Re: [R] Copula fitting

Puskás László wrote: Hi, Is anybody using Copula package for fitting copulas to own datas? I always got this message: Error in qnorm(p, mean, sd, lower.tail, log.p) : Non-numeric argument to mathematical function Please specify version of package and R as well as the code

[R] disaggregating table

Hi all, This should be easy, but I can't seem to figure it out. I have a table like this named newtable a1 a2 a3 a4 Cnts Score 1 100 4 3.28 1 011 2 2.63 I want the following: a1 a2 a3 a4 Cnts Score 1 100 4

Re: [R] disaggregating table

On Sun, 22 Oct 2006, Jeff Miller wrote: Hi all, This should be easy, but I can't seem to figure it out. ind - rep(1:nrow(newtable), times=newtable$Cnts) newtable[ind, -5] gives a1 a2 a3 a4 Score 11 1 0 0 3.28 1.1 1 1 0 0 3.28 1.2 1 1 0 0 3.28 1.3 1 1 0 0 3.28 2

[R] Lmer, heteroscedasticity and permutation, need help please

Hi everybody, I'm trying to analyse a set of data with a non-normal response, 2 fixed effects and 1 nested random effect with strong heteroscedasticity in the model. I planned to use the function lmer : lmer(resp~var1*var2 + (1|rand)) and then use permutations based on the t-statistic given

Re: [R] R tcl/tk

Charles Annis, P.E. [EMAIL PROTECTED] writes: Friends: I am a long-time R user, learning tcl/tk, and am tying myself in knots over something that should be simple. I want to create a frame and put that frame inside the toplevel frame. This works (i.e. it places text in col 1, and the

Re: [R] sqlSave, fast=F option, bug?

I've also reproduced this behaviour on WinXP + MS SQL Server and would agree that it's a bug with the fast=FALSE option. Have the package maintainers been contacted about this? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of chao gai Sent: 18 October

[R] calculate area of outer polygon

Dear all, Does anyone know of a function that calculates the area of the outer polygon constructed from a data frame with co-ordinates? For example, library(splancs) test = rbind(c(0,0), c(10,0),c(10,10),c(0,20)) plot(test) areapl(test) [1] 150 This is OK, but I want the same area to be returned

[R] Adjusted residuals

Dear users, Given a equation of the form y=a(1-exp(bt), where a,b parameters and t=age and given prevalences for t=1,2,3,4,5 What is a nice way to plot a kind of adjusted residuals at those values for t? How should one scale them to account for small counts at some values for t? Thanks --

Re: [R] Key colour problem with lattice plot

Hi Geoffrey, I replicated your problem, and I came up with the same solution as Deepayan, so I won't reprint it here but: Can anyone explain why the key is inverted versus the bar order? I'd also like to thank you for showing me a different approach to lattice

Re: [R] calculate area of outer polygon

Tord Snäll wrote: Dear all, Does anyone know of a function that calculates the area of the outer polygon constructed from a data frame with co-ordinates? For example, If by 'outer polygon' you mean 'convex hull', then look at help(chull). Barry

[R] How can I calculate adjusted means?

Hi, I have been looking for help about adjusted means but it seems like there is no specific information about it. My problem is following: In a 2 level ANOVA my model is - anova(Y~treat1+treat2+covarX) I have 4 factors in treat1 and 2 factors in treat2. Now I want the adjusted means for my

Re: [R] getting the by() function to work properly

Hi maybe somebody can help you more but in meantime I would recommend to debug your function with debug(f3) and call by(ss3, sub, f3) to see where exactly comes the error from. HTH Petr On 22 Oct 2006 at 22:49, Jancik, Jasper F. wrote: Date sent: Sun, 22 Oct 2006 22:49:23

Re: [R] Book for Maximum Likelihood Methods in R

On 23-Oct-06 Ben Bolker wrote: Milton Cezar Ribeiro milton_ruser at yahoo.com.br writes: Hi R-guys, Is there a good book for maximum likelihood methods in R? I´m looking mainly to Ecological approaches to apply ML. ** BLATANT PLUG warning **: I'm working on a book on

