
Hi Jim, Two thoughts come to me, unencumbered by the thought process or knowledge of zicounts: 1. Is Poisson really NOT appropriate? (do you have to use zicounts?) 2. Are you 110% certain that all variables are the same length? Would NA's interfere? Cheers, Hank On Aug 13, 2007, at 5:10 PM,

[R] Question about unicode characters in tcltk

2007-08-14 Thread R Help
hello list, Can someone help me figure out why the following code doesn't work? I'm trying to but both Greek letters and subscripts into a tcltk menu. The code creates all the mu's, and the 1 and 2 subscripts, but it won't create the 0. Is there a certain set of characters that R won't

Re: [R] Problem with by: does not work with ttest (but with lme)

2007-08-14 Thread Chuck Cleland
Daniel Stahl wrote: Hello, I would like to do a large number of e.g. 1000 paired ttest using the by-function. But instead of using only the data within the 1000 groups, R caclulates 1000 times the ttest for the full data set(The same happens with Wilcoxon test). However, the by-function

[R] labelling plots with ancillary data in data.frame

2007-08-14 Thread Wesley Roberts
Hi All, I am busy using R to do some regression modelling and have been using plot(x,y,) to visualise my variables. I would now like to label my points using data stored in the data.frame used for the regression analysis. For example each of my data points is made up of a field measured forest

Re: [R] invert 160000x160000 matrix

2007-08-14 Thread Jiao Yang
Tir, Thank you very much for the note. I'm using an algorithm to analyze a data set of 400 variables and the algorithm uses the inverse of a 16x16 positive definite matrix. The matrix is stored as a text file. Can you please give some reference to in-place inverse technique? I

[R] Using sunflowerplot to add points in a xyplot panel

2007-08-14 Thread Ronaldo Reis Junior
Hi, I use panel.points to add points to a xyplot graphic. But I like to use the sunflowerplot to plot my points because this is very superimposed. It is possible to use this? I try but it dont work directly. It may be need to put this function inside a panel.??? Thanks Ronaldo -- Where

Re: [R] State Space Modelling

2007-08-14 Thread Bernardo Ribeiro
Here is one of the codes. Thanks a lot... module(finmetrics) genvasicek.ssf = function(param, tau=NULL, freq=1/12){ ## 1. Check for valid inputs if(length(param) 5) stop(Parameters must have length greater than 4) N = length(param) - 13 if (length(tau) != N)

[R] {grid} plain units with non NULL data arguments

2007-08-14 Thread Wolfram Fischer
In help(unit) I read: The 'data' argument must be a list when the 'unit.length()' is greater than 1. For example, 'unit(rep(1, 3), c(npc, strwidth, inches), data=list(NULL, my string, NULL))'. In the newest R-versions it is not anymore allowed to let strings in the data-argument

Re: [R] Using sunflowerplot to add points in a xyplot panel

2007-08-14 Thread Sundar Dorai-Raj
Ronaldo Reis Junior said the following on 8/14/2007 7:08 AM: Hi, I use panel.points to add points to a xyplot graphic. But I like to use the sunflowerplot to plot my points because this is very superimposed. It is possible to use this? I try but it dont work directly. It may be need to

[R] Comparing long species lists via Sorenson’s dissimilarity

2007-08-14 Thread Richard Price
I have 4 very large species lists and I would like to compare them. I have the following results from running Sorenson’s dissimilarity tests: Norfolk Fens compared to Suffolk Coastal Fens: QS=0.583961142689298 Norfolk Fens compared to Breckland Edge Fens:

Re: [R] Linear Regression with slope equals 0

2007-08-14 Thread ONKELINX, Thierry
Dear Ed, In my opinion you don't need to set the slope to zero. Just test if the slope in lm(d ~ t) is significant. If it is significant then you have evidence that the slope is NOT zero. But when it is not significant (and in your example it is), you can't say that it is zero. But doing some

Re: [R] Question about unicode characters in tcltk

2007-08-14 Thread Peter Dalgaard
R Help wrote: hello list, Can someone help me figure out why the following code doesn't work? I'm trying to but both Greek letters and subscripts into a tcltk menu. The code creates all the mu's, and the 1 and 2 subscripts, but it won't create the 0. Is there a certain set of characters