[R] Cube plots

Hi does anyone know of any R functions or packages for the following :- . generating cube plots for displaying the results from a response surface experiment design . generating ternary plots from a mixture design . tetrahedral plot or quaternary plot for displaying results from a four

Re: [R] Cube plots

On 10/23/2006 7:17 AM, Robert Kinley wrote: Hi does anyone know of any R functions or packages for the following :- . generating cube plots for displaying the results from a response surface experiment design . generating ternary plots from a mixture design . tetrahedral plot or

Re: [R] R tcl/tk

Peter: Thank you for your response. I apologize for not sending a reproducible example. I have attached a reproducible example of the problem here. This is a much abbreviated version of my problem and even so it's rather long for an example. Run with tcl.tk.example(PROBLEM = TRUE)

[R] Recurrence plot in package tseriesChaos

Hi, I'm a new user of the R package, and I need to generate recurrence plots for a set of 56 time series data. The package tseriesChaos has the function recurr that gives a plot. But what I really need are the recurrence plot parameters that are calculated from each plot (like %recur, %det,

Re: [R] Cube plots

I don't think I've see tetrahedral plots, but the strategy above might turn them up. There was a userR presentation on them - http://www.r-project.org/useR-2006/Abstracts/Matthews.pdf With a little work, you could also do them in GGobi (http://www.ggobi.org), which would generalise to more

Re: [R] Multilevel model (lme) question

On 10/22/06, Lukas Rode [EMAIL PROTECTED] wrote: Thanks Douglas for the detailed explanation; it was very helpful (I'll definitely give lme4 a try as well). For the record: I also found it helpful to play with model.matrix (e.g. p. 14ff and p.28 of the book by Jose Pinheiro and Douglas) to see

[R] likelihood question not so related to R but probably requires the use of R

I have a question and it's only relation to R is that I probably need R after I understand what to do. Both models are delta y_t = Beta + epslion and suppose I have a null hypothesis and alternative hypothesis H_0 : delta y_t = zero+ epsilonepsilon is normal ( 0,

[R] FW: Debug package question

Dear list, I received the response below from the package author of 'debug'. I post it to the list, with Mark's approval, in case it is useful to others too. Regards, Matthew -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: 22 October 2006 23:53 To: Matthew

Re: [R] Recurrence plot in package tseriesChaos

Hi Joy. 2006/10/23, Joydeep [EMAIL PROTECTED]: Hi, I'm a new user of the R package, and I need to generate recurrence plots for a set of 56 time series data. The package tseriesChaos has the function recurr that gives a plot. But what I really need are the recurrence plot parameters that

Re: [R] R tcl/tk

Charles Annis, P.E. [EMAIL PROTECTED] writes: Peter: Thank you for your response. I apologize for not sending a reproducible example. I have attached a reproducible example of the problem here. This is a much abbreviated version of my problem and even so it's rather long for an example.

Re: [R] R tcl/tk

D'oh! You are right of course. How very obvious these things are on the other side of the solution. I spent the entire weekend and completely missed it. Thanks! Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com

[R] R tcl/tk

This must be dumbest question ever asked, but... When I ask help.search(tcltk), I get a reference to tcltk-package. When I ask help(tcltk-package), I get rtfm(s) in 'R_HOME/Tcl/doc'. But then when I ask help.search(R_HOME), I get nothing. Is something missing here in those help pages?

[R] Agnes Help

Hi, I'm trying to use the cluster package and I'm having some trouble... I always get the message: myagnes - agnes(datafile.dat) Error: could not find function agnes the package cluster is listed in the library() command, and I can reach the help files from Agnes as well I know that this can

[R] Citation for tseries help pages for R

Good Morning/Afternoon! I am editing a document and am not sure how to cite the Time series analysis and computational finance help pages that are accessible at this url: www.maths.lth.se/help/R/.R/library/tseries/html/00Index.html. Can anyone on this list help me with this? Thank you for

Re: [R] one is not one

On Sat, 21 Oct 2006, Philipp Pagel wrote: On Sat, Oct 21, 2006 at 11:04:13AM +0200, Patrick Giraudoux wrote: Which means that actually sum(x) is NOT considered equal to 1... Any idea about what is going wrong? Others have already pointed out the problem and I would like to add a reference

Re: [R] Citation for tseries help pages for R

On Mon, 23 Oct 2006, Jenny Vander Pluym wrote: Good Morning/Afternoon! I am editing a document and am not sure how to cite the Time series analysis and computational finance help pages that are accessible at this url: www.maths.lth.se/help/R/.R/library/tseries/html/00Index.html. Can anyone

[R] problem of using list element in for cycle

sorry, pressed sent by mistake. for example data - read.csv(data.txt) data V1 V2 1 YHR165C CG8877 2 YJL130C CG18572 3 YDL171C CG9674 4 YKR054C CG7507 5 YDL140C CG1554 6 YLR106C CG13185 7 YGL206C CG9012 8 YNL262W CG6768 9 YER172C

Re: [R] problem about using list element in for cycle

sorry, pressed sent by mistake. for example data - read.csv(data.txt) single V1 V2 1 YHR165C CG8877 2 YJL130C CG18572 3 YDL171C CG9674 4 YKR054C CG7507 5 YDL140C CG1554 6 YLR106C CG13185 7 YGL206C CG9012 8 YNL262W CG6768 9 YER172C

[R] Agnes Help

Hi I'm trying to use the cluster package and I'm having some trouble... I always get the message: myagnes - agnes(datafile.dat) Error: could not find function agnes the package cluster is listed in the library() command, and I can reach the help files from Agnes as well I know that this

Re: [R] R tcl/tk

On 10/23/2006 10:11 AM, Alberto Monteiro wrote: This must be dumbest question ever asked, but... When I ask help.search(tcltk), I get a reference to tcltk-package. When I ask help(tcltk-package), I get rtfm(s) in 'R_HOME/Tcl/doc'. But then when I ask help.search(R_HOME), I get nothing.

[R] problem about using list element in for cycle

for example data - read.csv(data.txt) typeof(data) [1] list for (i in 1:nrow(data)){ [[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] Latex editor recommendations

Tom Backer Johnsen [EMAIL PROTECTED] writes: This question is not oriented towards R, but is posted here because I have the impression that there are at least some Latex users among the contributors. The question is: What editors for Latex are to be recommended? I have located one: EMACS.

Re: [R] R tcl/tk

On 10/23/06, Duncan Murdoch [EMAIL PROTECTED] wrote: On 10/23/2006 10:11 AM, Alberto Monteiro wrote: This must be dumbest question ever asked, but... When I ask help.search(tcltk), I get a reference to tcltk-package. When I ask help(tcltk-package), I get rtfm(s) in 'R_HOME/Tcl/doc'.

Re: [R] R tcl/tk

On Mon, 23 Oct 2006, Alberto Monteiro wrote: This must be dumbest question ever asked, but... When I ask help.search(tcltk), I get a reference to tcltk-package. When I ask help(tcltk-package), I get rtfm(s) in 'R_HOME/Tcl/doc'. But then when I ask help.search(R_HOME), I get nothing. Is

[R] character manipulation

Dear R'helpers, I am reading lines in a .txt file Each line is stocked into a n elements object, as this: [958] 422 287 339 31 203 602 547 1026 500 366 346 227 [959] 410 67 11 220 110 451 562 598 732 163 163 220 [960] 179 513 95 186 102 595 333 1289 804 210 294 459 [961] 276 153 307

Re: [R] character manipulation

Forgot the second part. To replace multiple spaces with one: gsub( +, , your.data) On 10/23/06, Nicolas Degallier [EMAIL PROTECTED] wrote: Dear R'helpers, I am reading lines in a .txt file Each line is stocked into a n elements object, as this: [958] 422 287 339 31 203 602 547 1026