Re: [R] {grid} plain units with non NULL data arguments

2007-08-14 Thread Prof Brian Ripley
On Tue, 14 Aug 2007, Wolfram Fischer wrote: In help(unit) I read: The 'data' argument must be a list when the 'unit.length()' is greater than 1. For example, 'unit(rep(1, 3), c(npc, strwidth, inches), data=list(NULL, my string, NULL))'. In the newest R-versions it is not

Re: [R] diffusing GIS data in maps

2007-08-14 Thread Paul Hiemstra
Hi Lawrence, You could use the gstat (geostatistics) package to perform an interpolation, it also requires the package sp. It offers inverse distance interpolation and several forms of kriging. Making an interpolation would look something like: library(gstat) # Also loads sp

Re: [R] invert 160000x160000 matrix

2007-08-14 Thread Douglas Bates
On 8/14/07, Jiao Yang [EMAIL PROTECTED] wrote: Tir, Thank you very much for the note. I'm using an algorithm to analyze a data set of 400 variables and the algorithm uses the inverse of a 16x16 positive definite matrix. The matrix is stored as a text file. A meta-theorem in

Re: [R] Problem with

2007-08-14 Thread Dieter Menne
Daniel Stahl daniel_stahl at operamail.com writes: I would like to do a large number of e.g. 1000 paired ttest using the by-function. Technical stuff aside: do you really want to do 1000 paired t-tests? Followed by a *** pick-nic? Mmm... Dieter

Re: [R] Using sunflowerplot to add points in a xyplot panel

2007-08-14 Thread Dieter Menne
Ronaldo Reis Junior chrysopa at gmail.com writes: Hi, I use panel.points to add points to a xyplot graphic. But I like to use the sunflowerplot to plot my points because this is very superimposed. It is possible to use this? I try but it dont work directly. It may be need to put this

[R] Limma - 2x2 factorial design matrix

2007-08-14 Thread tee` suesean
Hi all, I'm working on microarray and currently analyzing the microrarray data using limmaGUI. Loop design has been applied in this experiment. This is a 2X2 factorial experiment where there are control and treatment at 2 different time points, week 6 and 9. The experimental design is

[R] kernlab ksvm() cross-validation prediction response vector

2007-08-14 Thread strinz
Hello, I would like to know, whether for the support vector classification function ksvm() the response values stored in [EMAIL PROTECTED] are cross validated outputs/predictions: Example code from package kernlab, function ksvm: library(kernlab) ## train a support vector machine filter -

Re: [R] Problem with by: does not work with ttest (but with lme)

2007-08-14 Thread Greg Snow
I think at least part of your problem is that in the lm example you use data=x (correct), but in the t.test example you use data=warpbreaks, so in that case it is uing the full data set, not just the portion passed by the 'by' function. Try the t.test example again with data=x and see what

[R] glm(family=binomial) and lmer

2007-08-14 Thread Chris O'Brien
Dear R users, I've notice that there are two ways to conduct a binomial GLM with binomial counts using R. The first way is outlined by Michael Crawley in his Statistical Computing book (p 520-521): dose=c(1,3,10,30,100) dead = c(2,10,40,96,98) batch=c(100,90,98,100,100) response =

Re: [R] labelling plots with ancillary data in data.frame

2007-08-14 Thread Paul Hiemstra
Hi Wesley, Try the text() function. An example: a = rep(10,10) b = seq(1,10) plot(a,b) text(a,b, labels = b, pos = 4, offset = 0.7) ?text hth, Paul Wesley Roberts schreef: Hi All, I am busy using R to do some regression modelling and have been using plot(x,y,) to visualise my variables.

Re: [R] Import of Access data via RODBC changes column name (NO to Expr1014) and the content of t he column

2007-08-14 Thread Dieter Menne
Maciej Hoffman-Wecker Maciej.Hoffman-Wecker at bioskin.de writes: ... But I succeeded in developing a tiny example, that reproduces the bug (wherever it is). I generated a small Access data base test2.mdb with one table Tab1 and following columns: . library(RODBC) .con -

[R] weights in GAMs (package mgcv)

2007-08-14 Thread Julian Burgos
Dear list, I’m using the ‘mgcv’ package to fit some GAMs. Some of my covariates are derived quantities and have an associated standard error, so I would like to incorporate this uncertainty into the GAM estimation process. Ideally, during the estimation process less importance would be given