Re: [R] character manipulation

nchar(gsub([^ ], '', your.data)) This replaces all non-blanks with nulls leaving only blanks and then determines number of characters. On 10/23/06, Nicolas Degallier [EMAIL PROTECTED] wrote: Dear R'helpers, I am reading lines in a .txt file Each line is stocked into a n elements object, as

Re: [R] R tcl/tk

Gabor Grothendieck wrote: But then when I ask help.search(R_HOME), I get nothing. Is something missing here in those help pages? Note that R_HOME corresponds to the R.home() path So I guess there _is_ something missing in those help pages, after all! Instead of R_HOME, the help page should

[R] libz lib

Hi all, Please, what libz must/could I use to build RMySQL in my Mac OS X 10.4.8 box? Thanks! Best, Ricardo -- Ricardo Rodríguez Your EPEC ICT Team __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

Re: [R] problem about using list element in for cycle

Your problem is that you are using cat() on a factor. Use as.character() or format() to convert the factor to character data, which cat will then print in the way you want. x - data.frame(L=letters[1:3]) x L 1 a 2 b 3 c x$L [1] a b c Levels: a b c cat(x$L, \n) 1 2 3

[R] Construction of Dataset for time varying COXPH analysis

Question: When survfit() function is used upon a coxph object, the 'n' returned is vastly smaller (n=6) than the number of distinct loans in the dataset used. I am trying to estimate a Cox proportional hazards model for a set of loans (over 6000) using using time varying covariates. For this

Re: [R] Hi,about the png device

Hi Li, Sadly, the png and jpg devices are not really appropriate for your needs, since they rely on the X11 device for their operation. In your case, the X11 device is not necessary, although if you did use it as you describe, it would let the png device work.

Re: [R] getting the by() function to work properly

Hi Jasper, For me it seems that you are fooling around with attach() or something. For one thing, it will not work like this,: e.g. twodied=x[died==2,]is the first statement died is not locally defined, hence it is gotten from somewhere else... For the second thing, this will throw an error:

[R] Worm distribution :-)

I don't know if anyone has heard this tale, but it runs more or like this way: A biologist was studing a (semi-spherical) cave where bats lives. He fell asleep in the cave, and he woke up in the middle of the night. Half-dreaming, he thought that he was outside, because glow-worms were

Re: [R] Worm distribution :-)

You are talking about random point patterns, since the glow-worms appear as ``stars'' (= points). See the package ``spatial'' (which comes with R) and try simulating a pattern using Strauss(). Or install the package ``spatstat'' from CRAN --- in this package there is a variety of ways to

Re: [R] Worm distribution :-)

Have you heard of Boids? (google it if not) Depending upon what you want this for a simulation approach might be appropriate. Regards, Ana Nelson On 23 Oct 2006, at 18:18, Alberto Monteiro wrote: I don't know if anyone has heard this tale, but it runs more or like this way: A

[R] Methods of addressing multicollinearity in multiple linear regression with R

In searching the R help archives I find a number of postings in April of 2005, but nothing since then. If readers are aware of more recent contributions addressing the problems arising from multicollinearity (such as with the bootstrap, jackknife, or other techniques) I would appreciate a

Re: [R] Key colour problem with lattice plot

On 10/23/06, Alex Brown [EMAIL PROTECTED] wrote: Hi Geoffrey, I replicated your problem, and I came up with the same solution as Deepayan, so I won't reprint it here but: Can anyone explain why the key is inverted versus the bar order? Because the key goes from top to

[R] Bayesian Information Criterion

Hello! I calculate a Bayesian logistic regression with the function MCMClogit from the package MCMCpack. After the calculation I use the package CODA to test the model in respect to convergence. Is there a compatible package to calculate the BIC (bayesian information criterion)? So that it

[R] toggleDoc: clutter reduction mainly for S4 documentation files

The following perl-script is available from http://www.menne-biomed.de/download/toggleDoc.zip After it is tested on other systems (currently only Windows), I plan to upload it to http://cran.mirroring.de/other-software.html toggleDoc.pl: Clutter reduction for S4-R documentation files.

[R] Plotting Text on a graph

Hi, I plotted 12 graphs on a page and output to a png file. I wanted to have an overall title for all 12 graphs. What command can I use to do this? Below is the code that plotted the 12 graphs in one page. # FM10 by Month/ Export the plot to Wash2005FM10.png

Re: [R] Plotting Text on a graph

Have you thought of using split.screen instead? Something like might work for you: split.screen(c(1,1)) split.screen(c(3,4), 1) for (i in 1:12) { screen(i+1) par(mar=c(2,2,4,2)) plot(1:20,rnorm(20),xlab=,ylab=) } screen(1) title(Overall title) On 23/10/06, Dan Chan [EMAIL PROTECTED]

[R] Plotting text on a graph

Hi Daniel: Here is a sample code that I have used: z1 - rexp(100) z2 - rexp(100) z3 - rexp(100) par(mfrow=c(2,2),oma = c(0, 0, 3, 0)) curve(dexp,from=0,to=5) hist(z1,main=Size 5) hist(z2,main=Size 15) hist(z3,main=Size 30) mtext(Densities, outer = TRUE, cex = 1.5) And this will do the trick.

[R] Color eps/ps output from specialized plots?

Hello, First a disclaimer :) I am very new to using R. I am generating some plots and eventhough I can get colored output in the encapsulated postscript files in the simplest of commands (e.g. plot(1:10,1:10, type=l, col=red) ), it does not work for the particular plots I want. It works on

[R] Extended CR model

I was wondering if someone could point me to the R package that implements the partial proportional odds (PO) model discussed by Peterson and Harrell (1990). In Harrell (2001), the model is explained in Chapt. 13. Respectfully, Frank R. Lawrence __

[R] Help with recode and factor functions

I have a data set with seven inputs. Four of which are categorical. For my midterm, my professor wants us to scale all the inputs. This means, I pressume, that I have to use 'recode' or 'factor' to transform the categorical data in numerical. For example, one input variable is

[R] The Censummary Function...

Hi Forum, I am new and learning this research tool. was trying to run some tests on a censored dataset using the NADA library. Everything is hunky dory except 'censummary' throws an error and I am trying to figure out a reason for this. Please help! below you will see the error statement...

Re: [R] how to create a vector with different categories in a simple way?

Thank you so much, Marc and Phil. Unfortunenately, I misunderstood the problem myself and wasn't clear how i wanted the variables to be. I will describe the issue again and hope you can help me out. Here is part of data called layout Id Name block col row 1 a1 11

Re: [R] Color eps/ps output from specialized plots?

On 10/23/06, Turgut Durduran [EMAIL PROTECTED] wrote: Hello, First a disclaimer :) I am very new to using R. I am generating some plots and eventhough I can get colored output in the encapsulated postscript files in the simplest of commands (e.g. plot(1:10,1:10, type=l, col=red) ), it

[R] unexpected read.csv behavior

Example data in a recent post was: LandFill Ruminants United States (USA) .214280 5528.16 France 200.527083 1299.87 Australia185.878368 2448.17 Russian Federation 1752.833400 2024.29 Argentina283.987320 2567.02 Brazil

[R] nested if/else very slow, more efficient ways?

Hello, in the data.frame resultsfuzzy I would like to replace the characters in the second column (5a, 5b, ... 5e) with numbers from 1 to 5. The data.frame has 39150 entries. I seems to work on samples that are nrow(resultsfuzzy) but it takes suspicously long. Do you have any suggestions how

Re: [R] The Censummary Function...