Re: [R] glm(family=binomial) and lmer

2007-08-14 Thread Prof Brian Ripley
On Tue, 14 Aug 2007, Chris O'Brien wrote: Dear R users, I've notice that there are two ways to conduct a binomial GLM with binomial counts using R. The first way is outlined by Michael Crawley in his Statistical Computing book (p 520-521): and in the places he got it from (it is not his

Re: [R] Import of Access data via RODBC changes column name (NO to Expr1014) and the content of the column

2007-08-14 Thread Prof Brian Ripley
On Tue, 14 Aug 2007, Maciej Hoffman-Wecker wrote: Dear Professor Ripley, Thank you very much for your response. I send the problem, as I didn't have any more ideas were to search for the reason. I didn't say this is a R bug, knowing the responses on such mails.-) But I succeeded in

Re: [R] weights in GAMs (package mgcv)

2007-08-14 Thread Prof Brian Ripley
Let's simplify to a linear model. If your covariates have uncertainties, most likely a linear regression is not appropriate. This sounds like an 'errors in measurements' model, as covered in @Book{Fuller.87, author = Fuller, Wayne A., title= Measurement Error Models,

Re: [R] labelling plots with ancillary data in data.frame

2007-08-14 Thread Julian Burgos
Hi Wesley, You can use the text() function to add text to an existing plot. See ?text. Julian Wesley Roberts wrote: Hi All, I am busy using R to do some regression modelling and have been using plot(x,y,) to visualise my variables. I would now like to label my points using data

[R] weights in lmer

2007-08-14 Thread Chris O'Brien
Dear R users, Prof. Ripley just corrected my understanding of the use of weights in glm, which I thought would allow me to correctly use lmer. However I'm still having problems. My data takes the form of # of infected and uninfected individuals that were measured over time under different

[R] memory allocation glitches

2007-08-14 Thread Ben Bolker
(not sure whether this is better for R-devel or R-help ...) I am currently trying to debug someone else's package (they're not available at the moment, and I would like it to work *now*), which among other things allocates memory for a persistent buffer that gets used by various functions. The

[R] File Exchange?

2007-08-14 Thread Wojciech Gryc
Hi, I've been using R for a number of years, and must say I really like it. This past summer, however, I started using MatLab for a course at school and found the file exchange it has ( http://www.mathworks.com/matlabcentral/fileexchange/loadCategory.do) to be extremely useful. I know that R has

Re: [R] weights in lmer

2007-08-14 Thread Sundar Dorai-Raj
Try weights = as.numeric(total) BTW, there is a SIG (Special Interest Group) for lmer. https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models HTH, --sundar Chris O'Brien said the following on 8/14/2007 11:00 AM: Dear R users, Prof. Ripley just corrected my understanding of the use of

Re: [R] memory allocation glitches

2007-08-14 Thread Peter Dalgaard
Ben Bolker wrote: (not sure whether this is better for R-devel or R-help ...) Hardcore debugging is usually better off in R-devel. I'm leaving it in R-help though. I am currently trying to debug someone else's package (they're not available at the moment, and I would like it to work

[R] [R-pkgs] 'fda' 1.2.2 is now available on CRAN.

2007-08-14 Thread hadley wickham
The fda package supports Functional Data Analysis and Applied Functional Data Analysis by Bernard Silverman and James Ramsay. Functional data analysis, which lots of us like to call FDA, is about the analysis of information on curves or functions. FDA is a collection statistical techniques for

[R] factorial Design with a separate control group

2007-08-14 Thread lamack lamack
Dear all, in R, how can I run a Factorial designs with a separate control? Best regards. #A = 0 and B = 0 == then control ABrepresponse 0 0 1 24 0 0 2 27 0 0 3 36 0

Re: [R] Convert factor to numeric vector of labels

2007-08-14 Thread Matthew Keller
Hi all, If we, the R community, are endeavoring to make R user friendly (gasp!), I think that one of the first places to start would be in setting stringsAsFactors = FALSE. Several times I've run into instances of folks decrying R's rediculous usage of memory in reading data, only to come to find

Re: [R] File Exchange?

2007-08-14 Thread Dirk Eddelbuettel
On Tue, Aug 14, 2007 at 02:34:45PM -0400, Wojciech Gryc wrote: Hi, I've been using R for a number of years, and must say I really like it. This past summer, however, I started using MatLab for a course at school and found the file exchange it has (

Re: [R] Convert factor to numeric vector of labels

2007-08-14 Thread Bert Gunter
Matt: I believe you have confused issues. Setting stringsAsFactors = FALSE would dramatically **increase** the amount of memory used for storing character vectors, which is what factors are for. So your proposed solution does exactly the opposite of what you want. The issue you are worried

Re: [R] State Space Modelling

2007-08-14 Thread sj
If your looking at state space models for forecasting, the Hyndman's forecasting has quite a bit. On 8/14/07, Bernardo Ribeiro [EMAIL PROTECTED] wrote: Here is one of the codes. Thanks a lot... module(finmetrics) genvasicek.ssf = function(param, tau=NULL, freq=1/12){ ## 1.

[R] Mann-Whitney U

2007-08-14 Thread Natalie O'Toole
Hi, Could someone please tell me how to perform a Mann-Whitney U test on a dataset with 2 groups where one group has more data values than another? I have split up my 2 groups into 2 columns in my .txt file i'm using with R. Here is the code i have so far... group1 - c(LeafArea2) group2 -

Re: [R] Convert factor to numeric vector of labels

2007-08-14 Thread Marc Schwartz
I think that you grossly underestimate the frequency of use of factors in R, not to mention that factors are stored more efficiently than character vectors. All modeling functions depend upon them. Most testing, grouping and plotting functions (base R and Lattice) either use them directly as

Re: [R] Mann-Whitney U

2007-08-14 Thread Marc Schwartz
On Tue, 2007-08-14 at 14:45 -0600, Natalie O'Toole wrote: Hi, Could someone please tell me how to perform a Mann-Whitney U test on a dataset with 2 groups where one group has more data values than another? I have split up my 2 groups into 2 columns in my .txt file i'm using with R. Here

Re: [R] GML with tweedie: AIC=NA

2007-08-14 Thread Gordon Smyth
Dear Catarina, As I've already indicated, I have no plans to include AIC for tweedie families, because the AIC computation is much more computationally intensive and less reliable than the actually fitting of the glm. That fact that dtweedie() is not currently available for Windows is a

Re: [R] Mann-Whitney U

2007-08-14 Thread Prof Brian Ripley
On Tue, 14 Aug 2007, Natalie O'Toole wrote: Hi, Could someone please tell me how to perform a Mann-Whitney U test on a dataset with 2 groups where one group has more data values than another? I have split up my 2 groups into 2 columns in my .txt file i'm using with R. Here is the code i

[R] Panel data and imputed datasets

2007-08-14 Thread Nathan Paxton
Hi all, I am hardly an expert, so I expect that this code is not the easiest/ most efficient way of getting where I want. Any suggestions in that direction would also be helpful. I am working on panel analysis with five imputed datasets, generated by Amelia. To do

[R] CDF of a gamma distribution

2007-08-14 Thread Jake Verschuyl
Hi there, I have some bird flight height data that follows a gamma distribution. The data (x) goes from 0 to 700 meters (n=1055). The calculated parameters calculated from the fitdistr(x) are (shape = 5.1379, rate = 0.017541), and therefore the scale (1/rate) = 57.00929. I would like to

[R] Can I calculcate the percentage of a gamma function area below a cutoff value?

2007-08-14 Thread Jake Verschuyl
Hi there, I have some bird flight height data that follows a gamma distribution. The data (x) goes from 0 to 700 meters (n=1055). The calculated parameters calculated from the fitdistr(x) are (shape = 5.1379, rate = 0.017541), and therefore the scale (1/rate) = 57.00929. I would like to

Re: [R] CDF of a gamma distribution

2007-08-14 Thread Francisco J. Zagmutt
pgamma(q=50,shape=5.1379,rate=0.017541) Francisco Jake Verschuyl wrote: Hi there, I have some bird flight height data that follows a gamma distribution. The data (x) goes from 0 to 700 meters (n=1055). The calculated parameters calculated from the fitdistr(x) are (shape =

[R] ANOVA: Factorial designs with a separate control

2007-08-14 Thread lamack lamack
Dear all, I would like to run in R the anova showed in the following pamphlet. http://www.for.gov.bc.ca/hre/biopamph/pamp14.pdf For A = 0 and B =0 I have de control group. Best regards. AB replication response 0 0 1 24 0 0