Try: censummary(AsExample$AsLow, AsExample$AsHigh, AsExample$AsCen) From the Introduction to R (http://cran.r-project.org/doc/manuals/R- intro.html#Lists-and-data-frames): Components of lists may also be named, and in this case the component may be referred to either by giving the component

Re: [R] unexpected read.csv behavior

On 10/23/2006 5:54 PM, Robert Baer wrote: Example data in a recent post was: LandFill Ruminants United States (USA) .214280 5528.16 France 200.527083 1299.87 Australia185.878368 2448.17 Russian Federation 1752.833400 2024.29

Re: [R] Key colour problem with lattice plot

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 really be any other way by default, if you think about it. I did promise someone that I would add an option to

Re: [R] nested if/else very slow, more efficient ways?

One way that might do what you want is to change the character column to a factor, and then apply as.numeric. resultsfuzzy$x-as.numeric(factor(resultsfuzzy$x,levels=c(5a,5b,5c,5d,5e))) This assumes, of course, that you know that the levels are going to be in the set {5a,5b,5c,5d,5e}. However,

Re: [R] nested if/else very slow, more efficient ways?

There are a number of ways this might be approached. Can you please give a sample of your data, and your desired output? Are 5a ... 5e the only values that appear in that column, or are there other values, 4e for instance, that should stay the same during your conversion? Do you wish to use

Re: [R] nested if/else very slow, more efficient ways?

On 10/23/2006 6:03 PM, Kim Milferstedt wrote: Hello, in the data.frame resultsfuzzy I would like to replace the characters in the second column (5a, 5b, ... 5e) with numbers from 1 to 5. The data.frame has 39150 entries. I seems to work on samples that are nrow(resultsfuzzy) but it

Re: [R] pdf/ convert/ font problem

Hi Sam McClatchie wrote: Background: OS: Linux Ubuntu Dapper R : Version 2.3.1 (2006-06-01) Emacs 21.4.1 ESS Colleagues This is neither a bug report, nor a complaint, so I think this is the appropriate list. I am getting an odd font problem with a pdf generated using pdf(file

Re: [R] Key colour problem with lattice plot

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 really be any other way by default, if you think about it.

[R] Replacing for loop with apply type function.

Hi Everyone, I want to replace the following for loop with an apply type function to (possibly) speed up the process. # The for loop I want to replace x - numeric(10) for(i in 2:10) x[i] - x[i-1]+1 x To give you some more background, I am running a Metropolis Hastings MCMC chain with k

Re: [R] Extended CR model

The posting guide (see below) suggests using something like RSiteSearch(continuation ratio) before posting to the list. There are many relevant hits including several to packages on CRAN. On Mon, 23 Oct 2006, Cougar Lawrence wrote: I was wondering if someone could point me to the

Re: [R] Extended CR model

Or better still RSiteSearch(partial proportional odds) and see the second hit. On Mon, 23 Oct 2006, Charles C. Berry wrote: The posting guide (see below) suggests using something like RSiteSearch(continuation ratio) before posting to the list. There are many relevant

[R] why it returns list level number instead of its content?

for example: I have a data frame. data$V4 returns: . [6936] P05796 P11096 P76174 P04475 P18775 [6941] P33225 P76387 P76388 P76388 P09375 [6946] P15300 P15723 1375 Levels: O50190 O65938 O69415 P00274 P00363 P00364 P00370 P00373 ... Q9AJ15

Re: [R] linear mixed effects models with breakpoints

Are you familiar with how to include include the desired serial correlation structure in 'lme', ignoring the breakpoint question? If no, please consult Pinheiro and Bates (2000) Mixed-Effects Models in S and S-Plus (Springer)? If yes, it should be a relatively easy matter to add that

Re: [R] why it returns list level number instead of its content?

The class factor is defined for vectors, not matrices. The attempt to use a factor in a matrix setting coerces it to numeric. See the documentation for factor where it says In particular, as.numeric applied to a factor is meaningless, and may happen by implicit coercion. tmp - matrix(1:8, 4)

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

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 the same. What do I need