Re: [R] CDF of a gamma distribution

2007-08-14 Thread Rolf Turner
On 15/08/2007, at 9:53 AM, Jake Verschuyl wrote: I have some bird flight height data that follows a gamma distribution. The data (x) goes from 0 to 700 meters (n=1055). The calculated parameters calculated from the fitdistr(x) are (shape = 5.1379, rate = 0.017541), and therefore

[R] OT - use of R

2007-08-14 Thread Andy Bunn
Hello, is there an up-to-date reference for how many people use R? I'm giving an R demo and want to cite wonderful R usage stats. How many people use it (or download it)? How often is R used in peer-reviewed pubs, etc. Is there any whiz-bang citation that says something like R is great and

Re: [R] Can I calculcate the percentage of a gamma function area below a cutoff value?

2007-08-14 Thread Roland Rau
Hi Jake Verschuyl wrote: Hi there, I have some bird flight height data that follows a gamma distribution. The data (x) goes from 0 to 700 meters (n=1055). The calculated parameters calculated from the fitdistr(x) are (shape = 5.1379, rate = 0.017541), and therefore the scale

Re: [R] Mann-Whitney U

2007-08-14 Thread Peter Dalgaard
Prof Brian Ripley wrote: On Tue, 14 Aug 2007, Natalie O'Toole wrote: Hi, Could someone please tell me how to perform a Mann-Whitney U test on a dataset with 2 groups where one group has more data values than another? I have split up my 2 groups into 2 columns in my .txt file i'm using

Re: [R] simulate data from multivariate normal with pre-specified correlation matrix

2007-08-14 Thread Thomas Harte
# here's your example correlation matrix: sigma- matrix(c(1.00, 0.75, 0, 0.75, 1.00, 0, 0.00, 0.00, 0), nr=3, byrow=TRUE) chol(sigma) # Error in chol(sigma) : the leading minor of order 3 is not positive definite # DUH! # let's chop off that dangling row and

[R] X11 problems

2007-08-14 Thread Pau Marc Munoz Torres
Hi I'm working in a ubuntu feisty OS, when I try to start X11() i get the following message X11() Error in X11() : could not find any X11 fonts Check that the Font Path is correct. In addition: Warning messages: 1: locale not supported by Xlib: some X ops will operate in C locale 2: X cannot

[R] vertically oriented color key in heatmaps

2007-08-14 Thread adrian
Rajarshi Guha [EMAIL PROTECTED] writes: Hi, I have some data which I was plotting using image(). I wanted to add a vertical color key to the plot and I found that heatmap.2 in gplots does let me add a color key. However, I was thinking of a vertical bar with the color range rather than the

Re: [R] X11 problems

2007-08-14 Thread Marc Schwartz
On Wed, 2007-08-15 at 04:03 +0200, Pau Marc Munoz Torres wrote: Hi I'm working in a ubuntu feisty OS, when I try to start X11() i get the following message X11() Error in X11() : could not find any X11 fonts Check that the Font Path is correct. In addition: Warning messages: 1:

Re: [R] X11 problems

2007-08-14 Thread De-Jian,ZHAO
Hi Pau, The error message indicates that the Font Path is perhaps wrong. I think you should set the font path. I do not use Linux. I never encounter this problem in Windows XP. About the warning messages, you can try ?locales to get some information. These warnings do not prevent the function

Re: [R] Mann-Whitney U

2007-08-14 Thread J Dougherty
Natalie, It's best to provide at least a sample of your data. Your field names suggest that your data might be collected in units of mm^2 or some similar measurement of area. Why do you want to use Mann-Whitney, which will rank your data and then use those ranks rather than your actual data?

Re: [R] OT - use of R

2007-08-14 Thread Chung-hong Chan
A quick search of google scholar found 2556 cites to the classic paper by Ihaka et al. http://scholar.google.com/scholar?hl=enlr=cites=15992947024900415641 On 8/15/07, Andy Bunn [EMAIL PROTECTED] wrote: Hello, is there an up-to-date reference for how many people use R? I'm giving an R demo

[R] installation of packages

2007-08-14 Thread robin . dobos
Dear All, Have just installed v2.5.1 on Windows XP. Works fine but I had quite a few pakages loaded for 2.5.0 (from contributed) and was wondering how I can get 2.5.1 to recognise them without having to reinstall them all. Is this possible or do I have to reinstall all the packages again? I

  1   2   >